diff --git a/.github/workflows/hugo.yml b/.github/workflows/hugo.yml
index ed38b90b0..4e458624a 100644
--- a/.github/workflows/hugo.yml
+++ b/.github/workflows/hugo.yml
@@ -31,7 +31,7 @@ jobs:
build:
runs-on: ubuntu-latest
env:
- HUGO_VERSION: 0.148.2
+ HUGO_VERSION: 0.155.2
steps:
- name: Install Hugo CLI
run: |
diff --git a/.gitignore b/.gitignore
index 8dd6d56b8..1034e558b 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,2 +1,3 @@
public/
.hugo_build.lock
+*.bak
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 000000000..ab6c2d74b
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,13 @@
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+ rev: v6.0.0 # Use the ref you want to point at
+ hooks:
+ - id: trailing-whitespace
+ - id: check-added-large-files
+ args: ['--maxkb=500']
+ - id: check-merge-conflict
+ - id: check-yaml
+ - id: end-of-file-fixer
+ - id: mixed-line-ending
+ - id: trailing-whitespace
+ args: ['--markdown-linebreak-ext=md']
diff --git a/README.md b/README.md
index b695a6fc8..173edc76b 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,6 @@
-# conversion of the obf website to GitHub pages
+[](https://results.pre-commit.ci/latest/github/OBF/OBF.github.io/main)
+
+# Conversion of the obf website to GitHub pages
Migration of the OBF WP site to a static site generator (Hugo)
@@ -67,10 +69,10 @@ hugo server &
Historic images from when the website was on WordPress live in a large separate
repo https://github.com/OBF/wp-content/ which is included as a git submodule.
If you want to view images in the web pages on `localhost:1313`, you will need
-to also initialise this repository, which is currently setup using the
+to also initialise this repository, which is currently setup using the
`git submodule` workflow.
-To load it you can run:
+To load it you can run:
```
cd OBF.github.io/
@@ -86,14 +88,18 @@ This may change.
For new images, you can place these into the `static/img/yyyy/` folder of this repository, where `yyyy` means the four digit year as a subfolder.
-When compiling the website during the build, Hugo will move everything in `static/` into the website root, i.e. to `open-bio.org/`. This means that when linking images you do not have to include the `static/` as part of the media/image link.
+When compiling the website during the build, Hugo will move everything in `static/` into the website root, i.e. to `open-bio.org/`. This means that when linking images you do not have to include the `static/` as part of the media/image link.
As an example: A file that resides in `static/img/2025/test-image.jpg` should be linked in the markdown files like this: ``
It is also good practice to name media files with the date you add them/the date of the page/post you want to add them to, e.g. `static/img/2025/2025-03-04-blogpost-image.jpg` (using `yyyy-mm-dd` as the start of the filename).
+Aim to keep within 1024 pixels high/wide to keep the file sizes reasonable for our pages to load quicky.
+
#### Some other random tips
+- Where is the menu?? It's in hugo.yaml.
+
- To set up a URL redirect, add an alias to the page you want to
redirect *to*. This goes in the header part of the .md (the part
between the three dashes) and looks like this:
@@ -127,7 +133,7 @@ image, use this html:
```
```
-
+
- To make two columns (e.g. to run text next to an image), use
"columns" (look for an example in one of our .mds)
- You can make a button like this:
@@ -140,7 +146,7 @@ image, use this html:
- To get posts to show up on the BOSC news page, include the category "bosc" (the tag doesn't seem to matter).
- Note that new posts may not show up on the main OBF home page until you kill and restart hugo.
- Photos/Images in posts
- - Images in the arcticle preview on the frontpage/blog page will only show up if they are part of the first paragraph
+ - Images in the arcticle preview on the frontpage/blog page will only show up if they are part of the first paragraph
## Steps taken to port content from old WP site
@@ -150,6 +156,3 @@ image, use this html:
not deployed on open-bio.org). (For now, the first line of
hugo.yaml should say "baseURL: https://OBF.github.io" but that will
change later)
-
-
-
diff --git a/content/_index.md b/content/_index.md
index b633049dc..1d9561a82 100644
--- a/content/_index.md
+++ b/content/_index.md
@@ -25,7 +25,7 @@ OBF runs the annual [Bioinformatics Open Source Conference (BOSC)](events/bosc/a
-
+
{{< endcolumns >}}
diff --git a/content/page/about-bosc.md b/content/page/about-bosc.md
index 0326734b1..7f18053bf 100644
--- a/content/page/about-bosc.md
+++ b/content/page/about-bosc.md
@@ -1,5 +1,5 @@
---
-author:
+author:
cover:
alt: BOSC-room - 1
image: /wp-content/uploads/2024/08/BOSC-room-1.jpeg
@@ -7,16 +7,16 @@ date: "2019-02-08T16:46:51+00:00"
guid: https://www.open-bio.org/wp/?page_id=2705
title: About BOSC
url: /events/bosc/about
-bosc: yes
+bosc: yes
---
# What is BOSC?
The **B** ioinformatics **O** pen **S** ource **C** onference promotes and facilitates the [open source](https://en.wikipedia.org/wiki/open_source) development of [bioinformatics](https://en.wikipedia.org/wiki/bioinformatics) tools and open science.
-Since it launched in 2000, BOSC has been part of ISMB every year except for 2018 and 2020. In 2020, BOSC partnered with GCC to form the Bioinformatics Community Conference, BCC2020. In 2018, BOSC was held jointly with GCC as a combined [GCCBOSC2018](https://gccbosc2018.sched.com/).
+Since it launched in 2000, BOSC has been part of ISMB every year except for 2018 and 2020, when it partnered with the Galaxy Community Conference.
-**[BOSC 2025](/events/bosc-2025) will be part of [ISMB/ECCB 2025](https://www.iscb.org/ismbeccb2025/home) in Liverpool, UK, July 21-22, 2025.**
+**[BOSC 2026](/events/bosc/) will take place July 14-15 as part of [ISMB 2026](https://www.iscb.org/ismb2026/home)) in Washington DC (and online).**
@@ -24,7 +24,7 @@ Since it launched in 2000, BOSC has been part of ISMB every year except for 2018
{{< columns >}}
-- Inform the research community of important developments in open source bioinformatics
+- Inform the research community of important developments in open source bioinformatics and open science
- Provide a focused environment for developers and users to interact and share ideas about open source approaches in bioinformatics
- Make connections between participants that could enhance the open source ecosystem and lead to collaborations
- Promote open science, with its focus on sharing data and tools, transparency, reproducibility, and data provenance
@@ -37,6 +37,7 @@ Since it launched in 2000, BOSC has been part of ISMB every year except for 2018
### Previous BOSCs
+- [BOSC 2025](/events/bosc-2025/) took place July 21-22, 2025 in Liverpool, UK (as part of [ISMB/ECCB 2025](https://www.iscb.org/ismbeccb2025/home)).
- [BOSC 2024](/events/bosc-2024/) The 25th annual BOSC was held July 15-16, 2024, as part of [ISMB 2024](https://www.iscb.org/ismbeccb2024), in person in Montréal, Canada, and online.
- [BOSC 2023](/events/bosc-2023/) took place July 26-27, 2023 as part of [ISMB/ECCB 2023](https://www.iscb.org/ismbeccb2023), in person in Lyon, France, and online.
- [BOSC 2022](/events/bosc-2022/) took place July 13-14, 2022, as part of [ISMB 2022](https://www.iscb.org/ismb2022), in person in Madison, Wisconsin, USA, and also online.
@@ -74,7 +75,7 @@ Since it launched in 2000, BOSC has been part of ISMB every year except for 2018
### CollaborationFest
-In recent years, the BOSC meetings have been preceded or followed by a two day [CollaborationFest](/events/bosc/collaborationfest/), an informal collaborative work event. Initially called CodeFest, the event was renamed CollaborationFest in 2018 to reflect the fact that it's not just about coding.
+In recent years, the BOSC meetings have been preceded or followed by a two-day [CollaborationFest](/events/bosc/collaborationfest/), an informal collaborative work event. Initially called CodeFest, the event was renamed CollaborationFest in 2018 to reflect the fact that it's not just about coding.
@@ -97,13 +98,11 @@ There's no conference without attendees! Your presence is crucial to the success
### Present your work
-Our focus is on open source work and communities. Code presented at BOSC must be open and properly licensed. If your work is more about training materials than code, we'd like your materials to be open and licensed so others can benefit from it!
-
-In the early days of BOSC, an abstract that was basically "I wrote some bioinformatics code, and it's open source" was good enough to merit at least a short talk, but we've grown since then. Even if a project is new and therefore doesn't yet have a community, there should be some sort of plan for building a community of users and/or developers.
+Our focus is on open source work and communities. Code presented at BOSC must be open and properly licensed. If your work is more about training materials than code, we want your materials to be open and licensed so others can benefit from it!
We try to provide a platform to everyone who wants to present appropriate work. We have "long" talks (typically 17 minutes + 3 minutes for questions), short/"lightning" talks (5 minutes), and posters.
-Submit an abstract
+Submit an abstract
### Review abstracts
@@ -114,7 +113,8 @@ We try to provide a platform to everyone who wants to present appropriate work.
{{< column >}}
-Conference abstracts are reviewed by volunteers who express their interest. We encourage reviewers to be constructive in their comments, and some choose to sign their reviews. Most reviewers are assigned about 6 abstracts to review. We acknowledge our reviewers on the conference website and in the program.
+Conference abstracts are reviewed by volunteers who express their interest and have appropriate experience. We encourage reviewers to be constructive in their comments, and some choose to sign their reviews. Reviewers are typically assigned about 6-8 abstracts to review.
+We acknowledge our reviewers on the conference website.
More about the review process
@@ -125,10 +125,8 @@ Conference abstracts are reviewed by volunteers who express their interest. We e
The organizing committee does most of the work to make BOSC a successful meeting. Committee members help write communications to reviewers, participants, and attendees; decide on the program; design conference materials; find dinner locations; chair sessions during the conference; and more! The workload gets heavy in two waves: first when abstracts are being reviewed and the program is being put together, and again as the conference gets closer. Most organizing committee members start out by becoming abstract reviewers.
-We acknowledge organizing committee members on the conference website and in the program, and they are entitled to complimentary conference registration if their institution/employer can't cover it.
-
### Sponsor BOSC and/or CollaborationFest
-The Open Bioinformatics Foundation welcomes donations to help support the BOSC and [CollaborationFest](/events/bosc/collaborationfest/) events. Please see the [Sponsors](/events/bosc/sponsors/) page for more information.
+The Open Bioinformatics Foundation welcomes sponsorships to help support the BOSC and [CollaborationFest](/events/bosc/collaborationfest/) events. Please see the [Sponsors](/events/bosc/sponsors/) page for more information.
diff --git a/content/page/about-obf.md b/content/page/about-obf.md
index c18e46c6c..32e7d9575 100644
--- a/content/page/about-obf.md
+++ b/content/page/about-obf.md
@@ -55,7 +55,7 @@ The OBF is open to anyone who is interested in promoting open source bioinformat
# Main Activities
-- Running the yearly [BOSC](events/bosc/) conference.
+- Running the yearly [BOSC](/events/bosc/about/) conference.
- Organizing the [CollaborationFest](/events/bosc/collaborationfest/) collaborative work events (which usually follow or precede BOSC).
- Running the [OBF Event Award program](/event-awards/) (launched March 2016), aimed at increasing diverse participation at events promoting open-source bioinformatics or open science.
- Participating in the Google Summer of Code program as an umbrella mentoring organization for member projects and related open source bioinformatics efforts, when there is sufficient interest.
diff --git a/content/page/adding-projects.md b/content/page/adding-projects.md
index 1053a6219..84a32a048 100644
--- a/content/page/adding-projects.md
+++ b/content/page/adding-projects.md
@@ -108,7 +108,7 @@ A project not currently affiliated with OBF can seek to attain Candidate OBF Pro
#### Removal of affiliation status
The ballot can include a vote on removing OBF affiliation from a project. Possible reasons for such a vote include consistent failure to meet expectations for OBF affiliated projects; consistent failure to adhere to OBF's Code of Conduct; and a project being no longer maintained.
-## Maintenance of affiliation status
+## Maintenance of affiliation status
The status of Affiliated and Candidate OBF Projects that are not voted on stays the same, unless one of the following conditions occurs:
@@ -165,5 +165,3 @@ If by signing over ownership you only mean assigning intellectual property right
### I'm interested in taking donations for my project, or I've recently received a grant. Can the OBF handle my cash flow?
The OBF can accept donations and grants on behalf of its member projects through SPI, the OBF's fiscal sponsor. The OBF also can, again through SPI, request the disbursement of funds earmarked for a member project. Management of cash flow with a high rate of transactions, will, however, likely exceed the capacity of SPI's (almost entirely volunteer) financial administrators, and we therefore advise projects expecting this need to apply independently for fiscal sponsorship. Organisations providing fiscal sponsorship for software projects include SPI, Software Freedom Conservancy, NumFocus, and OpenCollective.
-
-
diff --git a/content/page/board.md b/content/page/board.md
index dec45df0e..30f4037c1 100644
--- a/content/page/board.md
+++ b/content/page/board.md
@@ -6,7 +6,7 @@ title: Board
url: /board/
---
-# Board of Directors
+# Board of Directors
The Board can be contacted via email at board@open-bio.org (or, in case of mailing list problems, try obf-board@googlegroups.com as a fallback) You can also find us on [LinkedIn](https://www.linkedin.com/groups/9539620/). The minutes of the previous public Board meetings can be found on our [GitHub repository](https://github.com/OBF/obf-docs/tree/master/minutes) ([pre-2019 meeting minutes are linked here](https://open-bio.org/board/meeting-minutes/)).
@@ -17,7 +17,7 @@ The Board can be contacted via email at board@open-bio.org (or, in case of maili
alt="Image of Iddo Friedberg"
title= "Iddo Friedberg"
caption=`
-_At-large Member_
+_At-large Member_
Associate Professor at Iowa State University. Chair, Function COSI. Early contributor to the Biopython project.
`
>}}
@@ -28,7 +28,7 @@ Associate Professor at Iowa State University. Chair, Function COSI. Early contri
title= "[Hilyatuz Zahroh](https://www.linkedin.com/in/hilyatuz-zahroh-6671ab100/)"
link= "https://www.linkedin.com/in/hilyatuz-zahroh-6671ab100"
caption=`
-_At-large Member_
+_At-large Member_
[APBioNET](https://www.apbionet.org/current-exco-officers-2020-2022/) ExCo
`
>}}
@@ -39,7 +39,7 @@ _At-large Member_
title= "[Caleb Kibet](https://kipkurui.github.io/)"
link= "https://kipkurui.github.io"
caption=`
-_At-large Member_
+_At-large Member_
Bioinformatician at the [International Center of Insect Physiology and Ecology, Kenya](http://www.icipe.org/research/research-support-units/molecular-biology-bioinformatics-and-biostatistics); Founder [OpenScienceKE](https://medium.com/openscienceke).
`
>}}
@@ -48,10 +48,10 @@ Bioinformatician at the [International Center of Insect Physiology and Ecology,
src="/img/Hilmar-Lapp-1.jpg"
alt="Image of Hilmar Lapp"
link= "https://lappland.io"
- title= "[Hilmar Lapp](https://lappland.io/)"
+ title= "[Hilmar Lapp](https://orcid.org/0000-0001-9107-0714)"
caption=`
-_At-large Member_
-Representing [BioPerl](http://www.bioperl.org/), Director of Informatics at the [Center for Genomic and Computational Biology](http://genome.duke.edu/) (GCB) at Duke University. Former OBF President.
+_At-large Member_
+Representing [BioPerl](http://www.bioperl.org/), Open Research Faculty at [Neuromatch](https://neuromatch.io/). Former OBF President.
`
>}}
@@ -60,7 +60,7 @@ Representing [BioPerl](http://www.bioperl.org/), Director of Informatics at the
alt="Image of Peter Cock"
title= "[Peter Cock](#)"
caption=`
-_President_
+_President_
[Biopython](https://biopython.org/) core developer, bioinformatician at the James Hutton Institute for 16 years, currently at the University of Strathclyde. [BOSC 2016 co-chair](https://open-bio.org/wiki/BOSC_2016).
`
>}}
@@ -125,7 +125,7 @@ Co-founder of [openSNP](https://opensnp.org) and Director of Research at [Open H
# Joining the Board
-Nominations for the Board of Directors may be made by the general membership at any time throughout the year by contacting any Board Member.
+Nominations for the Board of Directors may be made by the general membership at any time throughout the year by contacting any Board Member.
The Board tries on an ongoing basis to create opportunities for members of the community to serve, while also ensuring stability of the Board, through expansion of the Board, by replacing a Board member whose term expires, or by volunteers from the community interested in serving.
## Board Expectations
diff --git a/content/page/bosc-2019-collaborationfest-for-reference.md b/content/page/bosc-2019-collaborationfest-for-reference.md
index 5372fe751..c8fb2f2a4 100644
--- a/content/page/bosc-2019-collaborationfest-for-reference.md
+++ b/content/page/bosc-2019-collaborationfest-for-reference.md
@@ -57,10 +57,10 @@ The CoFest will be covered by [ISMB’s Code of Conduct](https://www.iscb.org/i
The host venue for CoFest will be:
-[DayOne - The Swiss Innovation Hub for Personalized Medicine](https://www.dayone.swiss/dayone.html)
+[DayOne - The Swiss Innovation Hub for Personalized Medicine](https://www.dayone.swiss/dayone.html)
Hochbergerstrasse 60C, 4057 Basel, Switzerland.
-[https://goo.gl/maps/AvZkyjvsm1DQrGmL6](https://goo.gl/maps/AvZkyjvsm1DQrGmL6)
+[https://goo.gl/maps/AvZkyjvsm1DQrGmL6](https://goo.gl/maps/AvZkyjvsm1DQrGmL6)
[https://osm.org/go/0CdsbPozF?node=3215472544](https://osm.org/go/0CdsbPozF?node=3215472544)
More details like building access arrangements will be forthcoming.
diff --git a/content/page/bosc-2019.md b/content/page/bosc-2019.md
index 2234fcd53..dfd816531 100644
--- a/content/page/bosc-2019.md
+++ b/content/page/bosc-2019.md
@@ -77,15 +77,15 @@ If you would like to be a sponsor of BOSC, please contact us at bosc@open-bio.or
## Organizing Committee
-**Chair: Nomi L. Harris** (Lawrence Berkeley National Laboratory)
-**Co-Chair: Heather Wiencko** ( [Hosted Graphite](https://www.hostedgraphite.com/))
+**Chair: Nomi L. Harris** (Lawrence Berkeley National Laboratory)
+**Co-Chair: Heather Wiencko** ( [Hosted Graphite](https://www.hostedgraphite.com/))
-- [Peter Cock](http://www.scri.ac.uk/staff/petercock) ( [Biopython developer](http://biopython.org/); [James Hutton Institute](http://www.hutton.ac.uk/))
+- [Peter Cock](http://www.scri.ac.uk/staff/petercock) ( [Biopython developer](http://biopython.org/); [James Hutton Institute](http://www.hutton.ac.uk/))
- Christopher Fields (National Center for Supercomputing Applications)
- Bastian Greshake Tzovaras ( [Open Humans](https://www.openhumans.org/))
- [Michael Heuer](https://github.com/heuermh) ( [UC Berkeley](https://rise.cs.berkeley.edu/))
-- Karsten Hokamp (Smurfit Institute of Genetics, Trinity College Dublin, Ireland)
+- Karsten Hokamp (Smurfit Institute of Genetics, Trinity College Dublin, Ireland)
- Monica Munoz-Torres (Oregon State University)
- [Yo Yehudi](http://yo-yehudi.com/)(University of Cambridge)
diff --git a/content/page/bosc-2020-online.md b/content/page/bosc-2020-online.md
index a64d7c42c..1ac984278 100644
--- a/content/page/bosc-2020-online.md
+++ b/content/page/bosc-2020-online.md
@@ -62,7 +62,7 @@ BOSC is usually preceded or followed by what we now call [CollaborationFest (CoF
## Sponsoring BOSC
-[Sponsorships](/events/bosc/sponsors/) from private companies and organizations help to defray some of our costs. This year, BOSC will be part of [BCC2020](https://bcc2020.github.io/).
+[Sponsorships](/events/bosc/sponsors/) from private companies and organizations help to defray some of our costs. This year, BOSC will be part of [BCC2020](https://bcc2020.github.io/).
See the BCC [Partners](https://bcc2020.github.io/partners/) page for information about the BCC sponsors and how you can become one!
@@ -76,7 +76,7 @@ See the BCC [Partners](https://bcc2020.github.io/partners/) page for information
- Technology Chair: Karsten Hokamp (Smurfit Institute of Genetics, Trinity College Dublin, Ireland)
- **Program Chair: Chris Fields** ( [Bioperl developer](http://bioperl.org/); [HPCBio](https://hpcbio.illinois.edu/), University of Illinois)
-- [Peter Cock](http://www.scri.ac.uk/staff/petercock) ( [Biopython developer](http://biopython.org/); [James Hutton Institute](http://www.hutton.ac.uk/))
+- [Peter Cock](http://www.scri.ac.uk/staff/petercock) ( [Biopython developer](http://biopython.org/); [James Hutton Institute](http://www.hutton.ac.uk/))
- Jessica Maia (BD)
- Monica Munoz-Torres (Oregon State University)
diff --git a/content/page/bosc-2021-keynotes.md b/content/page/bosc-2021-keynotes.md
index 1a2fc628f..5bb9e395f 100644
--- a/content/page/bosc-2021-keynotes.md
+++ b/content/page/bosc-2021-keynotes.md
@@ -20,10 +20,10 @@ Christie Bahlai, PhD, is a computational ecologist in the Department of Biologic
### Thomas Hervé Mboa Nkoudou ( [Mboalab](https://www.mboalab.africa/) and [Open AIR](https://openair.africa/))
-_Contribution du mouvement maker dans le domaine de la biotechnologie en Afrique: Une perspective de la science ouverte
+_Contribution du mouvement maker dans le domaine de la biotechnologie en Afrique: Une perspective de la science ouverte
(Contribution of the maker movement to biotechnology in Africa: An open science perspective)_
-_
-Note: This talk will be delivered in French with English subtitles._
+_
+Note: This talk will be delivered in French with English subtitles._
ABSTRACT: The maker movement is a community-based movement driven by a common understanding that democratizing access to tools and technologies will revolutionize the distribution of material goods and disrupt existing socio-economic systems. With the Internet, the maker movement is reinforced by trends of openness, better, open science. Indeed, nowadays, information circulates instantaneously from one end of the world to the other, offering the possibility to exchange, share and contribute to the enrichment of knowledge with implications in the fields of health, environment, education, etc.
In this presentation, I will show evidence of the contribution of the maker movement to the democratisation of biotechnology in Africa. I will also discuss the local realities that need to be considered in order to ensure the success of such an undertaking. To do this, I will address the following points:
@@ -38,7 +38,7 @@ He founded the [Mboalab](https://www.mboalab.africa/) innovation lab in Cameroon
-### Lara Mangravite ( [Sage Bionetworks](https://sagebionetworks.org/))
+### Lara Mangravite ( [Sage Bionetworks](https://sagebionetworks.org/))
(Talk co-hosted with [Function-COSI](https://www.biofunctionprediction.org/meetings/))
_Open approaches to advance data-intensive biomedicine_
diff --git a/content/page/bosc-2021.md b/content/page/bosc-2021.md
index a25b995d4..8c1cd7e54 100644
--- a/content/page/bosc-2021.md
+++ b/content/page/bosc-2021.md
@@ -107,7 +107,7 @@ Monica Munoz-Torres (University of Colorado, Denver)
## Review Committee
-Kai Blin\*, Christian Brueffer, Scott Cain\*, J. Harry Caufield\*, Tyrone Chen, Luis Pedro Coelho\*, Gianluca Della Vedova, Scott Edmunds, Christopher Fields\*, Bastian Greshake Tzovaras\*, Nomi L. Harris, Janna Hastings, Michael Heuer, Karsten Hokamp, Matúš Kalaš\*, Aziz Khan, Radhika Khetani, Aleix Lafita-Masip, Hilmar Lapp, Hervé Ménager, Kieran O'Neill, Tazro Ohta, Konstantin Okonechnikov, Lorena Pantano, Surya Saha\*, Sonika Tyagi, Deepak Unni, Jason Williams, Yo Yehudi
+Kai Blin\*, Christian Brueffer, Scott Cain\*, J. Harry Caufield\*, Tyrone Chen, Luis Pedro Coelho\*, Gianluca Della Vedova, Scott Edmunds, Christopher Fields\*, Bastian Greshake Tzovaras\*, Nomi L. Harris, Janna Hastings, Michael Heuer, Karsten Hokamp, Matúš Kalaš\*, Aziz Khan, Radhika Khetani, Aleix Lafita-Masip, Hilmar Lapp, Hervé Ménager, Kieran O'Neill, Tazro Ohta, Konstantin Okonechnikov, Lorena Pantano, Surya Saha\*, Sonika Tyagi, Deepak Unni, Jason Williams, Yo Yehudi
\\* = also reviewed Late Poster abstracts
## Previous BOSCs
diff --git a/content/page/bosc-2022-1.md b/content/page/bosc-2022-1.md
index 2e691a72a..600f36cad 100644
--- a/content/page/bosc-2022-1.md
+++ b/content/page/bosc-2022-1.md
@@ -108,7 +108,7 @@ To participate in BOSC 2022, you will need to [register for ISMB 2022](https://w
## BOSC 2022 Review Committee
-Melissa Black\*, Scott Cain\*, Seth Carbon, J. Harry Caufield\*, Tyrone Chen, Christopher Fields\*, Bastian Greshake Tzovaras\*, Karsten Hokamp, Aziz Khan\*, Hilmar Lapp, Lara Mangravite, Hande McGinty, Hervé Ménager, Steffen Möller, Monica Munoz-Torres, Kieran O'Neill, Tazro Ohta, Konstantin Okonechnikov, Caralyn Reisle, Surya Saha\*, Ian Simpson, Stian Soiland-Reyes, David Twesigomwe, Deepak Unni\*, Jason Williams
+Melissa Black\*, Scott Cain\*, Seth Carbon, J. Harry Caufield\*, Tyrone Chen, Christopher Fields\*, Bastian Greshake Tzovaras\*, Karsten Hokamp, Aziz Khan\*, Hilmar Lapp, Lara Mangravite, Hande McGinty, Hervé Ménager, Steffen Möller, Monica Munoz-Torres, Kieran O'Neill, Tazro Ohta, Konstantin Okonechnikov, Caralyn Reisle, Surya Saha\*, Ian Simpson, Stian Soiland-Reyes, David Twesigomwe, Deepak Unni\*, Jason Williams
\\* = also reviewed Late Poster abstracts
## Previous BOSCs
diff --git a/content/page/bosc-2022-keynotes.md b/content/page/bosc-2022-keynotes.md
index a33ed6358..9d79cf0ad 100644
--- a/content/page/bosc-2022-keynotes.md
+++ b/content/page/bosc-2022-keynotes.md
@@ -36,7 +36,7 @@ _I will describe the work of an international group of scientist-educators to de
_- “Core Principles” (“Best Evidence”, “Catalytic”, Effective”, and “Inclusion”) apply to all SFT and are grounded in research and work in education, diversity, equity, and inclusion._
_- “Community Principles” (“Reaching”, “Scaling”, and “Sustaining”) apply when SFT is organized by groups to achieve the objectives of a community (e.g., science discipline, institution, career stage)._
-_Community refinement, adoption, and adaptation of the Bicycle Principles will help accelerate scientific progress by making SFT more effective, inclusive, and career-spanning for all.
+_Community refinement, adoption, and adaptation of the Bicycle Principles will help accelerate scientific progress by making SFT more effective, inclusive, and career-spanning for all.
_
[Jason Williams](https://jasonjwilliamsny.github.io/profile/) has worked at Cold Spring Harbor Laboratory since 2004, first at the bench in the Plant Science group and currently as an Assistant Director at the lab’s [DNA Learning Center](https://www.cshl.edu/dna-learning-center/). Jason is on numerous Advisory Boards and Diversity/Equity/Inclusion committees for organizations including the Earth BioGenome Project, Data Dryad, Global Alliance for Genomics and Health, BioData Catalyst, and ELIXIR UK. In 2020, he was chosen as a Kavli Frontiers of Science Fellow by the National Academy of Sciences, and won the [NSF 2026 Idea Machine Competition](https://www.cshl.edu/jason-williams-wins-nsf-2026-idea-machine-competition/).
diff --git a/content/page/bosc-2022-panel-1.md b/content/page/bosc-2022-panel-1.md
index 260a94bac..98c233257 100644
--- a/content/page/bosc-2022-panel-1.md
+++ b/content/page/bosc-2022-panel-1.md
@@ -9,7 +9,7 @@ title: BOSC 2022 Panel
url: /events/bosc-2022/bosc-2022-panel/
---
-# BOSC 2022 Panel: Building and Sustaining Inclusive Open Science Communities
+# BOSC 2022 Panel: Building and Sustaining Inclusive Open Science Communities
Building open source software is a great start, but to maximize the impact, it’s also necessary to put effort into maintaining it. Similarly, open source / open science communities don’t just need to be built; they also need to be maintained and expanded. We’ve seen increasing calls for inclusion and diversity, but once you’ve reached out to a new community, attracted new contributors, or recruited a new team member, how do you go beyond surface-level changes and achieve meaningful and sustainable inclusion? What difficult work, self-education, and research is needed to make more diverse groups thrive?
diff --git a/content/page/bosc-2022-panel.md b/content/page/bosc-2022-panel.md
index 36ebfc5e1..2d5bcb745 100644
--- a/content/page/bosc-2022-panel.md
+++ b/content/page/bosc-2022-panel.md
@@ -10,7 +10,7 @@ title: BOSC 2022 Panel
url: /
---
-# BOSC 2022 Panel: Building and Sustaining Inclusive Open Science Communities
+# BOSC 2022 Panel: Building and Sustaining Inclusive Open Science Communities
Building open source software is a great start, but to maximize the impact, it’s also necessary to put effort into maintaining it. Similarly, open source / open science communities don’t just need to be built; they also need to be maintained and expanded. We’ve seen increasing calls for inclusion and diversity, but once you’ve reached out to a new community, attracted new contributors, or recruited a new team member, how do you go beyond surface-level changes and achieve meaningful and sustainable inclusion? What difficult work, self-education, and research is needed to make more diverse groups thrive?
diff --git a/content/page/bosc-2022.md b/content/page/bosc-2022.md
index c082604be..e85efc297 100644
--- a/content/page/bosc-2022.md
+++ b/content/page/bosc-2022.md
@@ -109,7 +109,7 @@ Deepak Unni (European Molecular Biology Laboratory)
## BOSC 2022 Review Committee
-Melissa Black\*, Scott Cain\*, Seth Carbon, J. Harry Caufield\*, Tyrone Chen, Christopher Fields\*, Bastian Greshake Tzovaras\*, Karsten Hokamp, Aziz Khan\*, Hilmar Lapp, Lara Mangravite, Hande McGinty, Hervé Ménager, Steffen Möller, Monica Munoz-Torres, Kieran O'Neill, Tazro Ohta, Konstantin Okonechnikov, Caralyn Reisle, Surya Saha\*, Ian Simpson, Stian Soiland-Reyes, David Twesigomwe, Deepak Unni\*, Jason Williams
+Melissa Black\*, Scott Cain\*, Seth Carbon, J. Harry Caufield\*, Tyrone Chen, Christopher Fields\*, Bastian Greshake Tzovaras\*, Karsten Hokamp, Aziz Khan\*, Hilmar Lapp, Lara Mangravite, Hande McGinty, Hervé Ménager, Steffen Möller, Monica Munoz-Torres, Kieran O'Neill, Tazro Ohta, Konstantin Okonechnikov, Caralyn Reisle, Surya Saha\*, Ian Simpson, Stian Soiland-Reyes, David Twesigomwe, Deepak Unni\*, Jason Williams
\\* = also reviewed Late Poster abstracts
## Previous BOSCs
diff --git a/content/page/bosc-2023-1.md b/content/page/bosc-2023-1.md
index ee4b728ca..b934d86ff 100644
--- a/content/page/bosc-2023-1.md
+++ b/content/page/bosc-2023-1.md
@@ -99,7 +99,7 @@ Monica Munoz-Torres (University of Colorado Anschutz Medical Campus)
### Review Committee
-Arpita Joshi, Aziz Khan, Chris Fields, David Twesigomwe , Deepak Unni\*, Gianluca Della Vedova, Harsh Sharma, Hervé Ménager, Hilmar Lapp, Ian Simpson, J. Harry Caufield, Jenea Adams, Kai Blin, Karsten Hokamp\*, Konstantin Okonechnikov, Luis Pedro Coelho, Milen Nikolov, Monica Munoz-Torres, Rachel Torchet, Radhika Khetani, Seth Carbon, Surya Saha\*, Swapnil Sawant, Tazro Ohta, Tyrone Chen, Varsha Khodiyar
+Arpita Joshi, Aziz Khan, Chris Fields, David Twesigomwe , Deepak Unni\*, Gianluca Della Vedova, Harsh Sharma, Hervé Ménager, Hilmar Lapp, Ian Simpson, J. Harry Caufield, Jenea Adams, Kai Blin, Karsten Hokamp\*, Konstantin Okonechnikov, Luis Pedro Coelho, Milen Nikolov, Monica Munoz-Torres, Rachel Torchet, Radhika Khetani, Seth Carbon, Surya Saha\*, Swapnil Sawant, Tazro Ohta, Tyrone Chen, Varsha Khodiyar
\\* Also reviewed Late Poster abstracts
## Previous BOSCs
diff --git a/content/page/bosc-2023-keynotes.md b/content/page/bosc-2023-keynotes.md
index 335ffde7c..aff04f28f 100644
--- a/content/page/bosc-2023-keynotes.md
+++ b/content/page/bosc-2023-keynotes.md
@@ -17,7 +17,7 @@ url: /events/bosc-2023/bosc-2023-keynotes/
###### _A New Odyssey: Pioneering the Future of Scientific Progress Through Open Collaboration_
-_Join us in humanity's quest for knowledge and understanding, on a transformative odyssey of scientific progress, fueled by the power of open collaboration. This presentation will navigate the realms of scientific discovery, exploring the profound impact of globally inclusive and collaborative efforts that have the potential to revolutionize the very fabric of scientific advancement.
+_Join us in humanity's quest for knowledge and understanding, on a transformative odyssey of scientific progress, fueled by the power of open collaboration. This presentation will navigate the realms of scientific discovery, exploring the profound impact of globally inclusive and collaborative efforts that have the potential to revolutionize the very fabric of scientific advancement.
_
_As we embark on this journey, we will delve into the principles of diverse global alliances and pioneering scientific institutions, illustrating how their values align with real-world initiatives that promote open science, and provide examples of the groundbreaking opportunities that arise when individuals from various backgrounds, disciplines, and experiences unite in pursuit of a common goal._
@@ -36,7 +36,7 @@ With a strong background in life science and a PhD in cancer research, Sara is a
###### _The Dissonance between Scientific Altruism & Capitalist Extraction: The Zero Trust and Federated Data Sovereignty Solution_
-_The history that led to the roadbuilding of Open Data’s current pathway is a murky one and one that isn’t fully transparent as to causes, sponsors or decision makers. The philosophical underpinnings and moral obligation of Open Data is flawed and over prioritizes funding commitments and scientists’ rights to data rather than the privacy, development and implementation obligations that are often left to the unjust realm of commercial capitalization. Mr. Yracheta will discuss from the USA’s American Indian perspective (as sovereign Domestic Dependent Nations) and their relationship with states’ and federal governments. Several U.S. policy documents and legislative acts that were created in and out of consultation with American Indian nations will be shared and discussed. Key gaps in the moral obligation to society at large will be demonstrated via this special relationship with tribes. Where possible, Mr. Yracheta will employ game theory to move the Open Data argument into a more socially just and philosophically robust posture. Interrogated are two possible pathways to our current landscape 1) Is the current Open Data environment well intended but ignorant? Neglectful? Aligned with or against the Belmont Principle of Non-Coercion? Or 2) Is the current Open Data environment obfuscatory, purposely predatory and extractive? The answers to either position will determine the timing and delivery of benefits to societies and individuals.
+_The history that led to the roadbuilding of Open Data’s current pathway is a murky one and one that isn’t fully transparent as to causes, sponsors or decision makers. The philosophical underpinnings and moral obligation of Open Data is flawed and over prioritizes funding commitments and scientists’ rights to data rather than the privacy, development and implementation obligations that are often left to the unjust realm of commercial capitalization. Mr. Yracheta will discuss from the USA’s American Indian perspective (as sovereign Domestic Dependent Nations) and their relationship with states’ and federal governments. Several U.S. policy documents and legislative acts that were created in and out of consultation with American Indian nations will be shared and discussed. Key gaps in the moral obligation to society at large will be demonstrated via this special relationship with tribes. Where possible, Mr. Yracheta will employ game theory to move the Open Data argument into a more socially just and philosophically robust posture. Interrogated are two possible pathways to our current landscape 1) Is the current Open Data environment well intended but ignorant? Neglectful? Aligned with or against the Belmont Principle of Non-Coercion? Or 2) Is the current Open Data environment obfuscatory, purposely predatory and extractive? The answers to either position will determine the timing and delivery of benefits to societies and individuals.
_
Joseph M. Yracheta is an Amerindigenous Scientist (P’urhepecha y Raramuri from Mexico) and Executive Director of the Native BioData Consortium within the Cheyenne River Lakota Nation (Sioux). Mr. Yracheta has been a scientist since 1990; he started as a bench biotechnician and worked across many disciplines. In 2014 he graduated from UW Seattle with a master’s in Pharmaceutics and Bioethics under Drs. Ken Thummel and Wylie Burke. He is currently finishing a DrPH in Environmental Health and Engineering from Johns Hopkins under Drs. Ana Navas-Acien and Paul Locke.
diff --git a/content/page/bosc-2023.md b/content/page/bosc-2023.md
index ee0102698..a09116e5b 100644
--- a/content/page/bosc-2023.md
+++ b/content/page/bosc-2023.md
@@ -100,7 +100,7 @@ Monica Munoz-Torres (University of Colorado Anschutz Medical Campus)
### Review Committee
-Arpita Joshi, Aziz Khan, Chris Fields, David Twesigomwe , Deepak Unni\*, Gianluca Della Vedova, Harsh Sharma, Hervé Ménager, Hilmar Lapp, Ian Simpson, J. Harry Caufield, Jenea Adams, Kai Blin, Karsten Hokamp\*, Konstantin Okonechnikov, Luis Pedro Coelho, Milen Nikolov, Monica Munoz-Torres, Rachel Torchet, Radhika Khetani, Seth Carbon, Surya Saha\*, Swapnil Sawant, Tazro Ohta, Tyrone Chen, Varsha Khodiyar
+Arpita Joshi, Aziz Khan, Chris Fields, David Twesigomwe , Deepak Unni\*, Gianluca Della Vedova, Harsh Sharma, Hervé Ménager, Hilmar Lapp, Ian Simpson, J. Harry Caufield, Jenea Adams, Kai Blin, Karsten Hokamp\*, Konstantin Okonechnikov, Luis Pedro Coelho, Milen Nikolov, Monica Munoz-Torres, Rachel Torchet, Radhika Khetani, Seth Carbon, Surya Saha\*, Swapnil Sawant, Tazro Ohta, Tyrone Chen, Varsha Khodiyar
\\* Also reviewed Late Poster abstracts
## Previous BOSCs
diff --git a/content/page/bosc-2024-sponsors.md b/content/page/bosc-2024-sponsors.md
index 974807b80..88bf46194 100644
--- a/content/page/bosc-2024-sponsors.md
+++ b/content/page/bosc-2024-sponsors.md
@@ -63,7 +63,7 @@ BOSC participants come from a wide variety
- Biological researchers, students, and post-docs who are learning bioinformatics analysis tools and techniques
- Power bioinformatics users
-- Bioinformatics tool and workflow developers
+- Bioinformatics tool and workflow developers
- Bioinformatics-focused principal investigators and researchers
- Sequencing core facility staff
@@ -72,7 +72,7 @@ BOSC participants come from a wide variety
# Previous Events
-The OBF has organized BOSC [every year since 2000](/events/bosc/about/). From 2000 to 2017 and again in 2019, BOSC was run as part of the large ISMB conference. In 2018 (and again in 2020) it partnered with the Galaxy Community Conference. The OBF CodeFests (now renamed CollaborationFest, or CoFest) have been held every year after BOSC since 2010.
+The OBF has organized BOSC [every year since 2000](/events/bosc/about/). From 2000 to 2017 and again in 2019, BOSC was run as part of the large ISMB conference. In 2018 (and again in 2020) it partnered with the Galaxy Community Conference. The OBF CodeFests (now renamed CollaborationFest, or CoFest) have been held every year after BOSC since 2010.
The table below shows the approximate number of participants in BOSC and the CoFest. Figures for the CoFest and BOSC are number of people registered for at least one day of the meeting. The BOSC figures do not include drop-in attendees from the parallel sessions organized by other groups. The figures for CoFest do not include remote participants.
@@ -142,8 +142,8 @@ We acknowledge our sponsors before, during and after the event in multiple ways:
## BOSC 2021 Silver Sponsors
-[](https://elifesciences.org/)
-[](https://geneviatechnologies.com/)
+[](https://elifesciences.org/)
+[](https://geneviatechnologies.com/)
[](https://oup.com/)[](https://bioteam.net)
If you are interested in becoming a sponsor, please contact us at bosc@open-bio.org!
diff --git a/content/page/bosc-2025.md b/content/page/bosc-2025.md
index 549c3d61d..b73f8fe6b 100644
--- a/content/page/bosc-2025.md
+++ b/content/page/bosc-2025.md
@@ -14,13 +14,19 @@ bosc: yes
---
+
+
+[BOSC 2026](/events/bosc-2026/) will take place in Washington, DC, as part of [ISMB 2026](https://www.iscb.org/ismb2026/home), July 12-16, 2026. We hope you will join us!
+
+
+
Since 2000, BOSC has covered all aspects of open source bioinformatics and open science.
-**BOSC 2025, the 26th annual Bioinformatics Open Source Conference,
+BOSC 2025, the 26th annual Bioinformatics Open Source Conference,
took place July 21-22, 2025 in Liverpool, UK (as part of
- [ISMB/ECCB 2025](https://www.iscb.org/ismbeccb2025/home))**. Read our [BOSC 2025 report on F1000Research](https://f1000research.com/articles/14-887/v1)!
+ [ISMB/ECCB 2025](https://www.iscb.org/ismbeccb2025/home)). Read our [BOSC 2025 report on F1000Research](https://f1000research.com/articles/14-887/v1)!
-BOSC 2025 included two days of [keynote talks](/events/bosc-2025/bosc-2025-keynotes/), talks from submitted abstracts, a panel discussion, and posters.
+BOSC 2025 included two days of [keynote talks](/events/bosc-2025/bosc-2025-keynotes/), talks from submitted abstracts, a panel discussion, and posters.
The full lineup of talks and posters is available on our [schedule page](/events/bosc-2025/bosc-2025-schedule/).
The talk videos are linked from our [schedule page](/events/bosc-2025/bosc-2025-schedule/) as well as on our [YouTube channel](https://www.youtube.com/@OBFBOSC/videos).
@@ -29,8 +35,6 @@ BOSC 2025 included a [joint session](/2025/03/17/BOSC-BOKR-2025) with the
It featured a [joint keynote by Chris Mungall](/events/bosc-2025/bosc-2025-keynotes/) and talks on some of our favorite topics, including open data and reusable and reproducible science.
The program concluded with a [panel discussion on Data Sustainability](/events/bosc-2025/panel/).
-BOSC 2026 will take place in Washington, DC, as part of [ISMB 2026](https://www.iscb.org/ismb2026/home), July 12-16, 2026. We hope you will join us!
-
@@ -140,7 +144,7 @@ The Bioinformatics Open Source Conference (BOSC) has been [held annually since 2
Since its inception, BOSC has provided a forum for developers and users to interact and share research results and ideas in open source bioinformatics. BOSC’s broad spectrum of topics includes practical techniques for solving bioinformatics problems; software development practices; standards and ontologies; approaches that promote open science and sharing of data, results and software; and ways to grow and sustain open source communities.
-BOSC is usually preceded or followed by
+BOSC is usually preceded or followed by
[CollaborationFest](/events/bosc/collaborationfest/)
(CoFest for short), a two-day collaborative work session. This is an
opportunity for anyone interested in open science, biology and
@@ -174,7 +178,7 @@ CollaborationFest will be part of ISMB/ECCB!
{{< endcolumns >}}
#### BOSC 2025 Review Committee
-Aziz Khan*, Bastian Greshake Tzovaras*, Bhavesh Patel, Christopher Fields*, Damien Goutte-Gattat*, Daniel Korn, Deepak Unni, Fortune Ogo-Ndah Awala, Gayathri Jonnalagadda, J. Harry Caufield*, Karsten Hokamp, Kartik Khosa, Konstantin Okonechnikov,
+Aziz Khan*, Bastian Greshake Tzovaras*, Bhavesh Patel, Christopher Fields*, Damien Goutte-Gattat*, Daniel Korn, Deepak Unni, Fortune Ogo-Ndah Awala, Gayathri Jonnalagadda, J. Harry Caufield*, Karsten Hokamp, Kartik Khosa, Konstantin Okonechnikov,
Luis Pedro Coelho, Monica C Munoz-Torres, Naouel Karam, Nomi Harris, Olawumi Olasunkanmi, Peter Cock, Rafael Gonçalves, Sayali Talware, Sepideh Mazrouee*, Tanya Berardini, Tazro Ohta*, Tyrone Chen, Van Truong, Yuvanesh Vedaraju
* indicates reviewers who did extra reviews
diff --git a/content/page/bosc-2026.md b/content/page/bosc-2026.md
index 8520e36e8..841613c1f 100644
--- a/content/page/bosc-2026.md
+++ b/content/page/bosc-2026.md
@@ -13,12 +13,52 @@ bosc: yes
---
-**BOSC 2026**, the 27th annual Bioinformatics Open Source Conference, will take place July 13-14 or July 15-16 in Washington, DC, as part of [ISMB 2026](https://www.iscb.org/ismb2026/home). We hope you will join us in person or online!
+Since 2000, BOSC has covered all aspects of open source bioinformatics and open science. **BOSC 2026**, the 27th annual Bioinformatics Open Source Conference, will take place **July 14-15 in Washington, DC**, as part of [ISMB 2026](https://www.iscb.org/ismb2026/home). We are excited to announce our two [keynote speakers, **Eric Green and Maryam Zaringhalam**](/events/bosc-2026/bosc-2026-keynotes/), and two [panels](/events/bosc-2026/panels/) on important and timely topics: *Policies and Strategies for Resilient Open Science* and *Open Source in the Age of AI*.
+We will again join forces with [Bio-Ontologies and Knowledge Representation (BOKR)](https://www.open-bio.org/events/bosc-2026/) for half a day.
-Since 2000, BOSC has covered all aspects of open source bioinformatics and open science. [BOSC 2025](/events/bosc-2025/) took place July 21-22, 2025 in Liverpool, UK (as part of
- [ISMB/ECCB 2025](https://www.iscb.org/ismbeccb2025/home)). Read our [BOSC 2025 report on F1000Research](https://f1000research.com/articles/14-887/v1)!
-BOSC 2025 included two days of [keynote talks](/events/bosc-2025/bosc-2025-keynotes/), talks from submitted abstracts, a [panel discussion on data sustainability](/events/bosc-2025/panel), and posters. It also featured a [joint session](/2025/03/17/BOSC-BOKR-2025) with the
-[Bio-Ontologies and Knowledge Representation (BOKR)](https://www.bio-ontologies.org.uk/2025-meeting), which opened with a [joint keynote by Chris Mungall](/events/bosc-2025/bosc-2025-keynotes/) followed by talks on some of our favorite topics, including open data and reusable and reproducible science. The full lineup of BOSC 2025 talks and posters, including links to talk videos, is available on our [Schedule page](/events/bosc-2025/bosc-2025-schedule/).
+[CollaborationFest](https://www.open-bio.org/events/bosc-2026/collaborationfest/), our post-BOSC collaborative work event, will be held in central Washington DC the two days after ISMB (July 17-18, 2026).
+
+
+
+## [BOSC 2026 keynote speakers](/events/bosc-2026/bosc-2026-keynotes/)
+
+{{< columns >}}
+
+
+
+[KEYNOTE: Eric Green](/events/bosc-2026/bosc-2026-keynotes)
+
+From the Human Genome Project to the Realization of Genomic Medicine: A Scientific, Medical, and Societal Journey
+
+{{< column >}}
+
+
+
+[KEYNOTE: Maryam Zaringhalam](/events/bosc-2026/bosc-2026-keynotes)
+
+Science for the People: Open science to engage and build trust with communities
+
+{{< endcolumns >}}
+
+
+
+## [Panels](/events/bosc-2026/panels/)
+
+{{< columns >}}
+
+
+
+[Panel 1: Policies and Strategies for Resilient Open Science](/events/bosc-2026/panels/)
+
+{{< column >}}
+
+
+
+
+
+[Panel 2: Open Source in the Age of AI](/events/bosc-2026/panels/)
+
+{{< endcolumns >}}
@@ -27,27 +67,27 @@ BOSC 2025 included two days of [keynote talks](/events/bosc-2025/bosc-2025-keyno
## BOSC 2026 Key Dates
{{< columns >}}
-- April 1: [OBF Event Award application deadline](/event-awards/)
-- **April 9: Abstract submission deadline (talks and posters)**
+- April 9: Abstract submission deadline (talks and posters)
- May 5: Talk/poster acceptance notifications
-- May 7: Late poster submission deadline
+- **May 7: Late poster submission deadline**
- July 12-16: [ISMB 2026](https://www.iscb.org/ismb2026/home) (Washington, DC and online)
-- **July 13-14 or July 15-16:** **BOSC 2026** (part of ISMB 2026)
+- **July 14-15:** **BOSC 2026** (part of ISMB 2026)
+- July 17-18: [CollaborationFest](https://www.open-bio.org/events/bosc-2026/collaborationfest/) - free (registration required) post-BOSC collaborative work event. Central Washington DC location.
{{< column >}}
-
+
{{< endcolumns >}}
-### Topics
-
{{< columns >}}
-
+
+
{{< column >}}
+### Topics
- Open Science and Reproducible Research
- Open Biomedical Data
@@ -68,14 +108,14 @@ BOSC 2025 included two days of [keynote talks](/events/bosc-2025/bosc-2025-keyno
-
+
### Registration and Financial Assistance
-To participate in BOSC 2026 or the ISMB CollaborationFest, you will need to register for [ISMB 2026](https://www.iscb.org/ismb2026/home).
+To participate in BOSC 2026, you will need to register for [ISMB 2026](https://www.iscb.org/ismb2026/home).
Those who submit abstracts to BOSC can request a fee waiver on the submission form.
You can also apply for an [OBF Event Award](/event-awards/); the deadline is April 1.
-
+
The NIH Office of Data Science Strategy (ODSS) leads the implementation of the NIH Strategic Plan for Data Science through scientific, technical, and operational collaboration with the institutes, centers, and offices that comprise NIH.
Seqera, built by the creators of Nextflow, is the enterprise-first bioinformatics platform trusted by leading pharma and diagnostics companies to build, validate, and scale bioinformatics with confidence.
Dryad is a non-profit open data publishing platform operating in the community interest, and committed to the open availability and routine re-use of all research data. Dryad makes FAIR-complaint data publishing simple through robust open-source infrastructure, hands-on researcher support, and an easy-to-use submission interface.
-{{< endcolumns >}}
+
-### BOSC 2025 Organizing Committee
+## BOSC 2026 Organizing Committee
{{< columns >}}
***Chair: Nomi L. Harris*** (Lawrence Berkeley National Laboratory)
- Karsten Hokamp (Trinity College Dublin)
-- Deepak Unni (SIB, Swiss Institute of Bioinformatics)
- Jessica Maia (BD)
+- Hervé Ménager (Institut Pasteur)
+- Mónica Muñoz Torres (Univ. of Colorado Anschutz)
- Tazro Ohta (Chiba University)
+- Van Truong (University of Pennsylvania)
+- Deepak Unni (SIB, Swiss Institute of Bioinformatics)
- Jason Williams (Cold Spring Harbor Laboratory)
-- Monica Munoz-Torres (Univ. of Colorado Anschutz Medical Campus)
-- Hervé Ménager (Institut Pasteur)
{{< column >}}
-
+
{{< endcolumns >}}
-#### BOSC 2025 Review Committee
-Aziz Khan*, Bastian Greshake Tzovaras*, Bhavesh Patel, Christopher Fields*, Damien Goutte-Gattat*, Daniel Korn, Deepak Unni, Fortune Ogo-Ndah Awala, Gayathri Jonnalagadda, J. Harry Caufield*, Karsten Hokamp, Kartik Khosa, Konstantin Okonechnikov,
-Luis Pedro Coelho, Monica C Munoz-Torres, Naouel Karam, Nomi Harris, Olawumi Olasunkanmi, Peter Cock, Rafael Gonçalves, Sayali Talware, Sepideh Mazrouee*, Tanya Berardini, Tazro Ohta*, Tyrone Chen, Van Truong, Yuvanesh Vedaraju
- * indicates reviewers who did extra reviews
+#### BOSC 2026 Review Committee
+Robert Aboukhalil, Olaitan Awe, Seth Carbon, J. Harry Caufield*, Tyrone Chen, Chris Fields*, Aydan Gasimova, Damien Goutte-Gattat, Bastian Greshake Tzovaras, Nomi Harris, Karsten Hokamp*, Aziz Khan, Hilmar Lapp, Tiago Lubiana Alves, Marcos Martínez-Romero*, Monica C Munoz-Torres, Hervé Ménager, Pitiporn Noisagul, Tazro Ohta*, Konstantin Okonechnikov, Olawumi Olasunkanmi, Seun Olufemi, Ziwei Pan, Bhavesh Patel, Esther Plomp, Aakanksha Rangnekar*, Sayali Talware, Van Truong, Deepak Unni*
-**Interested in reviewing abstracts for BOSC 2026?** [Contact us on Slack](https://join.slack.com/t/obf-bosc/shared_invite/zt-n5ur1gsj-z2C~69_4lYTFPg5tbWA8Ew)
+\* indicates reviewers who did extra reviews
@@ -157,20 +189,25 @@ Luis Pedro Coelho, Monica C Munoz-Torres, Naouel Karam, Nomi Harris, Olawumi Ola
The Bioinformatics Open Source Conference (BOSC) has been [held annually since 2000](/events/bosc/about/). BOSC is organized by the [Open Bioinformatics Foundation (OBF)](/wiki/Main_Page), a non-profit group dedicated to promoting the practice and philosophy of open source software development and open science within the biological research community.
-Since its inception, BOSC has provided a forum for developers and users to interact and share research results and ideas in open source bioinformatics. BOSC’s broad spectrum of topics includes practical techniques for solving bioinformatics problems; software development practices; standards and ontologies; approaches that promote open science and sharing of data, results and software; and ways to grow and sustain open source communities.
+Since 2000, BOSC has covered all aspects of open source bioinformatics and open science. BOSC’s broad spectrum of topics includes practical techniques for solving bioinformatics problems; software development practices; standards and ontologies; approaches that promote open science and sharing of data, results and software; and ways to grow and sustain open source communities.
-BOSC is usually preceded or followed by [CollaborationFest](/events/bosc/collaborationfest/)
-(CoFest for short), a two-day collaborative work session. This is an
-opportunity for anyone interested in open science, biology and
-programming to meet, talk and work collaboratively.
+Last year's conference, [BOSC 2025](/events/bosc-2025/), took place July 21-22, 2025 in Liverpool, UK (as part of [ISMB/ECCB 2025](https://www.iscb.org/ismbeccb2025/home)). Read our [BOSC 2025 report on F1000Research](https://f1000research.com/articles/14-887/v1)!
+BOSC 2025 included two days of [keynote talks](/events/bosc-2025/bosc-2025-keynotes/), talks from submitted abstracts, a [panel discussion on data sustainability](/events/bosc-2025/panel), and posters. It also featured a [joint session](/2025/03/17/BOSC-BOKR-2025) with the
+[Bio-Ontologies and Knowledge Representation (BOKR)](https://www.bio-ontologies.org.uk/2025-meeting), which opened with a [joint keynote by Chris Mungall](/events/bosc-2025/bosc-2025-keynotes/) followed by talks on some of our favorite topics, including open data and reusable and reproducible science. The full lineup of BOSC 2025 talks and posters, including links to talk videos, is available on our [Schedule page](/events/bosc-2025/bosc-2025-schedule/).
+
+
+
+BOSC will be followed on July 17-18 by a [CollaborationFest](/events/bosc/collaborationfest/)
+(CoFest for short), a two-day collaborative work session. This is an opportunity for anyone interested in open science, biology or programming to meet, talk and work collaboratively.
In 2025, CollaborationFest was part of ISMB/ECCB.
More about BOSC
+
-
+
#### Code of Conduct
-As part of ISMB 206, BOSC 2026 is covered by the [ISCB Code of Ethics and Professional Conduct](https://www.iscb.org/iscb-policy-statements/iscb-code-of-ethics-and-professional-conduct).
+As part of ISMB 2026, BOSC 2026 is covered by the [ISCB Code of Ethics and Professional Conduct](https://www.iscb.org/about-iscb/policy-statements-bylaws-and-legal-documents/code-of-ethics-and-professional-conduct).
diff --git a/content/page/code-of-conduct.md b/content/page/code-of-conduct.md
index 44724766e..4d4b19df6 100644
--- a/content/page/code-of-conduct.md
+++ b/content/page/code-of-conduct.md
@@ -1,5 +1,4 @@
---
-author: kushinauwu
date: "2019-02-05T16:19:05+00:00"
guid: https://www.open-bio.org/wp/?page_id=2578
title: Code of Conduct
@@ -8,4 +7,4 @@ url: /code-of-conduct/
---
The [OBF Code of Conduct](https://github.com/OBF/obf-docs/tree/master/code-of-conduct) was adopted after being [voted on by our members in January 2022](/2022/01/27/approved-by-obf-membership-vote/), following the OBF Public Board meeting in September 2021.
-Our annual conference, [BOSC](/events/bosc/), is normally run as part of the ISMB meeting, where it therefore follows the [OBF Code of Conduct](https://www.iscb.org/iscb-policy-statements/iscb-code-of-conduct).
+Our annual conference, [BOSC](/events/bosc/), is normally run as part of the ISMB meeting, where it therefore follows the [ISCB code of conduct](https://www.iscb.org/about-iscb/policy-statements-bylaws-and-legal-documents/iscb-a-safe-space-code-of-conduct).
diff --git a/content/page/donate.md b/content/page/donate.md
index 90cf91486..26200a7fc 100644
--- a/content/page/donate.md
+++ b/content/page/donate.md
@@ -16,5 +16,5 @@ Our annual meetings, [BOSC](/events/bosc/) and the [CollaborationFest](/events/b
Through our fiscal sponsor, [Software in the Public Interest, Inc.](http://spi-inc.org/donations), you can donate to the OBF via [PayPal](http://spi-inc.org/projects/obf/) or [online by credit card](https://co.clickandpledge.com/advanced/default.aspx?wid=66788#). Donations made through SPI are 501(c)3 tax-exempt in the US. Your contribution helps fund a growing community of people committed to developing reusable open-source software for advancing biological research.
-[Donate!
+[Donate!
](https://co.clickandpledge.com/advanced/default.aspx?wid=66788#)
diff --git a/content/page/events.md b/content/page/events.md
index 5882c9762..26e66aabe 100644
--- a/content/page/events.md
+++ b/content/page/events.md
@@ -6,4 +6,3 @@ title: Events
url: /events/
---
-
diff --git a/content/page/get-involved.md b/content/page/get-involved.md
index f495512dc..5ac2c1458 100644
--- a/content/page/get-involved.md
+++ b/content/page/get-involved.md
@@ -22,7 +22,7 @@ There are many ways you can become part of our growing community, regardless of
The OBF community has a number of different online spaces that are open to everyone and can be used to network and discuss anything related to open bioinformatics. You can:
-* Follow our [blog](https://www.open-bio.org/posts/)
+* Follow our [blog](/blog/)
* [Subscribe to our OBF newsletter](https://mailman.open-bio.org/mailman/listinfo/open-bio-l/) (and if you have news to share, you can [also suggest topics](https://github.com/OBF/newsletter/issues)).
* [Join our community _Slack_](https://join.slack.com/t/open-bio/shared_invite/zt-1pnswao9y-8igcckVxBXhQHCMweHt_NA), where you will find fellow open bioinformatics folks to chat with.
* We also have an open [_LinkedIn_ group](https://www.linkedin.com/groups/9539620/), where you can hear about open bioinformatics events, job opportunities and more.
@@ -33,24 +33,24 @@ The OBF community has a number of different online spaces that are open to every
We organize an annual conference, the [_Bioinformatics Open Source Conference_](/events/bosc) (BOSC), and the associated [_CollaborationFest_](/events/bosc/collaborationfest/).
These events are a great way to meet others engaged in open source/science around biology.
-BOSC features talks, posters and panel discussions on the latest research in open bioinformatics, while
+BOSC features talks, posters and panel discussions on the latest research in open bioinformatics, while
CollaborationFest offers the chance to work together with others on improving open bioinformatics tools, by coding but also writing documentation and other non-coding tasks.
# Applying to become a voting member of OBF
-You can also apply to become a voting member of the Open Bioinformatics Foundation, which allows voting on larger OBF issues, including changes to the OBF's governing document, the [bylaws](https://github.com/OBF/obf-docs/blob/master/OBF%20Bylaws.pdf).
+You can also apply to become a voting member of the Open Bioinformatics Foundation, which allows voting on larger OBF issues, including changes to the OBF's governing document, the [bylaws](https://github.com/OBF/obf-docs/blob/master/OBF%20Bylaws.pdf).
To be considered as a voting member, you must already be actively and demonstrably engaged in biology-related open science or open source in some form.
Examples of such engagement could include contributing to existing open bioinformatics projects, publishing in the field, or attending open source bioinformatics conferences such as BOSC.
The reason for this requirement is that we expect voting members to have a long-term engagement with both the field and the OBF itself.
The OBF requires a quorum for voting, so we want OBF members to remain actively involved.
-The best time and place to join is at the annual [BOSC](/events/bosc/) conference, because attendees are automatically deemed eligible based on the fact that they attended BOSC, but you can apply for membership at any time.
+The best time and place to join is at the annual [BOSC](/events/bosc/) conference, because attendees are automatically deemed eligible based on the fact that they attended BOSC, but you can apply for membership at any time.
## History and Bylaws
-The OBF membership body was formally established at the 2005 Board of Directors meeting. As laid out in the [OBF Bylaws](https://github.com/OBF/obf-docs/blob/master/OBF%20Bylaws.md), the Board of Directors elects new Directors when terms expire or new seats are added. The membership of the OBF can nominate candidates for these elections.
+The OBF membership body was formally established at the 2005 Board of Directors meeting. As laid out in the [OBF Bylaws](https://github.com/OBF/obf-docs/blob/master/OBF%20Bylaws.md), the Board of Directors elects new Directors when terms expire or new seats are added. The membership of the OBF can nominate candidates for these elections.
Voting members are invited to attend the annual public Board meetings, which are announced via the (low-traffic) OBF members mailing list, as well as on our blog and via our social media channels.
diff --git a/content/page/how-bosc-supports-diversity-inclusion-and-accessibility.md b/content/page/how-bosc-supports-diversity-inclusion-and-accessibility.md
index 41a71cdf1..ebc73ef62 100644
--- a/content/page/how-bosc-supports-diversity-inclusion-and-accessibility.md
+++ b/content/page/how-bosc-supports-diversity-inclusion-and-accessibility.md
@@ -7,7 +7,7 @@ date: "2023-08-19T17:48:09+00:00"
guid: https://www.open-bio.org/?page_id=7251
title: How we support diversity, inclusion and accessibility
url: /obf-dei/
-aliases:
+aliases:
- /bosc-dei/
---
Diversity, inclusion and accessibility (also known as Diversity, Equity and Inclusion, DEI) are a major part of OBF and [BOSC's](/?obf-events=bosc-2023) mission and core values.
@@ -31,8 +31,8 @@ The Open Bioinformatics Foundation, **funds the [OBF event fellowships](/event-a
Since we introduced this option three years ago, we've been able to offer free registration to dozens of people, most of whom are from groups underrepresented at ISMB/BOSC:
-* In 2022, 19 people (of whom 18 were from groups that are underrepresented in our community) were granted free registration thanks to a combination of these registration fee waivers and OBF event fellowships.
-* In 2023, 15 people (13 from underrepresented groups) were given free registration to ISMB/BOSC.
+* In 2022, 19 people (of whom 18 were from groups that are underrepresented in our community) were granted free registration thanks to a combination of these registration fee waivers and OBF event fellowships.
+* In 2023, 15 people (13 from underrepresented groups) were given free registration to ISMB/BOSC.
* In 2024, 14 people (13 from underrepresented groups) received free registration.
@@ -100,7 +100,7 @@ Although there is not a formal rubric for choosing [BOSC organizing committee](/
{{< columns >}}
-Some recent BOSCs have included **DEI-focused sessions** such as ["Inclusion & Open Science"](/events/bosc-2022/bosc-2022-schedule) in 2022, and BOSC's landscape of open science includes citizen science, in which the research subjects themselves (for example, those with a disability) participate in the research. [BOSC 2023](/events/bosc-2023/bosc-2023-schedule/) included a talk entitled "AutSPACEs: a co-created and open source citizen science project to improve environments for sensory processing in autistic people".
+Some recent BOSCs have included **DEI-focused sessions** such as ["Inclusion & Open Science"](/events/bosc-2022/bosc-2022-schedule) in 2022, and BOSC's landscape of open science includes citizen science, in which the research subjects themselves (for example, those with a disability) participate in the research. [BOSC 2023](/events/bosc-2023/bosc-2023-schedule/) included a talk entitled "AutSPACEs: a co-created and open source citizen science project to improve environments for sensory processing in autistic people".
In a 2023 ISCBacademy webinar organized by BOSC, Long COVID sufferer and advocate Hannah Wei presented [Lessons from the Patient-Led Research Collaborative](/2023/03/07/iscbacademy-webinar-on-patient-led-research/).
diff --git a/content/page/keynotes-2025.md b/content/page/keynotes-2025.md
index 9aa26075f..1d51a401d 100644
--- a/content/page/keynotes-2025.md
+++ b/content/page/keynotes-2025.md
@@ -15,13 +15,15 @@ bosc: yes
#### _Open Knowledge Bases in the Age of Generative AI_
#### (Keynote talk for [joint BOSC/BOKR session](/2025/03/17/BOSC-BOKR-2025/))
+#### [Talk video](https://www.google.com/url?q=https://www.youtube.com/watch?v%3DLz7I2nB4Q5k&sa=D&source=editors&ust=1760741772335658&usg=AOvVaw2c9PAHMKhy_6LSqyRljd__)
+
ABSTRACT: The scientific and clinical community relies on the active development of a wide range of interlinked knowledge bases in order to plan experiments, interpret omics data, and to help with the diagnosis and treatment of disease. These knowledge bases make use of expert curation and the use of community ontologies in order to provide accurate and structured information that can be used algorithmically.
The advent of generative AI and agentic methods presents fantastic opportunities for accelerating curation, increasing the breadth and depth of coverage. Open knowledge bases also present opportunities to generative AI, in the form of a trusted backbone of knowledge that can mitigate the hallucinations that plague large language models. However, the pace of development of AI, combined with misunderstandings about both strengths and weaknesses, poses significant dangers.
In this talk, I will present our recent work on the use of agentic AI to assist with manual knowledge base tasks, particularly those involving complex ontology development and maintenance tasks. I will present a realistic picture of challenges we face, but also strategies to mitigate them, and a path towards a future where agents, curators, and others can work together to leverage and integrate open source tools and data along with the combined knowledge of the scientific community.
-Dr. Chris Mungall is a Senior Scientist at Berkeley Lab, where he heads the [Biosystems Data Science department](https://biosciences.lbl.gov/egsb/biosystems-data-science/) in the Environmental Genomics and Systems Biology Division. Chris’s research interests center around the capture, computational integration, and dissemination of biological research data, and the development of methods for using this data to elucidate biological mechanisms underpinning the health of humans and of the planet. He and his team have led the creation of key biological ontologies for the integration of resources covering gene function, anatomy, phenotypes and the environment, including the the Uberon anatomy ontology, the Cell Ontology (CL), and the Mondo disease ontology. He is also one of the cofounders of the [OBO Foundry](https://obofoundry.org/). For decades, he has been a strong advocate for open-source bioinformatics software, open standards, and open science.
+**Dr. Chris Mungall** is a Senior Scientist at Berkeley Lab, where he heads the [Biosystems Data Science department](https://biosciences.lbl.gov/egsb/biosystems-data-science/) in the Environmental Genomics and Systems Biology Division. Chris’s research interests center around the capture, computational integration, and dissemination of biological research data, and the development of methods for using this data to elucidate biological mechanisms underpinning the health of humans and of the planet. He and his team have led the creation of key biological ontologies for the integration of resources covering gene function, anatomy, phenotypes and the environment, including the the Uberon anatomy ontology, the Cell Ontology (CL), and the Mondo disease ontology. He is also one of the cofounders of the [OBO Foundry](https://obofoundry.org/). For decades, he has been a strong advocate for open-source bioinformatics software, open standards, and open science.
Chris, who has a PhD in bioinformatics from the University of Edinburgh, is a PI on the [Gene Ontology](http://geneontology.org/) (GO), the [Monarch Initiative](https://monarchinitiative.org/), the [Alliance of Genome Resources](https://www.alliancegenome.org/), [Phenomics First](https://biosciences.lbl.gov/2020/10/08/phenomics-first-project-receives-10m-to-unite-genetic-disease-data/), and the [NCATS Biomedical Data Translator](https://ncats.nih.gov/translator), as well as metadata lead for the [National Microbiome Data Collaborative](https://microbiomedata.org/) (NMDC).
In 2017, Chris was the first person to be awarded the [Exceptional Contributions to Biocuration Award](https://www.biocuration.org/2017-biocuration-awards/) by the International Society for Biocuration. In 2020, he received a Berkeley Lab Early Scientific Career Director’s Award.
@@ -34,12 +36,14 @@ In 2017, Chris was the first person to be awarded the [Exceptional Contributions
#### _Working together to develop, promote and protect our data resources: Lessons learnt developing CATH and TED_
+#### [Talk video](https://www.google.com/url?q=https://www.youtube.com/watch?v%3DmHxr4oUCsNQ&sa=D&source=editors&ust=1760741772319332&usg=AOvVaw0RgpvcUJoizEGILRiCq8CW)
+
ABSTRACT: The CATH protein domain structure classification was the vision of the pioneering computational scientist Janet Thornton. Algorithms developed by Orengo and Taylor in the lab of Willie Taylor enabled the analyses that laid the foundations for CATH. Since then, the Orengo team have taken CATH forward in many ways. Working closely with the protein sequence, structural and evolutionary biology communities provided the focus and feedback to shape the resource.
Maintaining the value and integrity of CATH has necessitated continuously embracing new types of data as it became relevant and developing the appropriate tools for this. For example, CATH was recently expanded >400-fold with predicted structures from AlphaFold Database (AFDB) using novel AI-based tools.
CATH is also a partner resource in InterPro and was used by the Structural Genomics Consortia in the US for more than 15 years to probe novel fold and function space. All CATH data and tools are publicly available. The talk will present landmark developments and describe how the resource has benefitted from extensive collaborations with the wider community to handle the data expansions and to provide accurate data needed by the community. It will also draw on CATH experience to reflect on strategies for supporting open data and open source.
-Dr. Christine Orengo is a Professor of Bioinformatics at University College London (UCL).
+**Dr. Christine Orengo** is a Professor of Bioinformatics at University College London (UCL).
Her research focuses on the development of algorithms to capture relationships between protein structures, sequences and functions.
She has built one of the most comprehensive protein classifications, [CATH](https://www.cathdb.info/). CATH structural and functional data for hundreds of millions of proteins has enabled studies that revealed essential universal proteins and their biological roles, and extended characterisation of biological systems implicated in disease e.g. in cell division, cancer and aging.
[The Encyclopedia of Domains (TED)](https://data.niaid.nih.gov/resources?id=zenodo_10788941) is a joint effort by CATH (Orengo group) and the Jones group at University College London to identify and classify protein domains in AlphaFold2 models from AlphaFold Database version 4, covering over 188 million unique sequences and 365 million domain assignments.
diff --git a/content/page/keynotes-2026.md b/content/page/keynotes-2026.md
new file mode 100644
index 000000000..6ac00e43d
--- /dev/null
+++ b/content/page/keynotes-2026.md
@@ -0,0 +1,61 @@
+---
+author: nlharris
+date: "2026-03-06T04:29:08+00:00"
+title: BOSC 2026 Keynotes
+url: /events/bosc-2026/bosc-2026-keynotes/
+bosc: yes
+
+---
+
+
+
+## Eric Green (Illumina)
+
+### From the Human Genome Project to the Realization of Genomic Medicine: A Scientific, Medical, and Societal Journey
+
+#### Abstract
+
+The coming decade offers great promise for human genomics and genomic medicine. Since the completion of the Human Genome Project over two decades ago, genomics has become progressively entrenched within the bedrock of the biomedical research enterprise. Capitalizing on the momentum of the project’s successful completion, the field of genomics has increasingly expanded and matured, such that genomics is now central and catalytic in basic and translational research, and studies now regularly demonstrate the vital role that genomic information can play in clinical care. Looking ahead, the anticipated advances in technologies, biological insights, and clinical applications (among others) will lead to more widespread dissemination of genomics throughout biomedical research, a growing adoption of genomics into medical and public health practices, and an increasing relevance of genomics in everyday life. At the same time, many challenges remain and require ongoing attention, such as understanding the biological complexities of the human genome, untangling the complex roles that genomic variants play in health and disease, and ensuring that genomics gets broadly and equitably integrated in medicine around the world.
+
+#### Biography
+
+Dr. Eric Green, M.D., Ph.D., is the recently appointed Chief Medical Officer at Illumina. As Illumina’s medical leader, Dr. Green is responsible for guiding global efforts to advance the clinical application of genomics, expand access to precision medicine, and increase diversity in genomic data to improve healthcare for people worldwide.
+
+Prior to joining Illumina, Dr. Green was a genomics researcher and leader at the National Human Genome Research Institute (NHGRI) at the U.S. National Institutes of Health, including serving as the NHGRI Director for more than 15 years. Under his directorship, NHGRI became a driving force in integrating genomics into medicine and public health. Dr. Green was also the founding Director of the NIH Intramural Sequencing Center.
+
+For over two decades, Dr. Green directed a research program that included start-to-finish roles in the Human Genome Project; groundbreaking work on mapping, sequencing, and comparing mammalian genomes; discoveries about the genes involved in several rare genetic diseases; and efforts to accelerate applications of genomics in healthcare. Dr. Green earned his M.D. and Ph.D. in 1987 from Washington University in St. Louis; coincidentally, the word “genomics” was coined in that same year. Dr. Green’s awards include being elected to the National Academy of Medicine in 2023, honored with the 2025 Leadership Award by the American Society of Human Genetics, and designated a Fierce 50 Innovation Honoree of 2025 (which honors “Trailblazers Redefining Health, Science, & Patient Care”).
+
+
+
+
+
+## Maryam Zaringhalam (Center for Open Science)
+
+### Science for the People: Open science to engage and build trust with communities
+
+#### Abstract
+
+The open science movement positions scientific knowledge as a global public good — yet in practice, open science is often not designed with public participation in mind. Policy efforts, including landmark federal public access policies to expand access to research, have largely focused on lowering barriers to accessing scholarly literature, datasets, and code. But access alone does not guarantee that research can meet communities where they are and address their most pressing needs.
+
+This gap has real consequences. The research community is increasingly discussing the erosion of public trust in science without fully reckoning with the gap between the research we produce and whether it actually reaches or serves the broader public. Simply put, we can do more to include and engage the communities with whom we seek to build trust. Open science, intentionally practiced, is a way to do that.
+
+Drawing on her experience spanning federal open science policy, biomedical research, and science communication, Dr. Zaringhalam will argue that open science represents an underutilized opportunity to rebuild that trust. By layering science communication and community engagement onto open research outputs, researchers, institutions, and practitioners can create genuine on-ramps for diverse publics — connecting the products and process of science to the communities who stand to benefit from them.
+
+This talk will explore practical approaches to bridging open science and community engagement, centering the needs of communities as a starting point for more meaningful and trustworthy science.
+
+#### Biography
+
+Maryam Zaringhalam, Ph.D., is the Senior Director of Policy at the [Center for Open Science (COS)](https://www.cos.io/). In that position, she leads COS’s policy efforts to increase openness, integrity, and trustworthiness of research.
+
+Prior to joining COS, Maryam served as the Data Science and Open Science Officer at the National Library of Medicine (NLM) at the National Institutes of Health (NIH), working to enhance capacity in the biomedical research community for data science and open science. From 2022 to 2024, she also served as the Assistant Director for Public Access and Research Policy at the White House Office of Science and Technology Policy (OSTP) where she oversaw federal policy development around public access, open science, and scientific integrity.
+
+Maryam is also a Senior Producer for the Story Collider, where she co-hosts the science policy podcast Science Soapbox, bringing true, personal stories of science to live audiences in Washington, DC. She received her PhD in Molecular Biology from the Rockefeller University.
+
+
+
+
+### BOSC keynote speaker selection process
+
+BOSC usually includes two or three keynote talks given by prominent individuals or emerging leaders who are accomplished in areas relevant to the bioinformatics open source community and who represent a range of backgrounds and ideas. Please see our [invited speaker rubric](https://github.com/OBF/bosc_materials/blob/master/invited-speaker-process.md) for more information about our keynote speaker selection process and criteria.
+
+
diff --git a/content/page/news.md b/content/page/news.md
index a408ed018..14ad25f29 100644
--- a/content/page/news.md
+++ b/content/page/news.md
@@ -6,4 +6,3 @@ title: News
url: /blog/
---
-
diff --git a/content/page/obf-bosc-collaborationfest-2023.md b/content/page/obf-bosc-collaborationfest-2023.md
index c45d0a020..d64eb90a5 100644
--- a/content/page/obf-bosc-collaborationfest-2023.md
+++ b/content/page/obf-bosc-collaborationfest-2023.md
@@ -30,14 +30,14 @@ Saturday July 22nd to Sunday 23rd, from 9am to 5.30pm.
## Location
-The 2023 BOSC CoFest will take place in Condorcet meeting room, at the ENS Lyon:
+The 2023 BOSC CoFest will take place in Condorcet meeting room, at the ENS Lyon:
-Address:
-[1, place de l’École
+Address:
+[1, place de l’École
\
-69007 Lyon
+69007 Lyon
\
-France
+France
](https://goo.gl/maps/9qEpK8smZ8TpDFFh9)
GPS coordinates: (45.729846881035385, 4.828230822514165)
diff --git a/content/page/obf-bosc-collaborationfest-2024.md b/content/page/obf-bosc-collaborationfest-2024.md
index 0f94066b9..4972bbc36 100644
--- a/content/page/obf-bosc-collaborationfest-2024.md
+++ b/content/page/obf-bosc-collaborationfest-2024.md
@@ -8,7 +8,7 @@ guid: https://www.open-bio.org/?page_id=7453
title: OBF/BOSC CollaborationFest 2024
url: /events/bosc-2024/obf-bosc-collaborationfest-2024/
aliases:
- - /events/bosc/collaborationfest/
+ - /events/bosc/collaborationfest2024/
bosc: yes
---
In conjunction with our annual meeting, [BOSC](/events/bosc/), the [OBF](/) runs a collaborative event (formerly called CodeFest, short for coding festival, and now called CollaborationFest, or CoFest for short). At these events, participants work together to contribute code, documentation, training materials, and challenging analysis problems and use cases. If you are interested in learning and contributing in an intensely collaborative environment, then CollaborationFest is for you.
diff --git a/content/page/obf-bosc-collaborationfest-2025.md b/content/page/obf-bosc-collaborationfest-2025.md
index 3747aac3f..a8c36cd02 100644
--- a/content/page/obf-bosc-collaborationfest-2025.md
+++ b/content/page/obf-bosc-collaborationfest-2025.md
@@ -7,7 +7,7 @@ date: "2025-02-16T09:35:44+00:00" #creation date
title: ISMB CollaborationFest 2025
url: /events/bosc-2025/ismb-collaborationfest-2025/
aliases:
- - /events/bosc/collaborationfest/
+ - /events/bosc/collaborationfest2025/
bosc: yes
---
@@ -31,7 +31,7 @@ Limited remote participation will be possible, but engagement opportunities will
{{< column >}}
-
+
{{< endcolumns >}}
@@ -69,7 +69,7 @@ The emergence of generative AI and large language models (LLMs) presents new opp
**Objective**
-Learn how to manually assign Gene Ontology terms or develop innovative approaches using LLM tools to enhance the curation workflow, enabling efficient and accurate extraction of experimental data from scientific literature.
+Learn how to manually assign Gene Ontology terms or develop innovative approaches using LLM tools to enhance the curation workflow, enabling efficient and accurate extraction of experimental data from scientific literature.
https://github.com/anphan0828/ISMB_CollaborationFest_EBI
@@ -79,7 +79,7 @@ Integrate drop in GPU-accelerated MMseq2 into biopython for acceleration.
https://github.com/collaborativebioinformatics/GPU_MSA_Integration
-#### 5. Integrate iCn3D viewer with Jalview MSA
+#### 5. Integrate iCn3D viewer with Jalview MSA
Jalview shows MSA and structure alignment with Jmol. Jalview could also link to iCn3D to show MSA together with structure alignment.
https://github.com/jiywang3/Integrate-iCn3D-viewer-with-Jalview-MSA
@@ -103,7 +103,7 @@ https://github.com/osercinoglu/grinn-ismb-2025
#### 8. Improving how we describe and discover Bioinformatics tools
-Bioconductor hosts over 3,000 R packages, but finding the right one can be challenging. biocEDAM is an experimental tool that uses large language models and the EDAM ontology to suggest meaningful package tags.
+Bioconductor hosts over 3,000 R packages, but finding the right one can be challenging. biocEDAM is an experimental tool that uses large language models and the EDAM ontology to suggest meaningful package tags.
At CoFest, we’ll work on integrating Gemini (a free, key‑free option) and testing the tool on more packages. We also welcome input on Model Context Protocols (MCPs), exploring how they might help surface package metadata in the future.
diff --git a/content/page/obf-bosc-collaborationfest-2026.md b/content/page/obf-bosc-collaborationfest-2026.md
new file mode 100644
index 000000000..0faf8b454
--- /dev/null
+++ b/content/page/obf-bosc-collaborationfest-2026.md
@@ -0,0 +1,75 @@
+---
+author: hmenager
+
+date: "2025-02-16T09:35:44+00:00" #creation date
+title: CollaborationFest 2026
+url: /events/bosc-2026/collaborationfest
+aliases:
+ - /events/bosc/collaborationfest2026/
+ - /events/bosc/collaborationfest/
+bosc: yes
+---
+
+{{< columns >}}
+
+
+
+{{< column >}}
+
+CollaborationFest 2026 will be a collaborative work event at which participants work together to contribute code, documentation, training materials, and challenging analysis problems and use cases. If you are interested in learning and contributing in an intensely collaborative environment, then CollaborationFest is for you. Bring your own project ideas or come ready to collaborate with others on their projects!
+
+BOSC has organized CollaborationFests (aka CoFests) every year before or after ISMB since 2010.
+The 2026 CoFest will start the day after ISMB 2026, in a nearby location in Washington, DC.
+
+{{< endcolumns >}}
+
+### Dates and Location
+
+Friday July 17 to Saturday July 18 (right after ISMB 2026), 9:00am - 5:00pm both days.
+
+The location is in central Washington DC. The address will be shared with those who register.
+
+{{< columns >}}
+
+### How to sign up
+
+Due to space constraints, participation in CollaborationFest is limited. Participation is free, but registration is mandatory. A registration link will be available shortly.
+
+We encourage you to register for ISMB, but the CoFest itself is free. Three easy steps to sign up:
+
+- add yourself to this [spreadsheet](https://docs.google.com/spreadsheets/d/1HvB9nHCBiCrSLWR9BNG5ypMecEbn7MOOnWIZxagQwRo/edit?usp=sharing) to help us gauge interest, coordinate topic groups and logistics
+- add your project ideas to this [document](https://docs.google.com/document/d/1x7h4Tx3Y8IrcDSkSs_LylVFzQhjNKmQpwAbizQnyxYQ/edit?tab=t.0) if you have something in mind
+- join the #cofest2026 channel in the [OBF Slack](https://join.slack.com/t/obf-bosc/shared_invite/zt-3va3bz5qa-hR9nKXHXO9GmrkddIpJXcQ)!
+
+{{< column >}}
+
+
+
+{{< endcolumns >}}
+
+### Cost
+
+CoFest is free to attend, and lunches will be provided thanks to Seqera.
+
+### CollaborationFest News and Activities
+
+As we get closer to BOSC 2026 and the CollaborationFest, we will add relevant news and activities here. Note that some of
+these activities are on dynamically updated Github pages, and will only be fully ready "the day of", or shortly before.
+
+### Sponsors
+
+{{< columns >}}
+
+
+
Thanks to Computercraft, for generously providing the space for this event; we appreciate their support in making it possible.
+
+{{< column >}}
+
+
+
Thanks to Seqera for providing food throughout the event.
+
+{{< endcolumns >}}
+
+### Code of Conduct
+
+As an OBF-organized event, CollaborationFest 2026 is covered by the [OBF Code of Conduct](https://github.com/OBF/obf-docs/blob/master/code-of-conduct/CODE_OF_CONDUCT.md).
diff --git a/content/page/panel.md b/content/page/panel-2025.md
similarity index 99%
rename from content/page/panel.md
rename to content/page/panel-2025.md
index 4c221584a..918fa2e09 100644
--- a/content/page/panel.md
+++ b/content/page/panel-2025.md
@@ -86,7 +86,7 @@ For decades, he has been a strong advocate for open-source bioinformatics softwa
Dr Scott Edmunds is Editor in Chief of [GigaScience](https://academic.oup.com/gigascience), the Hong Kong based Open Science journal that publishes data and software papers (and which launched at ISMB in 2012).
After PhD and postdoctoral research experience in Cancer Molecular Pathology, he has spent nearly 20 years working in open access publishing and open data.
-He has co-founded Citizen Science organisations Bauhinia Genome and CitizenScience.Asia, and is on the Board of Directors of the Dryad Digital Repository and Make Data Count.
+He has co-founded Citizen Science organisations Bauhinia Genome and CitizenScience.Asia, and is on the Board of Directors of the Dryad Digital Repository and Make Data Count.
He has also taught data management and curation at Hong Kong University.
{{< column >}}
diff --git a/content/page/panels-2026.md b/content/page/panels-2026.md
new file mode 100644
index 000000000..047783a55
--- /dev/null
+++ b/content/page/panels-2026.md
@@ -0,0 +1,178 @@
+---
+author: monicacecilia
+date: "2026-06-12T19:20:23+00:00"
+title: BOSC 2026 Panels
+url: /events/bosc-2026/panels/
+bosc: yes
+
+---
+For the first time ever, BOSC will include **two** panel discussions featuring perspectives from across the open science, bioinformatics, policy, and AI landscapes.
+
+# Panel 1: Policies and Strategies for Resilient Open Science
+
+As we gather in Washington, D.C. for BOSC 2026, we stand at the literal and figurative crossroads of the policies that dictate the pulse of our field. For years, the open science community has operated under a steady wind of progress, but the past year has shifted the weather. We have moved from an era of "open by default" to an environment where the infrastructure of open science—funding, federal data repositories, and international collaborations—is increasingly under scrutiny. This panel moves beyond theoretical support for open science to focus on the strategies of resilience and active advocacy required to navigate a landscape that is being rapidly redefined.
+
+The current climate in the United States has seen federal agencies, which are the traditional engines of open research, reorienting under new mandates that prioritize "national interest" and "operational efficiency." While these shifts have created uncertainty, they have also demonstrated **the power of the community**; despite early threats of deep cuts, concerted advocacy has kept certain key research budgets remarkably stable. Resilience, therefore, is not just about surviving these shifts; it is about building a proactive presence in the rooms where these decisions are made. We will explore how these domestic tensions mirror global trends, from the rise of protectionist data policies to the decentralized alternatives emerging in the wake of federal volatility.
+
+Our discussion will range from high-level policy to the practical "how-to" of remaining principled and productive, addressing topics that include: the Advantage of Advocacy, Navigating Funding Fragility, Protecting the Digital Commons, and Institutional Fortification.
+
+# Panelists
+
+### Maryam Zaringhalam
+**Center for Open Science**
+
+{{< columns >}}
+
+Maryam Zaringhalam, PhD, is the Senior Director of Policy at the Center for Open Science (COS), where she leads strategic policy efforts to improve the openness, integrity, and reproducibility of scientific research. Prior to joining COS, she served as the Data Science and Open Science Officer at the National Library of Medicine (NLM) at the NIH and as the Assistant Director for Public Access and Research Policy at the White House Office of Science and Technology Policy (OSTP), where she oversaw the implementation of the landmark 2022 public access memo and coordinated the 2023 Federal Year of Open Science. A molecular biologist by training, Maryam received her PhD from Rockefeller University. She is also a Senior Producer for *The Story Collider*, utilizing narrative storytelling to foster community engagement and dismantle barriers to open, inclusive science.
+
+{{< column >}}
+
+
+
+{{< endcolumns >}}
+
+### Ann Nowakowski
+**Sage Bionetworks**
+
+{{< columns >}}
+
+
+
+{{< column >}}
+
+Ann Novakowski, MPH, is Associate Technical Director of Product Strategy at Sage Bionetworks, where she helps translate policy, governance, and community needs into products that support open and responsible biomedical research. Her work spans federated data ecosystems, data access and reuse, digital use conditions, and emerging approaches to AI-enabled research. Drawing on more than 20 years of experience in public health, global health, and research infrastructure, she is particularly interested in how technical systems, governance models, and community practices can work together to make open science more sustainable, trustworthy, and resilient. She holds an MPH from Yale University and a BS in Molecular and Cellular Biology from the University of Arizona.
+
+{{< endcolumns >}}
+
+### Mallory Freeberg
+**EMBL-EBI**
+
+{{< columns >}}
+
+Mallory Freeberg, PhD, is the Human Genomics Team Leader at EMBL’s European Bioinformatics Institute (EMBL-EBI). She directs major genomic variation resources, including the Ensembl Variant Effect Predictor (VEP) tool, human variation interpretation platforms (such as DECIPHER and Gene2Phenotype), and the European Genome-phenome Archive (EGA). Mallory’s career is dedicated to promoting the responsible and standardized sharing of FAIR human clinical and omics data. She actively guides international data harmonization frameworks and serves as Co-Lead of the Global Alliance for Genomics and Health (GA4GH) Implementation Forum, facilitating interoperability between clinical and research domains. She earned her PhD in Bioinformatics from the University of Michigan.
+
+{{< column >}}
+
+
+
+{{< endcolumns >}}
+
+### Guy Cochrane
+**Global BioData Coalition (GBC)**
+
+{{< columns >}}
+
+
+
+{{< column >}}
+
+Guy Cochrane, PhD, is the Scientific Head of the Global BioData Coalition (GBC) and a faculty member at EMBL-EBI. He works internationally to unite life science and biomedical funding organizations around long-term sustainability models for core data infrastructure. Guy previously served as the Head of the European Nucleotide Archive (ENA) and led critical pandemic-response infrastructure as a leader of the European COVID-19 Data Platform. His long-standing advocacy for open data encompasses policy development for access and benefit sharing, international metadata standards development, and leadership within the International Nucleotide Sequence Database Collaboration (INSDC).
+
+{{< endcolumns >}}
+
+### Sam Halabi
+**Georgetown University**
+
+{{< columns >}}
+
+Sam Halabi, JD, MPhil, is the Bette Jacobs Endowed Professor in Georgetown University's Department of Health Management and Policy and directs the Center for Transformational Health Law at the O'Neill Institute for National and Global Health Law. His research focuses on the law and ethics of pandemic preparedness, global vaccine deployment, and the complexities of international biomedical data sharing. He has authored over 100 manuscripts and five books covering data sharing, global health security, and liability in emergency public health responses. He regularly advises or has advised the World Health Organization (WHO), the World Bank, and the COVAX Facility, and is a member of the WHO’s Working Group on Regulatory Approaches to AI and Health. He holds a JD from Harvard University and an MPhil from the University of Oxford.
+
+{{< column >}}
+
+
+
+{{< endcolumns >}}
+
+### MODERATOR: Mónica Muñoz Torres
+
+{{< columns >}}
+
+
+
+{{< column >}}
+
+Dr. Muñoz Torres is an Associate Professor at the University of Colorado Anschutz. Her work focuses on the critical challenge of developing the socio-technical foundations needed to realize the promise of artificial intelligence in biomedical sciences. Her expertise includes genomics, biocuration, knowledge representation, and data harmonization. She leads the NIH-funded Bridge to Artificial Intelligence (Bridge2AI)’s team focused on Standards, Practices, and Quality Assessment. She is also Co-Lead of the Clinical & Phenotypic Data Capture Work Stream of the Global Alliance for Genomics and Health (GA4GH).
+
+{{< endcolumns >}}
+
+
+
+# Panel 2: Open Source in the Age of AI
+
+Open-source software has been a key part of the bioinformatics landscape for decades, enabling large-scale collaboration and supporting reproducible science.
+The emergence of generative AI represents a fundamental shift in how code is authored, maintained, and shared. This panel will examine the "elephant in the room": is generative AI a powerful advantage for open-source communities, or a threat to their long-term health, or both?
+We will explore how AI tools—which can generate thousands of lines of code in seconds—challenge our notions of contribution, reuse, and the value of human-authored frameworks.
+
+While AI makes it easier than ever to code solutions from scratch, it raises critical questions about the sustainability of existing projects and the scientific accuracy of machine-generated results. As the difficult part of software development shifts from writing code to verifying it for scientific integrity, our communities and the way they operate must evolve. From assessing pull requests submitted by AI agents to debating the merits of bans on AI-generated submissions, the open-source community is at a crossroads in defining how humans and AI agents can best work together.
+
+This panel will bring together a variety of perspectives to discuss topics including: Reuse, Attribution and Accountability, Licensing, Sustainability, and the Future of Open Data.
+
+# Panelists
+
+### Aida Miro-Herrans
+**University of Florida**
+
+{{< columns >}}
+
+
+
+{{< column >}}
+
+Aida Miro-Herrans is the Bioinformatics Librarian at the University of Florida Libraries, where she focuses on supporting open science, open education, and instruction in bioinformatics methods. Her current work investigates the intersection of artificial intelligence and life science education, specifically exploring how generative AI tools can optimize student learning. Her upcoming presentation at BOSC 2026 highlights a specialized workshop design that empowers life science instructors to leverage AI chatbots to craft active learning activities built entirely on open-source software and open-access datasets.
+
+{{< endcolumns >}}
+
+### Nahid Zeinali
+**California Medical Innovations Institute**
+
+{{< columns >}}
+
+Nahid Zeinali, PhD, is an AI Research Scientist at the California Medical Innovations Institute (CalMI2) and a core team member at the FAIR Data Innovations Hub (FAIRHub). She specializes in natural language processing, deep learning, and artificial intelligence architectures tailored for healthcare and biomedical data. She completed her PhD in Informatics at the University of Iowa in 2025, where her research focused on turning complex multi-modal data into deployable, trustworthy digital biomarkers and healthcare solutions. At CalMI2, her work bridges advanced machine learning methods with open data frameworks to build interoperable, AI-driven medical products.
+
+{{< column >}}
+
+
+
+{{< endcolumns >}}
+
+### Alex Bateman
+**EMBL-EBI**
+
+{{< columns >}}
+
+
+
+{{< column >}}
+
+Alex Bateman, PhD, is a Senior Team Leader for Protein Sequence Resources at EMBL-EBI. He serves as a Principal Investigator for the UniProt consortium and has broad oversight over protein and non-coding RNA databases, including RNAcentral. Before joining EMBL-EBI in 2012, Alex managed several of the community's most widely utilized biological resources at the Wellcome Sanger Institute, including Pfam and Rfam. He has driven open-source data standards as a former Chairman of the International Society for Biocuration (ISB) Executive Committee, and has served as the Executive Editor for *Bioinformatics* and the Editor of *Nucleic Acids Research* Database Issue.
+
+{{< endcolumns >}}
+
+### Eric Green
+**Illumina**
+
+{{< columns >}}
+
+Eric Green, MD, PhD, is the Chief Medical Officer at Illumina and a legendary figure in the history of genomics. He spent over two decades directing a premier research program at the National Human Genome Research Institute (NHGRI) at the U.S. National Institutes of Health, where he played a start-to-finish role in the historic Human Genome Project and founded the NIH Intramural Sequencing Center. He subsequently served as the Director of NHGRI for over 15 years, acting as a primary driver of the integration of genomics into clinical care and public health globally. An elected member of the National Academy of Medicine, he currently focuses on guiding global efforts to broaden access to precision medicine, ensure diversity in genomic data, and navigate the clinical applications of genomics in an era increasingly defined by advanced computational and AI tools.
+
+{{< column >}}
+
+
+
+{{< endcolumns >}}
+
+### MODERATOR: Jason Williams
+
+{{< columns >}}
+
+
+
+{{< column >}}
+
+Jason Williams, is the Assistant Director of Cold Spring Harbor's Dolan DNA Learning Center.
+He was elected an AAAS Fellow in 2026. In 2025, he won the Elizabeth W. Jones Award for Excellence in Education.
+Mr. Williams has been instrumental in bringing the latest technologies and teaching approaches for working with DNA into classrooms around the world through dedicated hands-on programs for students and teachers.
+He develops national and international biology education and professional development programs. In addition to his work at the DNALC, Williams is the founder of LifeSciTrainers.org, a global initiative promoting a community of practice among professionals who develop short-format training for life scientists.
+He is also the Lead Investigator of the [NSF Arecibo Center for STEM Education, Computing, and Community Engagement](https://areciboc3.org/).
+
+{{< endcolumns >}}
diff --git a/content/page/project-ideas.md b/content/page/project-ideas.md
index 16d4a1e59..4a673df3c 100644
--- a/content/page/project-ideas.md
+++ b/content/page/project-ideas.md
@@ -101,7 +101,7 @@ The overall goal of this project is to improve the configurability of the featur
**Project description**
-OpenMS is a framework for computational mass spectrometry. Modern mass spectrometers produce large files (e.g., 100 GB) that can’t be easily stored or accessed in the established XML file format mzML. Recently, an update to mzML has been developed that uses HDF5 to store Blosc compressed spectra in binary format: called mzMLb.
+OpenMS is a framework for computational mass spectrometry. Modern mass spectrometers produce large files (e.g., 100 GB) that can’t be easily stored or accessed in the established XML file format mzML. Recently, an update to mzML has been developed that uses HDF5 to store Blosc compressed spectra in binary format: called mzMLb.
In this project, the student will add a reader and writer for the mzMLb file format to OpenMS. To some extent, code from the OpenMS reader and writer for the mzML file format can be reused, as well as inspiration can be taken from reference implementations by other parties.
**Project size**
@@ -144,7 +144,7 @@ In this project, the student will add a reader and writer for the mzMLb file for
**Project description**
-OpenMS is a framework for computational mass spectrometry. It features a wide range of algorithms and data structures to process and analyze mass spectra. For some very computationally demanding parts, we performed manual code conversion to make the layout of our data better fit the data access patterns of our algorithms. We observed the biggest speedup switching the data layout from an Array of Structs (AoS) to a Structure of Arrays (SoA).
+OpenMS is a framework for computational mass spectrometry. It features a wide range of algorithms and data structures to process and analyze mass spectra. For some very computationally demanding parts, we performed manual code conversion to make the layout of our data better fit the data access patterns of our algorithms. We observed the biggest speedup switching the data layout from an Array of Structs (AoS) to a Structure of Arrays (SoA).
In this project, the GSoC contributor will adapt our core data structure for mass spectra to AoS. Ideally, the contributor should be using a modern C++ zero-cost abstraction (e.g., building on https://github.com/crosetto/SoAvsAoS) that makes the old code work without (or minimal) manual changes.
**Project size**
diff --git a/content/page/projects.md b/content/page/projects.md
index 0b0cfe90f..e263a08a2 100644
--- a/content/page/projects.md
+++ b/content/page/projects.md
@@ -48,4 +48,4 @@ The OBF has [a process for projects in the open bioinformatics realm to become m
* [BlipKit](https://github.com/cmungall/blipkit): Chris Mungall’s Prolog toolkit for Bioinformatics and BioMedical Informatics.
* [Biolib](https://github.com/biolib/obf-biolib): Cross-project/language C bindings for a shared codebase across the different Bio* projects (Pjotr Prins).
* DAS / BioDAS: The Distributed Annotation System defines a communication protocol used to exchange annotations on genomic or protein sequences.
-* [EMBOSS](https://emboss.sourceforge.net/): An analysis package developed for the needs of the molecular biology (e.g. EMBnet) user community.
+* [EMBOSS](https://emboss.sourceforge.net/): An analysis package developed for the needs of the molecular biology (e.g. EMBnet) user community.
diff --git a/content/page/schedule-2025.md b/content/page/schedule-2025.md
index 15d975d74..5aa31048b 100644
--- a/content/page/schedule-2025.md
+++ b/content/page/schedule-2025.md
@@ -32,7 +32,7 @@ Working together to develop, promote and protect our data resources: Lessons lea
+
+## [BOSC 2026 keynote speakers](/events/bosc-2026/bosc-2026-keynotes/)
+
+{{< columns >}}
+
+
+
+[KEYNOTE: Eric Green](/events/bosc-2026/bosc-2026-keynotes)
+
+From the Human Genome Project to the Realization of Genomic Medicine: A Scientific, Medical, and Societal Journey
+
+{{< column >}}
+
+
+
+[KEYNOTE: Maryam Zaringhalam](/events/bosc-2026/bosc-2026-keynotes)
+
+Science for the People: Open science to engage and build trust with communities
+
+{{< endcolumns >}}
+
+
+
+
+
+## [Panel: Policies and Strategies for Resilient Open Science](/events/bosc-2026/panels/)
+Panelists: Maryam Zaringhalam, Ann Nowakowski, Mallory Freeberg, Guy Cochrane, Sam Halabi
+Moderator: Mónica Muñoz Torres
+
+## [Panel: Open Source in the Age of AI](/events/bosc-2026/panels/)
+Panelists: Eric Green, Aida Miro-Herrans, Nahid Zeinali, Alex Bateman
+Moderator: Jason Williams
+
+
+
+## BOSC 2026 Schedule at a Glance
+(Keep scrolling to see the full schedule of talks and posters!)
+
+
+
+
+## Schedule of Talks
+
+
+
+
+## Schedule of Posters
+Posters are displayed for two days (July 13-14 or 15-16). The presenter is assigned one of those two days to stand by their posters.
+These dates are listed in the table below, and can also be found on [the ISMB poster schedule](https://www.iscb.org/ismb2026/scientific-programme/posters).
+On that page, there are four different BOSC links to see which posters are being presented each of the four days.
+
+
+
+
diff --git a/content/page/sponsors-1.md b/content/page/sponsors-1.md
index 8180f4612..ee1285c99 100644
--- a/content/page/sponsors-1.md
+++ b/content/page/sponsors-1.md
@@ -64,7 +64,7 @@ BOSC participants come from a wide variety
- Biological researchers, students, and post-docs who are learning bioinformatics analysis tools and techniques
- Power bioinformatics users
-- Bioinformatics tool and workflow developers
+- Bioinformatics tool and workflow developers
- Bioinformatics-focused principal investigators and researchers
- Sequencing core facility staff
@@ -73,7 +73,7 @@ BOSC participants come from a wide variety
# Previous Events
-The OBF has organized BOSC [every year since 2000](/events/bosc/about/). From 2000 to 2017 and again in 2019, BOSC was run as part of the large ISMB conference. In 2018 (and again in 2020) it partnered with the Galaxy Community Conference. The OBF CodeFests (now renamed CollaborationFest, or CoFest) have been held every year after BOSC since 2010.
+The OBF has organized BOSC [every year since 2000](/events/bosc/about/). From 2000 to 2017 and again in 2019, BOSC was run as part of the large ISMB conference. In 2018 (and again in 2020) it partnered with the Galaxy Community Conference. The OBF CodeFests (now renamed CollaborationFest, or CoFest) have been held every year after BOSC since 2010.
The table below shows the approximate number of participants in BOSC and the CoFest. Figures for the CoFest and BOSC are number of people registered for at least one day of the meeting. The BOSC figures do not include drop-in attendees from the parallel sessions organized by other groups. The figures for CoFest do not include remote participants.
@@ -143,8 +143,8 @@ We acknowledge our sponsors before, during and after the event in multiple ways:
## BOSC 2021 Silver Sponsors
-[](https://elifesciences.org/)
-[](https://geneviatechnologies.com/)
+[](https://elifesciences.org/)
+[](https://geneviatechnologies.com/)
[](https://oup.com/)[](https://bioteam.net)
If you are interested in becoming a sponsor, please contact us at bosc@open-bio.org!
diff --git a/content/page/sponsors-2.md b/content/page/sponsors-2.md
index 3f8ff8026..918667f50 100644
--- a/content/page/sponsors-2.md
+++ b/content/page/sponsors-2.md
@@ -55,7 +55,7 @@ BOSC participants come from a wide variety
- Biological researchers, students, and post-docs who are learning bioinformatics analysis tools and techniques
- Power bioinformatics users
-- Bioinformatics tool and workflow developers
+- Bioinformatics tool and workflow developers
- Bioinformatics-focused principal investigators and researchers
- Sequencing core facility staff
@@ -64,7 +64,7 @@ BOSC participants come from a wide variety
# Previous Events
-The OBF has organized BOSC [every year since 2000](/events/bosc/about/). From 2000 to 2017 and again in 2019, BOSC was run as part of the large ISMB conference. In 2018 (and again in 2020) it partnered with the Galaxy Community Conference. The OBF CodeFests (now renamed CollaborationFest, or CoFest) have been held every year after BOSC since 2010.
+The OBF has organized BOSC [every year since 2000](/events/bosc/about/). From 2000 to 2017 and again in 2019, BOSC was run as part of the large ISMB conference. In 2018 (and again in 2020) it partnered with the Galaxy Community Conference. The OBF CodeFests (now renamed CollaborationFest, or CoFest) have been held every year after BOSC since 2010.
The table below shows the approximate number of participants in BOSC and the CoFest. Figures for the CoFest and BOSC are number of people registered for at least one day of the meeting. The BOSC figures do not include drop-in attendees from the parallel sessions organized by other groups. The figures for CoFest do not include remote participants.
@@ -112,8 +112,8 @@ We acknowledge our sponsors before, during and after the event in multiple ways:
## BOSC 2021 Silver Sponsors
-[](https://elifesciences.org/)
-[](https://geneviatechnologies.com/)
-[](https://oup.com/)[](https://bioteam.net)
+[](https://elifesciences.org/)
+[](https://geneviatechnologies.com/)
+[](https://oup.com/)[](https://bioteam.net)
If you are interested in becoming a sponsor, please contact us at bosc@open-bio.org!
diff --git a/content/page/sponsors-2023.md b/content/page/sponsors-2023.md
index 266dfe780..6c750a56c 100644
--- a/content/page/sponsors-2023.md
+++ b/content/page/sponsors-2023.md
@@ -55,7 +55,7 @@ BOSC participants come from a wide variety
- Biological researchers, students, and post-docs who are learning bioinformatics analysis tools and techniques
- Power bioinformatics users
-- Bioinformatics tool and workflow developers
+- Bioinformatics tool and workflow developers
- Bioinformatics-focused principal investigators and researchers
- Sequencing core facility staff
@@ -64,7 +64,7 @@ BOSC participants come from a wide variety
# Previous Events
-The OBF has organized BOSC [every year since 2000](/events/bosc/about/). From 2000 to 2017 and again in 2019, BOSC was run as part of the large ISMB conference. In 2018 (and again in 2020) it partnered with the Galaxy Community Conference. The OBF CodeFests (now renamed CollaborationFest, or CoFest) have been held every year after BOSC since 2010.
+The OBF has organized BOSC [every year since 2000](/events/bosc/about/). From 2000 to 2017 and again in 2019, BOSC was run as part of the large ISMB conference. In 2018 (and again in 2020) it partnered with the Galaxy Community Conference. The OBF CodeFests (now renamed CollaborationFest, or CoFest) have been held every year after BOSC since 2010.
The table below shows the approximate number of participants in BOSC and the CoFest. Figures for the CoFest and BOSC are number of people registered for at least one day of the meeting. The BOSC figures do not include drop-in attendees from the parallel sessions organized by other groups. The figures for CoFest do not include remote participants.
@@ -126,8 +126,8 @@ We acknowledge our sponsors before, during and after the event in multiple ways:
## BOSC 2021 Silver Sponsors
-[](https://elifesciences.org/)
-[](https://geneviatechnologies.com/)
-[](https://oup.com/)[](https://bioteam.net)
+[](https://elifesciences.org/)
+[](https://geneviatechnologies.com/)
+[](https://oup.com/)[](https://bioteam.net)
If you are interested in becoming a sponsor, please contact us at bosc@open-bio.org!
diff --git a/content/page/sponsors-new-draft-2023.md b/content/page/sponsors-new-draft-2023.md
index 53abc92c5..d95a8ec3c 100644
--- a/content/page/sponsors-new-draft-2023.md
+++ b/content/page/sponsors-new-draft-2023.md
@@ -55,7 +55,7 @@ BOSC participants come from a wide variety
- Biological researchers, students, and post-docs who are learning bioinformatics analysis tools and techniques
- Power bioinformatics users
-- Bioinformatics tool and workflow developers
+- Bioinformatics tool and workflow developers
- Bioinformatics-focused principal investigators and researchers
- Sequencing core facility staff
@@ -64,7 +64,7 @@ BOSC participants come from a wide variety
# Previous Events
-The OBF has organized BOSC [every year since 2000](/events/bosc/about/). From 2000 to 2017 and again in 2019, BOSC was run as part of the large ISMB conference. In 2018 (and again in 2020) it partnered with the Galaxy Community Conference. The OBF CodeFests (now renamed CollaborationFest, or CoFest) have been held every year after BOSC since 2010.
+The OBF has organized BOSC [every year since 2000](/events/bosc/about/). From 2000 to 2017 and again in 2019, BOSC was run as part of the large ISMB conference. In 2018 (and again in 2020) it partnered with the Galaxy Community Conference. The OBF CodeFests (now renamed CollaborationFest, or CoFest) have been held every year after BOSC since 2010.
# Sponsorship
@@ -144,7 +144,7 @@ We acknowledge our sponsors before, during and after the event in multiple ways:
- Helicos Biosciences
-- Humboldt University of Berlin Institute
+- Humboldt University of Berlin Institute
of Biology
- Intel
diff --git a/content/page/sponsors.md b/content/page/sponsors.md
index b4cb5f4bf..94ab74443 100644
--- a/content/page/sponsors.md
+++ b/content/page/sponsors.md
@@ -1,120 +1,234 @@
---
author: nlharris
-cover:
- alt: ""
- image: /wp-content/uploads/2021/06/image-8.png
-date: "2024-02-15T16:33:21+00:00"
-draft: "true"
-guid: https://www.open-bio.org/?page_id=7658
+date: "2025-10-22T19:05:24+00:00"
title: Sponsors
-url: /
-
+url: /events/bosc/sponsors/
+bosc: yes
---
-# Sponsoring BOSC
-Page with BOSC 2023 Sponsors: [open-bio.org/events/sponsors/](/events/sponsors/)
+{{< columns >}}
+### Sponsoring BOSC
-## BOSC 2022 Platinum Sponsors
+Sponsorships from companies and non-profit organizations help enable us to provide free registration for some conference participants, offer honorariums to keynote speakers, and cover other expenses. Sponsors gain increased visibility and trust across the open source and open science ecosystem.
-[](https://chanzuckerberg.com/)[](http://aws.amazon.com)
+
-## BOSC 2022 Gold Sponsors
+#### Interested in sponsoring BOSC?
-[](https://www.broadinstitute.org/data-sciences-platform)[](https://datascience.nih.gov/)
+#### Please contact us: bosc@open-bio.org!
-### BOSC 2022 Silver Sponsors
+{{< column >}}
-[](https://arvados.org)[](https://academic.oup.com/gigascience)
+
-
+{{< endcolumns >}}
-Sponsorships from companies and organizations help to defray some of our costs and enable us to offer registration fee waivers for some conference participants. In 2021, thanks to our sponsors' generous support, we were able to grant free registration to 20 participants at [BOSC 2021](/events/bosc-2021/), offer honoraria to keynote speakers, and cover other expenses.
+
+
-If you’re interested in sponsoring BOSC 2022, please contact us at bosc@open-bio.org!
+## 2026 Gold Sponsors:
-Thanks to our 2021 sponsors, we were able to offer free ISMB/ECCB 2021 registration to 20 participants from all over the world!
-{{< googlemaps src="1z3D_j0fQYGDqMpCm1f8GQIi2KPvPzOEH" width=640 height=480 >}}
+
+
The NIH Office of Data Science Strategy (ODSS) leads the implementation of the NIH Strategic Plan for Data Science through scientific, technical, and operational collaboration with the institutes, centers, and offices that comprise NIH.
-## What is BOSC?
+
+
+
+
Seqera, built by the creators of Nextflow, is the enterprise-first bioinformatics platform trusted by leading pharma and diagnostics companies to build, validate, and scale bioinformatics with confidence.
+
+
-BOSC is an annual meeting organized by the Open Bioinformatics Foundation (OBF), a non-profit, volunteer-run group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community.
-Whether in-person or online, each BOSC includes talks, poster sessions, birds-of-a-feather gatherings, and lots of opportunities for networking. It is followed by collaborative working sessions at the CollaborationFest. These events bring together software engineers, bioinformaticians, and researchers to collaborate and extend open source bioinformatics tools.
+### 2026 Silver Sponsor:
-Most years, BOSC has been part of the Intelligent Systems for Molecular Biology meeting (ISMB/ECCB). In 2018, BOSC partnered with the Galaxy Community Conference (GCC) in a very successful joint meeting in Portland, [GCCBOSC 2018](https://gccbosc2018.sched.com/). In July 2020, BOSC again joined forces with GCC to form the [Bioinformatics Community Conference (BCC2020)](https://bcc2020.github.io/). Held online, BCC2020 attracted over 600 participants from 62 countries. [BOSC 2021](/events/bosc-2021/) was part of [ISMB/ECCB 2021](https://www.iscb.org/ismbeccb2021), and took place July 29-30, 2021 (followed by a two-day [CollaborationFest](/events/bosc-2021/collaborationfest/)).
+
+
Dryad is a non-profit open data publishing platform operating in the community interest, and committed to the open availability and routine re-use of all research data. Dryad makes FAIR-complaint data publishing simple through robust open-source infrastructure, hands-on researcher support, and an easy-to-use submission interface.
-BOSC 2022 will take place July 13-14, 2022, as part of [ISMB 2022](https://www.iscb.org/ismb2022). The meeting will be held both in person in Madison, Wisconsin, USA, and simultaneously online.
+
+
+## What is BOSC?
-
+BOSC is an annual meeting organized by the [Open Bioinformatics Foundation (OBF)](/), a non-profit, volunteer-run group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community.
-
+Each BOSC includes keynote talks, talks chosen from submitted abstracts, poster sessions, panel, and lots of opportunities for networking. It is followed by collaborative working sessions at the [CollaborationFest](/events/bosc/collaborationfest/). These events bring together software engineers, bioinformaticians, and researchers to collaborate on open source bioinformatics tools and frameworks and approaches to open science.
-
+ Most years, BOSC has been part of the Intelligent Systems for Molecular Biology meeting (ISMB), which typically attracts over 2000 participants.
-
+
BOSC participants come from a wide variety of research environments and backgrounds:
-- Biological researchers, students, and post-docs who are learning bioinformatics analysis tools and techniques
+- Biological researchers, students, and post-docs
- Power bioinformatics users
-- Bioinformatics tool and workflow developers
-
+- Bioinformatics tool and workflow developers
- Bioinformatics-focused principal investigators and researchers
- Sequencing core facility staff
- Industry scientists and bioinformaticians
-- Data producers
+- Data scientists
+
+## Previous Events
+
+BOSC has been held [every year since 2000](/events/bosc/about/). Most years, BOSC is part of the large Intelligent Systems for Molecular Biology meeting (ISMB).
+
+In 2018, BOSC partnered with the Galaxy Community Conference (GCC) in a very successful joint meeting in Portland, [GCCBOSC 2018](https://gccbosc2018.sched.com/). In July 2020, BOSC again joined forces with GCC to form the [Bioinformatics Community Conference (BCC2020)](https://bcc2020.github.io/). Held online, BCC2020 attracted over 600 participants from 62 countries.
+
+[BOSC 2021](/events/bosc-2021/) was part of [ISMB/ECCB 2021](https://www.iscb.org/ismbeccb2021), and took place July 29-30, 2021 (followed by a two-day [CollaborationFest](/events/bosc-2021/collaborationfest/)).
+
+[BOSC 2022](/events/bosc-2022/) was held July 13-14, 2022, as part of [ISMB 2022](https://www.iscb.org/ismb2022) in person in Madison, Wisconsin, USA, and simultaneously online.
+
+[BOSC 2023](/events/bosc-2023/) took place July 24-25, 2023 as part of [ISMB/ECCB 2023](https://www.iscb.org/ismbeccb2023) in Lyon, France and online. Like the previous year, we joined forces with Bio-Ontologies for part of a day!
+
+[BOSC 2024](/events/bosc-2024/), the 25th annual Bioinformatics Open
+Source Conference, took place July 15-16, 2024 as part of
+[ISMB 2024](https://www.iscb.org/ismb2024/home) in Montreal, Canada
+and online. It was followed by [CoFest 2024](/events/bosc-2024/ismb-collaborationfest-2024/).
+
+[BOSC 2025](/events/bosc-2025/) took place in Liverpool, UK, as part
+of the large [ISMB/ECCB 2025](https://www.iscb.org/ismbeccb2025/home)
+conference, which attracted a record 2238 participants. For the first time,
+[CollaborationFest](/events/bosc-2025/ismb-collaborationfest-2025/)
+was part of the main ISMB/ECCB conference.
+
+[BOSC 2026](/events/bosc/) will be held in Washington, DC (with an online participation option) July 14-15, 2026 as part of [ISMB 2026](https://www.iscb.org/ismb2026/home).
-# Previous Events
+More about BOSC
-The OBF has organized BOSC [every year since 2000](/events/bosc/about/). From 2000 to 2017 and again in 2019, BOSC was run as part of the large ISMB conference. In 2018 (and again in 2020) it partnered with the Galaxy Community Conference. The OBF CodeFests (now renamed CollaborationFest, or CoFest) have been held every year after BOSC since 2010.
+
-The table below shows the approximate number of participants in BOSC and the CoFest. Figures for the CoFest and BOSC are number of people registered for at least one day of the meeting. The BOSC figures do not include drop-in attendees from the parallel sessions organized by other groups. The figures for CoFest do not include remote participants.
+
-YearLocation BOSC ParticipantsCoFest Participants 2020BCC2020 (BOSC + Galaxy): virtual~300~1502019Basel, Switzerland109352018 Portland, OR, USA1501002017 Prague, Czech Republic 230652016 Orlando, FL, USA90362015Dublin, Ireland125352014Boston, MA, USA100602013Berlin, Germany100372012Long Beach, CA, USA 100132011 Vienna, Austria 12035
+## Benefits of Sponsorship
-# Sponsorship
+Sponsoring BOSC increases your visibility in the bioinformatics community.
+We acknowledge our sponsors before, during and after the event in multiple ways:
+
+- We list our sponsors on the BOSC website
+- Sponsors are thanked and named in the introduction/closing slides during the meeting
+- We show the sponsor logos on large BOSC posters displayed outside the meeting room and in the poster area
+- The sponsors are thanked in selected emails to our mailing list and social media posts (with your logo) that go out before, during and after the event
+- The sponsors are listed in our published reports after the meeting, e.g., [https://f1000research.com/articles/7-1309/v1](https://f1000research.com/articles/7-1309/v1)
+- Platinum sponsors can show a short video before the first keynote
+- Gold sponsors can show a short video some time during the conference
+- We are open to discussing specific requests, such as distributing stickers or leaflets, or earmarking the sponsorship for a specific activity.
+
+
+
+
+
+## How sponsorships help BOSC
We gratefully accept sponsorships from private companies and organizations. In the past these sponsorships have enabled us to
- offer free registration to some BOSC participants
-- support the [OBF's Event Fellowship program](/travel-awards/), increasing participation from underrepresented groups
+- support the [OBF's Event Fellowship program](/event-awards/), increasing participation from underrepresented groups
- provide child care at the conference
- underwrite the cost of conference events such as dinners or refreshments at poster sessions
- help defray the cost of videography
-- provide space and catering at the CoFest
+- provide space and catering at the CollaborationFest
- offer honoraria to keynote speakers
- pay for captioning and translations
-
-## Sponsoring BOSC
+
-Sponsorships from private companies and organizations help to defray some of our costs and allow us to offer registration fee waivers to some attendees. If you are interested in becoming a BOSC sponsor, please contact us at bosc@open-bio.org!
+In 2021, sponsorships enabled us to offer free registration to 20 participants from all over the world!
+{{< googlemaps src="1z3D_j0fQYGDqMpCm1f8GQIi2KPvPzOEH" width=640 height=480 >}}
-
+
-# Benefits of Sponsorship
-We acknowledge our sponsors before, during and after the event in multiple ways:
+# Sponsors from previous years
-- We list our sponsors on the BOSC website
-- Sponsors are thanked and named in the introduction/closing slides during the meeting
-- We show the sponsor logos on large BOSC posters displayed outside the meeting room and in the poster area
-- The sponsors are thanked in selected emails to our mailing list, tweets and blog posts (with your logo) that go out before, during and after the event
-- The sponsors are listed in our published reports after the meeting, e.g., [https://f1000research.com/articles/7-1309/v1](https://f1000research.com/articles/7-1309/v1)
-- We are open to discussing specific requests, such as distributing stickers or leaflets, or earmarking the sponsorship for a specific activity.
+## 2025 Platinum Sponsor:
-## BOSC 2021 Platinum Sponsors
+
+
The aim of CZI's Open Science program is the universal and immediate open sharing of all scientific knowledge, processes, and outputs.
+
+
+
+
+### 2025 Gold Sponsor:
+
+
+
Seqera, developed by the creators of Nextflow, empowers researchers to develop and deploy scalable bioinformatics pipelines faster
-## BOSC 2021 Silver Sponsors
+### If you are interested in becoming a BOSC sponsor, please contact us at bosc@open-bio.org!
+
-[](https://elifesciences.org/)
-[](https://geneviatechnologies.com/)
-[](https://oup.com/)[](https://bioteam.net)
-If you are interested in becoming a sponsor, please contact us at bosc@open-bio.org!
+
diff --git a/content/page/sponsors2022.md b/content/page/sponsors2022.md
new file mode 100644
index 000000000..9226f0e67
--- /dev/null
+++ b/content/page/sponsors2022.md
@@ -0,0 +1,120 @@
+---
+author: nlharris
+cover:
+ alt: ""
+ image: /wp-content/uploads/2021/06/image-8.png
+date: "2024-02-15T16:33:21+00:00"
+draft: "true"
+guid: https://www.open-bio.org/?page_id=7658
+title: Sponsors
+url: /
+
+---
+# Sponsoring BOSC
+
+Page with BOSC 2023 Sponsors: [open-bio.org/events/sponsors/](/events/sponsors/)
+
+## BOSC 2022 Platinum Sponsors
+
+[](https://chanzuckerberg.com/)[](http://aws.amazon.com)
+
+## BOSC 2022 Gold Sponsors
+
+[](https://www.broadinstitute.org/data-sciences-platform)[](https://datascience.nih.gov/)
+
+### BOSC 2022 Silver Sponsors
+
+[](https://arvados.org)[](https://academic.oup.com/gigascience)
+
+
+
+Sponsorships from companies and organizations help to defray some of our costs and enable us to offer registration fee waivers for some conference participants. In 2021, thanks to our sponsors' generous support, we were able to grant free registration to 20 participants at [BOSC 2021](/events/bosc-2021/), offer honoraria to keynote speakers, and cover other expenses.
+
+If you’re interested in sponsoring BOSC 2022, please contact us at bosc@open-bio.org!
+
+Thanks to our 2021 sponsors, we were able to offer free ISMB/ECCB 2021 registration to 20 participants from all over the world!
+{{< googlemaps src="1z3D_j0fQYGDqMpCm1f8GQIi2KPvPzOEH" width=640 height=480 >}}
+
+## What is BOSC?
+
+BOSC is an annual meeting organized by the Open Bioinformatics Foundation (OBF), a non-profit, volunteer-run group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community.
+Whether in-person or online, each BOSC includes talks, poster sessions, birds-of-a-feather gatherings, and lots of opportunities for networking. It is followed by collaborative working sessions at the CollaborationFest. These events bring together software engineers, bioinformaticians, and researchers to collaborate and extend open source bioinformatics tools.
+
+Most years, BOSC has been part of the Intelligent Systems for Molecular Biology meeting (ISMB/ECCB). In 2018, BOSC partnered with the Galaxy Community Conference (GCC) in a very successful joint meeting in Portland, [GCCBOSC 2018](https://gccbosc2018.sched.com/). In July 2020, BOSC again joined forces with GCC to form the [Bioinformatics Community Conference (BCC2020)](https://bcc2020.github.io/). Held online, BCC2020 attracted over 600 participants from 62 countries. [BOSC 2021](/events/bosc-2021/) was part of [ISMB/ECCB 2021](https://www.iscb.org/ismbeccb2021), and took place July 29-30, 2021 (followed by a two-day [CollaborationFest](/events/bosc-2021/collaborationfest/)).
+
+BOSC 2022 will take place July 13-14, 2022, as part of [ISMB 2022](https://www.iscb.org/ismb2022). The meeting will be held both in person in Madison, Wisconsin, USA, and simultaneously online.
+
+
+
+
+
+
+
+
+
+BOSC participants come from a wide variety of research environments and backgrounds:
+
+- Biological researchers, students, and post-docs who are learning bioinformatics analysis tools and techniques
+- Power bioinformatics users
+- Bioinformatics tool and workflow developers
+
+- Bioinformatics-focused principal investigators and researchers
+- Sequencing core facility staff
+- Industry scientists and bioinformaticians
+- Data producers
+
+# Previous Events
+
+The OBF has organized BOSC [every year since 2000](/events/bosc/about/). From 2000 to 2017 and again in 2019, BOSC was run as part of the large ISMB conference. In 2018 (and again in 2020) it partnered with the Galaxy Community Conference. The OBF CodeFests (now renamed CollaborationFest, or CoFest) have been held every year after BOSC since 2010.
+
+The table below shows the approximate number of participants in BOSC and the CoFest. Figures for the CoFest and BOSC are number of people registered for at least one day of the meeting. The BOSC figures do not include drop-in attendees from the parallel sessions organized by other groups. The figures for CoFest do not include remote participants.
+
+YearLocation BOSC ParticipantsCoFest Participants 2020BCC2020 (BOSC + Galaxy): virtual~300~1502019Basel, Switzerland109352018 Portland, OR, USA1501002017 Prague, Czech Republic 230652016 Orlando, FL, USA90362015Dublin, Ireland125352014Boston, MA, USA100602013Berlin, Germany100372012Long Beach, CA, USA 100132011 Vienna, Austria 12035
+
+# Sponsorship
+
+We gratefully accept sponsorships from private companies and organizations. In the past these sponsorships have enabled us to
+
+- offer free registration to some BOSC participants
+- support the [OBF's Event Fellowship program](/travel-awards/), increasing participation from underrepresented groups
+- provide child care at the conference
+- underwrite the cost of conference events such as dinners or refreshments at poster sessions
+- help defray the cost of videography
+- provide space and catering at the CoFest
+- offer honoraria to keynote speakers
+- pay for captioning and translations
+
+
+
+## Sponsoring BOSC
+
+Sponsorships from private companies and organizations help to defray some of our costs and allow us to offer registration fee waivers to some attendees. If you are interested in becoming a BOSC sponsor, please contact us at bosc@open-bio.org!
+
+
+
+# Benefits of Sponsorship
+
+We acknowledge our sponsors before, during and after the event in multiple ways:
+
+- We list our sponsors on the BOSC website
+- Sponsors are thanked and named in the introduction/closing slides during the meeting
+- We show the sponsor logos on large BOSC posters displayed outside the meeting room and in the poster area
+- The sponsors are thanked in selected emails to our mailing list, tweets and blog posts (with your logo) that go out before, during and after the event
+- The sponsors are listed in our published reports after the meeting, e.g., [https://f1000research.com/articles/7-1309/v1](https://f1000research.com/articles/7-1309/v1)
+- We are open to discussing specific requests, such as distributing stickers or leaflets, or earmarking the sponsorship for a specific activity.
+
+## BOSC 2021 Platinum Sponsors
+
+[](https://chanzuckerberg.com/)[](https://www.alzheimersdata.org/)
+
+## BOSC 2021 Gold Sponsors
+
+[](http://aws.amazon.com)[](https://www.broadinstitute.org/)
+
+## BOSC 2021 Silver Sponsors
+
+[](https://elifesciences.org/)
+[](https://geneviatechnologies.com/)
+[](https://oup.com/)[](https://bioteam.net)
+
+If you are interested in becoming a sponsor, please contact us at bosc@open-bio.org!
diff --git a/content/page/sponsors-3.md b/content/page/sponsors2025.md
similarity index 98%
rename from content/page/sponsors-3.md
rename to content/page/sponsors2025.md
index a2f3fa18f..0b33bbfe7 100644
--- a/content/page/sponsors-3.md
+++ b/content/page/sponsors2025.md
@@ -1,12 +1,9 @@
---
author: nlharris
-cover:
- alt: panel-with-Nomi - 1
- image: /wp-content/uploads/2022/11/panel-with-Nomi-1.jpeg
date: "2023-03-27T19:05:24+00:00"
guid: https://www.open-bio.org/?page_id=6961
-title: Sponsors
-url: /events/bosc/sponsors/
+title: Sponsors - BOSC 2025
+url: /events/bosc/sponsors-2025/
bosc: yes
---
@@ -101,7 +98,7 @@ will be part of the main ISMB/ECCB conference and will be open to all.
## Benefits of Sponsorship
-Sponsoring BOSC increases your visibility in the bioinformatics community.
+Sponsoring BOSC increases your visibility in the bioinformatics community.
We acknowledge our sponsors before, during and after the event in multiple ways:
- We list our sponsors on the BOSC website
diff --git a/content/page/submit-to-bosc-2023.md b/content/page/submit-to-bosc-2023.md
index 94f4f8777..85091b4ce 100644
--- a/content/page/submit-to-bosc-2023.md
+++ b/content/page/submit-to-bosc-2023.md
@@ -89,7 +89,7 @@ In addition to the requirements listed at left, we consider the following when s
-Watch a video of [BOSC organizing committee member Jason Williams discussing how to write a great BOSC abstract](https://youtu.be/DwJRrh1Tpew)!
+Watch a video of [BOSC organizing committee member Jason Williams discussing how to write a great BOSC abstract](https://youtu.be/DwJRrh1Tpew)!
[Submit Abstract](https://easychair.org/conferences/?conf=ismbeccb2023abstract)
@@ -97,7 +97,7 @@ Watch a video of [BOSC organizing committee member Jason Williams discussing how
The [Open Bioinformatics Foundation](/wiki/OBF), which coordinates BOSC, is dedicated to promoting the practice and philosophy of Open Source Software Development and Open Science within the biological research community.
-For this reason, if a submitted abstract concerns a specific software system for use by the research community, then that software must include a recognized Open Source License or Public Domain dedication, and be available for download, including source code. We recommend Open Source Initiative (OSI) Approved Licenses where appropriate.
+For this reason, if a submitted abstract concerns a specific software system for use by the research community, then that software must include a recognized Open Source License or Public Domain dedication, and be available for download, including source code. We recommend Open Source Initiative (OSI) Approved Licenses where appropriate.
Similarly, abstracts with a focus on data, analysis methods, and/or documentation must make these available in a manner consistent with Open Science standards, utilizing appropriate licensing and approaches that promote open sharing, reuse, and redistribution.
diff --git a/content/page/submit-to-bosc-2025.md b/content/page/submit-to-bosc-2025.md
index 4f3f3ca5c..9485ddcaa 100644
--- a/content/page/submit-to-bosc-2025.md
+++ b/content/page/submit-to-bosc-2025.md
@@ -103,7 +103,7 @@ In addition to the requirements listed above, we consider the following when sel
The [Open Bioinformatics Foundation](/), which coordinates BOSC, is dedicated to promoting the practice and philosophy of Open Source Software Development and Open Science within the biological research community.
-For this reason, if a submitted abstract concerns a specific software system for use by the research community, then that software must include a recognized Open Source License or Public Domain dedication, and be available for download, including source code. We recommend Open Source Initiative (OSI) Approved Licenses where appropriate.
+For this reason, if a submitted abstract concerns a specific software system for use by the research community, then that software must include a recognized Open Source License or Public Domain dedication, and be available for download, including source code. We recommend Open Source Initiative (OSI) Approved Licenses where appropriate.
Similarly, abstracts with a focus on data, analysis methods, and/or documentation must make these available in a manner consistent with Open Science standards, utilizing appropriate licensing and approaches that promote open sharing, reuse, and redistribution.
See the following websites for further information and examples of recognized Open Source Licenses and Public Domain Dedications:
diff --git a/content/page/submit-to-bosc-2026.md b/content/page/submit-to-bosc-2026.md
new file mode 100644
index 000000000..c8e10d450
--- /dev/null
+++ b/content/page/submit-to-bosc-2026.md
@@ -0,0 +1,151 @@
+---
+author: khokamp
+cover:
+ alt: BOSC2023-crowded-room-Bastian - 1 (1)
+ image: /wp-content/uploads/2023/08/BOSC2023-crowded-room-Bastian-1-1.png
+date: "2024-01-24T16:09:52+00:00"
+title: Submit to BOSC 2026
+url: /events/bosc-2026/submit/
+bosc: yes
+
+---
+# BOSC 2026 Abstract Submission
+
+{{< columns >}}
+**BOSC 2026**, the 27th annual Bioinformatics Open Source Conference, will take place **July 14-15** as part of [ISMB 2026](https://www.iscb.org/ismb2026/home) in Washington DC. We hope you will join us in person or online!
+
+Abstract submission is now closed.
+
+{{< column >}}
+
+
+
+{{< endcolumns >}}
+
+
+
+
+
+### Key Dates
+
+{{< columns >}}
+- April 1, 2026: [OBF Event Award application deadline](/event-awards/)
+- **April 9: Abstract submission deadline (talks and posters)**. Submission is via ISMB's EasyChair.
+- May 5: Talk/poster acceptance notifications
+- May 7: Late poster submission deadline
+- July 12-16: [ISMB 2026](https://www.iscb.org/ismb2026/home) (Washington, DC and online)
+- **July 14-15:** **BOSC 2026** (part of ISMB 2026)
+
+{{< column >}}
+
+{{< endcolumns >}}
+
+
+
+# Submission guidelines
+
+{{< columns>}}
+
+### What to submit: Overview
+
+- A 250-word short abstract (text only) is required for ALL submissions (talk and/or poster).
+- If you want to be considered for a talk, you also MUST attach a 1-2 page "long abstract" as a PDF. Figures are welcome as long as the total length is 2 pages or less.
+- In your long abstract, please describe how your work fits into the open source / open science ecosystem. We like to see examples of biological applications of your work, and a summary of the current and/or projected community aspects of your project.
+- Your abstract should not contain your title/position or any personal information (e.g., affiliation). These details will be collected through the EasyChair submission system.
+
+{{< column>}}
+
+### Requirements
+
+To be accepted, abstracts submitted to BOSC must be:
+
+- **Relevant**: Your abstract must describe how your work relates to some aspect of open source software, open science or open data applied to biology or biomedical science.
+- **Available**: Your code / data / materials must be available **at the time of review** at the URL you list.
+- **Open Content**: Work discussed in BOSC presentations must be open source / open content, with a recognized license (which should also be included in the repository). If your abstract concerns non-software products (e.g., educational materials), these should also be freely available with an appropriate open license (see below).
+- **Updated**: If you presented this work at a previous BOSC in any form, your abstract must describe progress since the last BOSC presentation.
+- **Human-written**: AI/LLMs must not be used to write sections your abstract--please see the "AI Use Policy" section below.
+
+{{< endcolumns >}}
+
+### Additional criteria
+
+In addition to the requirements listed above, we consider the following when selecting abstracts for short or long talks.
+
+- **Community impact**: Please describe how your work fits into the open source bioinformatics / open science ecosystem. A summary of the current and/or projected community aspect of your project is very helpful.
+- **Novelty**: Innovative approaches are interesting to hear about, but it’s fine to build on existing technology! If you can compare your approach with existing approaches, that’s a plus.
+- **Examples**: We like abstracts with examples of how your approach works (e.g. a figure showing the output of a visualization tool, an example of software input/output, or benchmarks on relevant data).
+- **Usable**: Although we are happy to consider abstracts that describe early-phase projects, our reviewers are likely to look at your code and try to run it. Reviewers like projects that they are able to download and run, and that are well-documented and easy to use.
+
+### How to Submit
+
+- Submissions are via the ISMB EasyChair. If you don't already have an EasyChair account, you will need to create one.
+ - After signing in, click "make a new submission"
+ - You will see "Please select the track relevant for your submission." Select BOSC (5th line down).
+ - Later in the submission process, you will be able to specify one or two other COSIs/tracks that your abstract might also fit into.
+- A 250-word short abstract is required for ALL submissions (talk and/or poster). (Confusingly, the submission form refers to this as simply "Abstract".)
+- If you want to be considered for a talk, you also MUST submit a 1-2 page "long abstract" as a PDF. (Yes, we did suggest to ISMB that calling both of these things "abstracts" was confusing.)
+- If you submit for a talk but your abstract is not chosen for a talk, it will automatically be considered for a poster.
+- You don't need to register before you submit your abstract, but to present your talk or poster you will need to register for ISMB.
+
+
+
+
+
+## BOSC open content requirement
+
+The [Open Bioinformatics Foundation](/), which coordinates BOSC, is dedicated to promoting the practice and philosophy of Open Source Software Development and Open Science within the biological research community.
+
+For this reason, if a submitted abstract concerns a specific software system for use by the research community, then that software must include a recognized Open Source License or Public Domain dedication, and be available for download, including source code. We recommend Open Source Initiative (OSI) Approved Licenses where appropriate.
+Similarly, abstracts with a focus on data, analysis methods, and/or documentation must make these available in a manner consistent with Open Science standards, utilizing appropriate licensing and approaches that promote open sharing, reuse, and redistribution.
+
+See the following websites for further information and examples of recognized Open Source Licenses and Public Domain Dedications:
+
+- [ChooseALicense](https://choosealicense.com/), with options for source code and non-source code licensing
+- [Open Source Initiative (OSI) Approved Licenses](http://www.opensource.org/licenses/)
+- [Definition of the Open Source Philosophy](http://www.opensource.org/docs/definition.php)
+- [Creative Commons licenses that support free “cultural works”](https://creativecommons.org/share-your-work/public-domain/freeworks/) : [CC0](https://creativecommons.org/share-your-work/public-domain/cc0), [CC-BY](https://creativecommons.org/licenses/by/3.0/), [CC-BY-SA](https://creativecommons.org/licenses/by-sa/3.0/)
+- [Public Domain Dedications](https://creativecommons.org/share-your-work/public-domain/) and [Public-domain-equivalent licenses](https://en.wikipedia.org/wiki/Public-domain-equivalent_license): [CC0](https://creativecommons.org/share-your-work/public-domain/cc0), [Unlicense](https://unlicense.org/)
+
+
+
+## AI use policy
+
+BOSC follows the [ISCB policy on acceptable use of large language models (LLMs)](https://www.iscb.org/about-iscb/policy-statements-bylaws-and-legal-documents/acceptable-use-of-large-language-models-policy). Key points:
+
+- Abstracts and papers **must be written by humans**. LLMs must not be used to draft or write sections of your submission.
+- Acceptable uses of LLMs include spell/grammar checking, language translation assistance, and code development support — but the submitting authors remain responsible for all content.
+- If you used AI tools as part of the research described in your submission, please describe that usage in the submission form.
+
+## ISMB rules
+
+**In-person presentation**: "ISCB strongly prefers that scientific research accepted for oral presentation be presented in-person at the conference venue. ISCB will grant remote presentation options for reasons associated with maternity/paternity leave, care for a family member, personal/medical disability, sickness, financial hardship, or potential visa problems."
+
+**Talk OR poster**: ISMB does not allow a presenting author to present both a talk and a poster on the same topic. If you want your work to be presented as both a talk and a poster, a different presenting author needs to submit for each.
+
+### Presentation formats
+
+At BOSC, talks chosen from submitted abstracts are generally either "long" (typically 16 minutes plus 4 minutes for questions) or short/"lightning" (5 minutes, scheduled in groups of three lightning talks followed by 5 minutes for questions for all three). Abstracts submitted in the Late Poster round are not eligible for talks.
+
+
+
+### BOSC review process
+
+Talk abstracts submitted to BOSC are typically reviewed by three reviewers; poster abstracts by two. Our review process and rubric can be found [here](https://github.com/OBF/bosc_materials/blob/master/BOSC_review_process.md).
+
+
+
+### Requesting registration fee assistance
+
+{{< columns >}}
+
+We realize that the cost of ISMB may be prohibitive for some. If you are submitting an abstract to BOSC and would have difficulty covering the cost of registration, you can request registration fee assistance. To make it easy, this request can be made right on the abstract submission form. (Only the conference chairs will see these fee assistance requests -- the abstract reviewers will not.) Last year, thanks to help from our [sponsors](/events/bosc/sponsors/), we were able to grant free registration to 15 participants.
+
+{{< column >}}
+
+
+{{< endcolumns >}}
+
+
+
+
+
diff --git a/content/posts/2025-03-04-Event-Awards.md b/content/posts/2025-03-04-Event-Awards.md
index efb90d0e8..6f4a03de0 100644
--- a/content/posts/2025-03-04-Event-Awards.md
+++ b/content/posts/2025-03-04-Event-Awards.md
@@ -13,7 +13,7 @@ tag:
- community
- event-fellowship
- travel-fellowship
-
+
title: Call for the first 2025 round of the OBF Event Fellowship & overview of the last round of 2024
url: /2025/03/02/event-fellowship-2025-1/
@@ -26,15 +26,15 @@ We invite applications from candidates seeking financial support to attend relev
### Overview of the third 2024 round of the OBF Event Fellowship
-The [Open Bioinformatics Foundation (OBF) Event Fellowship program](https://www.open-bio.org/event-awards/) is now in its 8th year. Since 2023, we have three application rounds per year with the following deadlines: 1 April, 1 August, and 1 December.
+The [Open Bioinformatics Foundation (OBF) Event Fellowship program](https://www.open-bio.org/event-awards/) is now in its 8th year. Since 2023, we have three application rounds per year with the following deadlines: 1 April, 1 August, and 1 December.
In the third round of 2024 (December 2024), we received numerous applications, and four applicants were selected for funding to support their participation in various events. **Congratulations to the following recipients**:
-1. Jacqueline Wahura: the Royal Entomological Society Conference 2024\.
-2. Kyra Feuer: 2025 International Statistical Genetics Workshop.
+1. Jacqueline Wahura: the Royal Entomological Society Conference 2024\.
+2. Kyra Feuer: 2025 International Statistical Genetics Workshop.
3. Zoé Pochon: ISBA11 (International Symposium on Biomolecular Archaeology) and SPAAM7 (Standards, Precautions, and Advances in Ancient Metagenomics) in Turin, Italy
-We require each awardee to write a blog post about their conference experience, to share what they learned with the wider community. Here are some examples from our recent awardees:
+We require each awardee to write a blog post about their conference experience, to share what they learned with the wider community. Here are some examples from our recent awardees:
{{< columns >}}
@@ -44,7 +44,7 @@ We require each awardee to write a blog post about their conference experience,
**Masturina Binti Md Mansor** (left) attended the 1st Asia & Pacific Bioinformatics Joint Congress 2024, supported by OBF Event Fellowships. [Read about their experience here](https://www.open-bio.org/2024/11/19/masturina-experience-at-apbjc2024/).
-**Erin Krichilsky** received the award to attend the 27th International Congress of Entomology (ICE2024 Kyoto) and shared [**their story here**](https://www.open-bio.org/2024/11/21/erin-rin-krichilsky/).
+**Erin Krichilsky** received the award to attend the 27th International Congress of Entomology (ICE2024 Kyoto) and shared [**their story here**](https://www.open-bio.org/2024/11/21/erin-rin-krichilsky/).
**Jacqueline Wahura** attended the Royal Entomological Society Conference 2024, virtually. They reported [**their experience here**](https://www.open-bio.org/2025/01/07/jacqueline-wahura-ento24-experience/).
diff --git a/content/posts/2025-03-04-new-website.md b/content/posts/2025-03-04-new-website.md
index 9cb974950..474b07eef 100644
--- a/content/posts/2025-03-04-new-website.md
+++ b/content/posts/2025-03-04-new-website.md
@@ -2,12 +2,12 @@
author: Bastian Greshake Tzovaras
category:
- community
- - obf
+ - obf
date: "2025-03-04T18:23:00+00:00"
tag:
- obf
- internal
-
+
title: "Welcome to the new OBF website!"
---
diff --git a/content/posts/2025-03-09-BOSC-BOKR.md b/content/posts/2025-03-09-BOSC-BOKR.md
index 71c044965..37deb508d 100644
--- a/content/posts/2025-03-09-BOSC-BOKR.md
+++ b/content/posts/2025-03-09-BOSC-BOKR.md
@@ -13,7 +13,7 @@ tag:
- bosc
- ismb
- conferences
-
+
title: BOSC and BOKR to join forces at ISMB/ECCB 2025
url: /2025/03/17/BOSC-BOKR-2025
diff --git a/content/posts/2025-03-20-award-opportunities-BOSC2025.md b/content/posts/2025-03-20-award-opportunities-BOSC2025.md
index e25b7c41b..12c95f34a 100644
--- a/content/posts/2025-03-20-award-opportunities-BOSC2025.md
+++ b/content/posts/2025-03-20-award-opportunities-BOSC2025.md
@@ -38,7 +38,7 @@ Awards are made three times a year; the next **deadline is April 1, 2025** (note
**[More info about applying for an OBF Event Fellowship](/2025/03/02/event-fellowship-2025-1/)**
-*Left:
+*Left:
[Awardee Ruth Nanjala and her poster at ICHG 2023](/2023/03/21/ruth-nanjala-experience-at-the-ichg-2023-conference/)*
{{< endcolumns >}}
@@ -58,7 +58,7 @@ Only presenting authors whose abstracts are accepted for talk or poster presenta
{{< endcolumns >}}
-Requests from early-career applicants and people from underrepresented geographical areas will be given priority.
+Requests from early-career applicants and people from underrepresented geographical areas will be given priority.
Applicants will be notified about whether their fee waiver request was granted around the same time that abstract acceptance notifications go out (May 14).
diff --git a/content/posts/2025-04-02-archiving-obf-posts.md b/content/posts/2025-04-02-archiving-obf-posts.md
index eabecc5a0..e06f9e131 100644
--- a/content/posts/2025-04-02-archiving-obf-posts.md
+++ b/content/posts/2025-04-02-archiving-obf-posts.md
@@ -2,7 +2,7 @@
author: Bastian Greshake Tzovaras
category:
- community
- - obf
+ - obf
date: 2025-04-02T14:49:50+00:00
tag:
- obf
@@ -18,6 +18,6 @@ Which is why this blog is now also archived for the long-term with the help of [
_Rogue Scholar_ makes use of open technologies to both archive the full-text of our blog posts itself, but also makes sure that they are archived in [The Wayback Machine](https://web.archive.org/) of the Internet Archive semiannually.
To ensure the long-term findability, _Rogue Scholar_'s archive contains rich metadata and also assigns a DOI for each blog post enlisted.
-Thanks to this, blog posts don't only have a stable identifier that can perpetually link to the correct places, this also means that our blog posts will have a stable and **citable identifier**, which allows them to become objects that are more easily citable within the scientific record.
+Thanks to this, blog posts don't only have a stable identifier that can perpetually link to the correct places, this also means that our blog posts will have a stable and **citable identifier**, which allows them to become objects that are more easily citable within the scientific record.
In the future, we plan to expose those DOIs more easily through our blog itself, but [already now you can find all of our posts listed on Rogue Scholar](https://rogue-scholar.org/communities/obf/records?q=&l=list&p=1&s=10&sort=newest).
diff --git a/content/posts/2025-04-30-Kyra-Feuer-2025-International-Statistical-Genetics-Workshop.md b/content/posts/2025-04-30-Kyra-Feuer-2025-International-Statistical-Genetics-Workshop.md
index 14e69fcc3..c77075f81 100644
--- a/content/posts/2025-04-30-Kyra-Feuer-2025-International-Statistical-Genetics-Workshop.md
+++ b/content/posts/2025-04-30-Kyra-Feuer-2025-International-Statistical-Genetics-Workshop.md
@@ -1,7 +1,7 @@
---
author: Kyra-Feuer
date: 2025-04-30
-category:
+category:
- community
- event-fellowship
- travel-fellowship
@@ -19,12 +19,12 @@ Thanks to the Event Fellowship from Open Bioinformatics Foundation (OBF), I was
*The workshop was a combination of lectures and collaborative hands-on practicals*
-The schedule was intensive and jam-packed with learning. Each day we gathered from 8am-5pm for a combination of lectures and hands-on practicals. We covered various aspects of genome-wide association studies, from the theory and principles behind the analyses, to the logistics of running them, to how to perform downstream analyses to investigate biological mechanisms. We learned how to perform analyses on multiple platforms including the terminal, RStudio, and Jupyter. On Monday we learned about classic and modern statistical approaches for genetic modeling; population genetics; how to generate, QC, and impute data using [plink](https://www.cog-genomics.org/plink/2.0/); and how to perform principal components analysis using plink and [GCTA](https://yanglab.westlake.edu.cn/software/gcta/#Overview). Topics on Tuesday included how to access different data, including recruiting participants for your own studies and accessing biobanks; theory and performance of GWAS association tests using [SAIGE](https://github.com/weizhouUMICH/SAIGE); meta-analysis of multiple GWAS using [METAL](https://github.com/statgen/METAL); and calculation of polygenic risk scores using [SBayesR](https://github.com/zhilizheng/SBayesRC). Wednesday was a relatively light day, with a only a few sessions which were focused on calculating SNP heritability and genetic correlations with [LD score regression](https://github.com/bulik/ldsc). We also had a poster session on Wednesday, during which I presented my work on using the open-access tool [PRS-CSx](https://github.com/getian107/PRScsx) for improving polygenic risk score prediction for severe mental illness in diverse populations.
+The schedule was intensive and jam-packed with learning. Each day we gathered from 8am-5pm for a combination of lectures and hands-on practicals. We covered various aspects of genome-wide association studies, from the theory and principles behind the analyses, to the logistics of running them, to how to perform downstream analyses to investigate biological mechanisms. We learned how to perform analyses on multiple platforms including the terminal, RStudio, and Jupyter. On Monday we learned about classic and modern statistical approaches for genetic modeling; population genetics; how to generate, QC, and impute data using [plink](https://www.cog-genomics.org/plink/2.0/); and how to perform principal components analysis using plink and [GCTA](https://yanglab.westlake.edu.cn/software/gcta/#Overview). Topics on Tuesday included how to access different data, including recruiting participants for your own studies and accessing biobanks; theory and performance of GWAS association tests using [SAIGE](https://github.com/weizhouUMICH/SAIGE); meta-analysis of multiple GWAS using [METAL](https://github.com/statgen/METAL); and calculation of polygenic risk scores using [SBayesR](https://github.com/zhilizheng/SBayesRC). Wednesday was a relatively light day, with a only a few sessions which were focused on calculating SNP heritability and genetic correlations with [LD score regression](https://github.com/bulik/ldsc). We also had a poster session on Wednesday, during which I presented my work on using the open-access tool [PRS-CSx](https://github.com/getian107/PRScsx) for improving polygenic risk score prediction for severe mental illness in diverse populations.
*The tabletop poster session - I presented a poster on using the open-source algorithm PRS-CSx*
-On Thursday we continued with post-GWAS analyses, including additional SNP heritability calculations with [GREML](https://yanglab.westlake.edu.cn/software/gcta/#GREML); pathway analysis with [MAGMA](https://cncr.nl/research/magma/); eQTL analysis with [PEER](https://www.sanger.ac.uk/tool/peer/) and [MatrixEQTL](https://github.com/andreyshabalin/MatrixEQTL); and fine mapping and colocalization with [SUSIE](https://github.com/stephenslab/susieR) and [coloc](https://github.com/chr1swallace/coloc/). Finally, on Friday we went through statistical power and how to calculate it with R and online tools; identifying causal and confounding factors with Mendelian Randomization in R; and performing rare variant analyses using [Hail](https://github.com/hail-is/hail).
+On Thursday we continued with post-GWAS analyses, including additional SNP heritability calculations with [GREML](https://yanglab.westlake.edu.cn/software/gcta/#GREML); pathway analysis with [MAGMA](https://cncr.nl/research/magma/); eQTL analysis with [PEER](https://www.sanger.ac.uk/tool/peer/) and [MatrixEQTL](https://github.com/andreyshabalin/MatrixEQTL); and fine mapping and colocalization with [SUSIE](https://github.com/stephenslab/susieR) and [coloc](https://github.com/chr1swallace/coloc/). Finally, on Friday we went through statistical power and how to calculate it with R and online tools; identifying causal and confounding factors with Mendelian Randomization in R; and performing rare variant analyses using [Hail](https://github.com/hail-is/hail).
A huge benefit of this workshop, besides the technical skills it imparted, was the ability to network with such an experienced and diverse group of people in an intimate setting. We had direct face time with world leaders in the statistical genetics field, who headed off any intimidation we might have felt by reminding us in the very first lecture that we were all colleagues and insisting that we call them by their first names. In addition to being extremely knowledgeable, they were friendly, warm, and happy to answer one-on-one questions and give advice. Meeting and working with the other attendees - many of whom were from across the country or the world - was also fantastic, and was an opportunity I would have never had otherwise. I was even able to meet some of my own collaborators from the PsycheMERGE consortium, who I had only previously met over Zoom, in person for the first time!
@@ -33,12 +33,12 @@ When the workshop wasn’t in session, I visited as many places in Boulder as I
*Enjoying some delicious cuisine at Rosetta Hall*
-Perhaps the best part of Boulder was its natural beauty. The hotel was located near the Boulder foothills which contain the famed Flatirons formation. This view was a stunning backdrop that we were able to enjoy during lunch, networking sessions, and on a group hike on Wednesday.
+Perhaps the best part of Boulder was its natural beauty. The hotel was located near the Boulder foothills which contain the famed Flatirons formation. This view was a stunning backdrop that we were able to enjoy during lunch, networking sessions, and on a group hike on Wednesday.
*The workshop was a short walk away from the stunning Flatirons and the Open Space park*
-I also found some time to take an Uber up into the mountains to visit the incredible Lost Gulch Overlook, which boasts views of the forest and snow-capped peaks of the Continental Divide. The combination of the stunning view, the peaceful silence, and the crisp, cold air was otherworldly.
+I also found some time to take an Uber up into the mountains to visit the incredible Lost Gulch Overlook, which boasts views of the forest and snow-capped peaks of the Continental Divide. The combination of the stunning view, the peaceful silence, and the crisp, cold air was otherworldly.
*Breaktaking views from the Lost Gulch Overlook*
diff --git a/content/posts/2025-07-15-Event-Awards.md b/content/posts/2025-07-15-Event-Awards.md
index 8a33f14c0..6e0f2e411 100644
--- a/content/posts/2025-07-15-Event-Awards.md
+++ b/content/posts/2025-07-15-Event-Awards.md
@@ -13,7 +13,7 @@ tag:
- community
- event-fellowship
- travel-fellowship
-
+
title: Call for the second 2025 round of the OBF Event Fellowship & overview of the first round of 2025
url: /2025/07/15/event-fellowship-2025-2/
@@ -26,7 +26,7 @@ We invite applications from candidates seeking financial support to attend relev
### Overview of the First 2025 round of the OBF Event Fellowship
-The [Open Bioinformatics Foundation (OBF) Event Fellowship program](https://www.open-bio.org/event-awards/) is now in its 8th year. Since 2023, we have three application rounds per year with the following deadlines: 1 April, 1 August, and 1 December.
+The [Open Bioinformatics Foundation (OBF) Event Fellowship program](https://www.open-bio.org/event-awards/) is now in its 8th year. Since 2023, we have three application rounds per year with the following deadlines: 1 April, 1 August, and 1 December.
In the first round of 2025 (April 2025), we received numerous applications, and four applicants were selected for funding to support their participation in various events. **Congratulations to the following recipients**:
@@ -35,7 +35,7 @@ In the first round of 2025 (April 2025), we received numerous applications, and
3. Seun Olufemi RSECon25 9-11 September 2025
4. Muhamad Haries Ramdhani ISMB/ECCB 2025 20th July 2025 - 24th July 2025
-We require each awardee to write a blog post about their conference experience, to share what they learned with the wider community. Here are some examples from our recent awardees:
+We require each awardee to write a blog post about their conference experience, to share what they learned with the wider community. Here are some examples from our recent awardees:
{{< columns >}}
diff --git a/content/posts/2025-08-25-Tayyaba-Alvi-ISMB2025.md b/content/posts/2025-08-25-Tayyaba-Alvi-ISMB2025.md
index 0837d5d74..2572e28f9 100644
--- a/content/posts/2025-08-25-Tayyaba-Alvi-ISMB2025.md
+++ b/content/posts/2025-08-25-Tayyaba-Alvi-ISMB2025.md
@@ -2,7 +2,7 @@
author: alviitayyaba
date: 2025-08-25 # format is YYYY-MM-DD
-category:
+category:
- community
- event-fellowship
- travel-fellowship
@@ -12,10 +12,11 @@ tag:
- travel-fellowship
title: "ISMB 2025: A Week of Learning, Teaching, and Connecting in Liverpool"
-url: /2025/08/25/2025-08-25-Tayyaba-Alvi-ISMB2025/
+url: /2025/08/25/2025-08-25-Tayyaba-Alvi-ISMB2025/
---
**_The_** [**_Open Bioinformatics Foundation (OBF) Event Fellowship program_**](/travel-awards) **_aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Tayyaba Alvi,_** _**a PhD student at**_ _**Fritz Lipmann Institute on Aging**_, **_was awarded an OBF Event Fellowship to attend_** **_[ISMB/ECCB2025](https://www.iscb.org/ismbeccb2025/home)_**.
+
Thanks to the Event Fellowship from the Open Bioinformatics Foundation (OBF), I had the chance to attend the 33rd Conference on Intelligent Systems for Molecular Biology (ISMB 2025) in Liverpool. It’s the annual meeting of the International Society for Computational Biology (ISCB) and the biggest conference in the field. This year, it brought together over 2,000 researchers from all over the world at ACC Liverpool, a beautiful venue right by the Albert Dock.
@@ -34,7 +35,7 @@ In the evening, we heard a fantastic keynote from John Jumper, who shared the st
The second day opened with a keynote from Amos Bairoch, who spoke about the ongoing challenges in biocuration. With so much biological data being generated, his talk highlighted just how important curated, high-quality data resources are, and how we need to keep investing in them.
After that, the days were packed with talks across different tracks and COSIs. I attended sessions from:
* GenComp (Comparative Genomics)
-* DREAM
+* DREAM
* BOSC (Bioinformatics Open Source Conference)
* And MICROBIOME, which had some especially interesting talks on Tuesday and Thursday
@@ -44,10 +45,8 @@ Outside the talks, the poster sessions and coffee breaks were great for meeting
The conference wrapped up with a conversation with David Baker, who shared his insights on protein design and creative science, followed by a final keynote from Fabian Theis. His talk focused on atlas-scale data integration and the Human Cell Atlas, a huge and ongoing effort to map cell types across tissues and conditions. It was a powerful reminder of how large-scale collaboration can really push the field forward.
-
-
## Exploring Liverpool
-In between conference sessions, I made sure to explore a bit of Liverpool. The dockside area near the venue was lovely to walk around—full of history, great views of the Mersey, and a surprisingly peaceful vibe despite all the conference hustle.
+In between conference sessions, I made sure to explore a bit of Liverpool. The dockside area near the venue was lovely to walk around—full of history, great views of the Mersey, and a surprisingly peaceful vibe despite all the conference hustle.
diff --git a/content/posts/2025-09-04-muhamad-haries-ramdhani-ismb-eccb-2025.md b/content/posts/2025-09-04-muhamad-haries-ramdhani-ismb-eccb-2025.md
index 22b59e9b3..4a001b86d 100644
--- a/content/posts/2025-09-04-muhamad-haries-ramdhani-ismb-eccb-2025.md
+++ b/content/posts/2025-09-04-muhamad-haries-ramdhani-ismb-eccb-2025.md
@@ -1,7 +1,7 @@
---
author: hariesramdhani
date: 2025-09-04 # format is YYYY-MM-DD
-category:
+category:
- community
- event-fellowship
- travel-fellowship
diff --git a/content/posts/2025-09-24-BOSC2025-report-and-video.md b/content/posts/2025-09-24-BOSC2025-report-and-video.md
index bbb0a31d9..23bfade46 100644
--- a/content/posts/2025-09-24-BOSC2025-report-and-video.md
+++ b/content/posts/2025-09-24-BOSC2025-report-and-video.md
@@ -1,7 +1,7 @@
---
author: nlharris
date: "2025-09-24"
-category:
+category:
- community
- conference
- bosc
diff --git a/content/posts/2025-09-30-gigascience.md b/content/posts/2025-09-30-gigascience.md
index 3f5028668..5b588ca92 100644
--- a/content/posts/2025-09-30-gigascience.md
+++ b/content/posts/2025-09-30-gigascience.md
@@ -2,7 +2,7 @@
author: inutano
date: 2025-09-30
draft: false
-category:
+category:
- community
tag:
- community
@@ -27,7 +27,7 @@ They act not merely for themselves, but for the whole of human society.
One of these organizations is the [GigaScience journal](https://academic.oup.com/gigascience).
Since its founding, GigaScience has been at the forefront of open data science.
Its initiative to build its own data repository, to assign curators, and to archive the data underlying accepted articles was truly pioneering, and other journals followed.
-Unlike traditional journals operated solely by editorial boards, GigaScience is, in effect, equivalent to establishing a full-fledged data center.
+Unlike traditional journals operated solely by editorial boards, GigaScience is, in effect, equivalent to establishing a full-fledged data center.
The recent news concerning GigaScience’s owners, BGI, laying off the entire editorial,
software and curation team in Hong Kong on short notice, has filled us with both surprise and deep disappointment.
@@ -85,6 +85,7 @@ by the end of October if you wish to add your name):
* Mark A. Jensen
* Lane Rasberry
* Hans-Rudolf Hotz
+* Maryann Martone
diff --git a/content/posts/2025-10-07-Events-Awards.md b/content/posts/2025-10-07-Events-Awards.md
index 715b91625..690e03d72 100644
--- a/content/posts/2025-10-07-Events-Awards.md
+++ b/content/posts/2025-10-07-Events-Awards.md
@@ -13,7 +13,7 @@ tag:
- community
- event-fellowship
- travel-fellowship
-
+
title: Call for the third 2025 round of the OBF Event Fellowship & overview of the second round of 2025
url: /2025/10/07/event-fellowship-2025-3/
@@ -36,9 +36,9 @@ In the second round of 2025 (August 2025), we received numerous applications, an
4. Hetvi Jethwani - BioHackathon Europe 2025
5. Rafał Miłodrowski - BioHackathon Europe 2025
-Notably, the OBF Events Fellowship sponsored three participants at the BioHackathon Europe 2025.
+Notably, the OBF Events Fellowship sponsored three participants at the BioHackathon Europe 2025.
-We require each awardee to write a blog post about their conference experience, to share what they learned with the wider community. Here are some examples from our recent awardees:
+We require each awardee to write a blog post about their conference experience, to share what they learned with the wider community. Here are some examples from our recent awardees:
{{< columns >}}
@@ -53,4 +53,3 @@ We require each awardee to write a blog post about their conference experience,
Congratulations to all of our awardees\! We are delighted to support their participation with OBF Event Fellowships, and we wish them all the best for their future work.
**Please share this post and [apply for the fellowship](https://forms.gle/D31zSs558aRwj2ig9) before 1 December 2025\.**
-
diff --git a/content/posts/2025-10-29-biopython-1-86-released.md b/content/posts/2025-10-29-biopython-1-86-released.md
new file mode 100644
index 000000000..7412d9374
--- /dev/null
+++ b/content/posts/2025-10-29-biopython-1-86-released.md
@@ -0,0 +1,36 @@
+---
+author: peterc
+category:
+ - biopython
+ - blogroll
+ - code
+ - development
+ - obf-projects
+cover:
+ alt: Biopython logo
+ image: /wp-content/uploads/2023/09/biopython_logo_s.png
+date: "2025-10-29"
+tag:
+ - biopython
+ - development
+ - obf-projects
+title: Biopython 1.86 released
+url: /2025/10/29/biopython-1-86-released/
+
+---
+Biopython 1.86 has been released and is available from our [website](https://biopython.org/wiki/Download) and [PyPI](https://pypi.python.org/pypi/biopython/1.86).
+
+This contains about nine months worth of updates, and is our first release with Python 3.14 support.
+See [change-log in the news file](https://github.com/biopython/biopython/blob/biopython-186/NEWS.rst)
+(most of the changes are in `Bio.Align` and `Bio.PDB`).
+There have also been a few [deprecations and removals of older code](https://github.com/biopython/biopython/blob/biopython-186/DEPRECATED.rst).
+
+Many thanks to the Biopython developers and community for making this release possible, especially the following contributors who were happy to be named:
+
+- Rachel Stern (first contribution)
+- Fabio Zanini
+- Michiel de Hoon
+- Oliver Wissett (first contribution)
+- Peter Cock
+- Samuel Prince (first contribution)
+- Cassie Bastress (first contribution)
diff --git a/content/posts/2025-11-03-Krasnow-ESIIL-Summit.md b/content/posts/2025-11-03-Krasnow-ESIIL-Summit.md
new file mode 100644
index 000000000..15a9886b0
--- /dev/null
+++ b/content/posts/2025-11-03-Krasnow-ESIIL-Summit.md
@@ -0,0 +1,71 @@
+---
+author: rmk118
+date: 2025-11-03
+category:
+ - community
+ - event-fellowship
+ - travel-fellowship
+tag:
+ - community
+ - event-fellowship
+ - travel-fellowship
+title: "2025 ESIIL Innovation Summit: Collaborative and Open Environmental Data Science in Boulder"
+url: /2025/11/03/2025-11-03-Krasnow-ESIIL-Summit/
+editor_options:
+ markdown:
+ wrap: sentence
+---
+
+***The*** [***Open Bioinformatics Foundation (OBF) Event Fellowship program***](/travel-awards) **aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Ruby Krasnow, a PhD student at the University of Maine, was awarded an OBF Event Fellowship to attend the [2025 ESIIL Innovation Summit](https://cu-esiil.github.io/Innovation-Summit-2025/)**.
+ *My team (Group 4) from the 2025 ESIIL Innovation Summit.*
+
+## Introduction
+
+Thanks to the support of an OBF Event Fellowship, I attended the 2025 [Environmental Data Science Innovation & Impact Lab](https://esiil.org/) (ESIIL) [Innovation Summit](https://cu-esiil.github.io/Innovation-Summit-2025/) in Boulder, Colorado.
+An annual event, this year’s ESIIL Summit had the following goals:
+
+- Explore big data to understand environmental tipping points and transformations by identifying data synthesis opportunities and utilizing ESIIL cloud-compute capabilities.
+- Promote best practices in ethical, open science by supporting accessibility and usability of environmental data by all stakeholders.
+- Champion ethical practices in environmental science, and encourage the responsible use of AI.
+- Support teams by establishing collaborations around data-inspired themes across different disciplines, sectors, and career stages.
+
+ *Summit participants at the Sustainability, Energy and Environment Community (SEEC) building, part of the University of Colorado Boulder.*
+
+The Summit was designed as an “unconference,” where much of the time was dedicated to forming teams that each tackled a specific research question related to understanding and predicting environmental tipping points and working in those teams to begin a collaborative project that ideally lasts far beyond the end of the in-person gathering.
+This event was a remarkable opportunity to meet and collaborate with other scientists from a variety of backgrounds.
+
+I learned a great deal about the conference theme as well as the open-source software tools that support the use of big data to answer questions related to the environmental transformations or disturbances.
+The topics chosen by the groups were extremely diverse, such as:
+
+- Examining how hydrology, governance, and management interact within and across the Snake, Green, and Wind River Basins in the western U.S. - Synthesizing forest management and intervention strategies that can mitigate the impacts of linked disturbances (e.g., drought, windstorm, wildfire, and insect/pathogen disturbances).
+- Creating a dashboard and interactive search tool for tribal decision-makers to access and understand meaningful information about extractive activities in the HeSapa (Black Hills) through \>2,400 Environmental Impact Statement/Assessment documents from the U.S.
+Forest Service, Bureau of Land Management, and other agencies.
+- Evaluating how the order, duration, frequency, and intensity of disturbances affect the likelihood of regime shifts from forests to nonforests.
+- Tackling broad questions about how to ensure greater data interoperability within the environmental data science community.
+
+My team chose to focus on environmental tipping points within freshwater food webs, exploring how the stability and resilience of food webs might be affected by—or serve as an early warning signal for—environmental tipping points or “regime shifts.” As an initial case study, we concentrated on Lake Champlain, a relatively data-rich system that one of our team members, [Dr. Alyssa Gleichsner](https://www.plattsburgh.edu/academics/schools/arts-sciences/biological-sciences/faculty/gleichsner-alyssa.html), knows well.
+
+  *Preliminary drafts of a simplified food web of the Lake Champlain ecosystem, with more (left) or less (right) abstraction of individual species into trophic groups. Dates in parentheses in the right figure indicate the year of first appearance for invasive species.*
+
+ESIIL staff encouraged us to use reproducible data analysis workflows from the very beginning of our project.
+Each team received a [template GitHub repository](https://cu-esiil.github.io/stressors-food-web-connectivity-stability-innovation-summit-2025__4/) to track progress and share code, which we used when presenting our initial results during report-back sessions to all participants.
+Looking ahead, we plan to submit a proposal to form an ESIIL working group, which would provide additional support to expand this project’s scope and impact.
+Whether or not we receive funding, we aim to publish an open-access paper describing our results.
+In keeping with OBF and ESIIL’s open science ethos, we will publish our data and code alongside the paper so other researchers can reproduce, reuse, and extend our analysis to other freshwater systems.
+
+In addition to the time spent in working groups, the Summit featured several keynote presentations, including discussions on causal inference to identify climate impacts on ecological systems, predicting and managing ecological transformations in climate-adapted landscapes, and the use of AI in environmental data science.
+Perhaps the most meaningful aspect of the event was the emphasis on learning from and co-creating knowledge with the Indigenous peoples whose land we live and work on.
+
+It was impossible not to be moved by the words of the Indigenous leaders present at the Summit, who spoke about the deep connection we have to every part of the natural world and our responsibility to honor and protect the land, water, and life around us.
+Although I was aware in an academic sense of Traditional Ecological Knowledge (TEK) and efforts to incorporate TEK with traditional western science, the Summit was the first place I’ve experienced it in action, and it was very powerful to see how diverse ways of knowing can be weaved together to support environmental protection and management efforts.
+
+  *Pictures of the mountains in Boulder and a grazing mule deer taken while walking to the University of Colorado Boulder East Campus, where the Summit was held.*
+
+In many ways, the Summit showed me the value of diversity in scientific communities and the importance of community itself in maintaining hope and joy when facing immense challenges.
+Having learned more about ESIIL and its core values, I see many similarities with OBF, and I hope that OBF’s support of my participation in this ESIIL event will be only one of many examples of collaboration between the two organizations.
+
+## Acknowledgements
+
+> "Thank you to my Group 4 team members and to the OBF Event Fellowship for supporting my travel to the 2025 ESIIL Innovation Summit!"
+
+------------------------------------------------------------------------
diff --git a/content/posts/2025-12-02-Hetvi-J-BioHackathon-Europe-2025.md b/content/posts/2025-12-02-Hetvi-J-BioHackathon-Europe-2025.md
new file mode 100644
index 000000000..0d56373f5
--- /dev/null
+++ b/content/posts/2025-12-02-Hetvi-J-BioHackathon-Europe-2025.md
@@ -0,0 +1,81 @@
+---
+author: hetvij
+date: 2025-12-02 # format is YYYY-MM-DD
+
+category:
+ - community
+ - event-fellowship
+ - travel-fellowship
+tag:
+ - community
+ - event-fellowship
+ - travel-fellowship
+
+title: "BioHackathon Europe 2025: A Week full of Brainstorming, Coding & Collaboration"
+url: /2025/12/02/2025-12-02-Hetvi-J-BioHackathon-Europe-2025/
+---
+
+**_The_** [**_Open Bioinformatics Foundation (OBF) Event Fellowship program_**](/travel-awards) **_aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Hetvi J,_** _**a PhD student at**_ _**Imperial College London**_, **_was awarded an OBF Event Fellowship to attend_** **_[BioHackathon Europe 2025](https://biohackathon-europe.org/)_**.
+
+Thanks to the Event Fellowship from the Open Bioinformatics Foundation (OBF), I had the opportunity to attend BioHackathon Europe 2025 located in the beautiful city of Bad Saarow, Germany. I’m currently a 3rd year PhD student in Biostatistics and my work focuses on human mitochondrial genetics. Specifically, I construct statistical models to test whether the presence or absence of somatic mitochondrial variants is associated with gene expression changes indicative of stress and aging. As part of my PhD, I work with single-cell -omics data, and run bioinformatics pipelines over high performance computing systems. My broader interests in the fields of open-source scientific computing and bioinformatics motivated me to participate in this hackathon.
+
+
+
+## Background on the Hackathon
+
+This event was a 5 day Hackathon with 31 projects, attended by 170+ in person and 200+ online. The hackathon began with presentations of each project & we started working with our chosen teams on day 1. Every day, we had hacking sessions from 9am until 5:30pm & the evenings were followed by social events to facilitate networking between people.
+
+During the hacking sessions, participants would work together with their project teams on assigned tasks & make progress by co-working with team members. On the last day, we had final presentations detailing work done and future plans from the diverse range of projects.
+
+
+
+
+The projects are all in bioinformatics but spanning a variety of topics— everything from sustainable cluster computing to metadata standardization to building new pipelines. A full list of projects can be found here: https://biohackathon-europe.org/projects/
+
+## Brief information about my project
+
+I was part of Project 4: _Beyond Beacons- Establishing genomic background in European and international biobanks_.
+
+We had 5 in person members and 1 online member working collaboratively on this project. The broad goal of this project was to assess the effect of genomic context as defined by haploblocks on the penetrance of mendelian variants.
+
+
+
+
+We segregated sequences from specific haploblocks that contain genes of interest and clustered them using mmseqs2 over 2600 individuals from the 1000 genomes project. Further, we developed a nomenclature system using binary strings to jointly-label the chromosomal, haploblock, cluster, and variant context per individual.
+
+
+
+
+We also made progress on sketching statistical models that would help associate these per-individual hashes with phenotypes. I contributed to building the nomenclature rules, and to model development and the codebase. More information on the project can be found at our Github repository. We will be releasing a Docker pipeline and a pre-print based on our work soon!
+
+Our Github: https://github.com/collaborativebioinformatics/Haploblock_Clusters_ElixirBH25
+
+
+
+
+## Social events
+
+The hackathon had some amazing social events I took part in.
+
+
+
+
+On Day 2, we had ‘Chain Reaction’ - an event where we made a creative obstacle course with all sorts of materials like wood or rubber ducks or even bubble machines to create a visual spectacle across 12 tables (the pictures will help!). A very unconventional but incredibly fun social activity- it was one of my favourite parts of the hackathon!
+
+
+
+
+On Day 3, we had a mid-week progress update from each team through a Poster session. This was a great opportunity to learn about other projects in more detail and learn about their technical & organizational approaches to the hackathon.
+
+Every day, we had walks at 6pm led by one of the hackathon organizers - which was a nice chance to see the lovely town of Baad Saarow with other participants.
+
+## Learning experiences
+
+Even with my limited background in the topic of recombination & haploblocks— I was able to rapidly understand the project context & make meaningful contributions through collaborating with others & learning from them. It was also fun working collaboratively on a codebase.
+
+Moreover, getting a chance to interact with people from the wider bioinformatics community across sub-disciplines was very valuable for me. It was fascinating to hear about the interesting and diverse backgrounds other participants came from— my learnings from these conversations will definitely guide me as I progress in my career.
+
+Thanks again to OBF for enabling my participation in this project.
+
+
+
diff --git a/content/posts/2025-12-04-BOSC-keynote-solicitation.md b/content/posts/2025-12-04-BOSC-keynote-solicitation.md
new file mode 100644
index 000000000..05c31a4ec
--- /dev/null
+++ b/content/posts/2025-12-04-BOSC-keynote-solicitation.md
@@ -0,0 +1,43 @@
+---
+author: nlharris
+date: "2025-12-04"
+category:
+ - community
+ - conference
+ - bosc
+
+tag:
+ - community
+ - conference
+ - bosc
+ - ismb
+
+title: "Call for Nominations: BOSC 2026 Keynote Speakers"
+url: /2025/12/02/2026-BOSC-keynote-nomination/
+
+---
+
+
+
+[BOSC 2026](/events/bosc) is planned for July 14-15, 2026, as part of ISMB 2026 in Washington, DC.
+
+We invite our community to [nominate potential keynote speakers](https://docs.google.com/forms/d/e/1FAIpQLSchUjaUlZw9n05kinPrYOohqukURIJrK6y662E2jjqUlT1dRQ/viewform) who would be of interest to our community.
+You may submit as many nominations as you wish. The [form](https://docs.google.com/forms/d/e/1FAIpQLSchUjaUlZw9n05kinPrYOohqukURIJrK6y662E2jjqUlT1dRQ/viewform) may be filled out multiple times. Please submit nominations by **December 15, 2025**.
+
+### Why this matters
+Keynote talks are always a highlight at BOSC.
+We traditionally open and close the conference with invited speakers—prominent contributors or emerging leaders whose work resonates with the bioinformatics open-source community.
+
+### About the selection process
+Prior to 2023, keynote selection was handled internally by the BOSC Organizing Committee.
+In 2023, we introduced a more consistent, transparent, and community-aligned process, including a public rubric for evaluating candidates.
+The results were excellent, and we are continuing this open nomination process for 2026.
+(See our selection rubric: [https://github.com/OBF/bosc_materials/blob/master/invited-speaker-process.md](https://github.com/OBF/bosc_materials/blob/master/invited-speaker-process.md))
+
+### Key Dates
+
+- December 15, 2025 – Deadline for [keynote speaker nominations](https://docs.google.com/forms/d/e/1FAIpQLSchUjaUlZw9n05kinPrYOohqukURIJrK6y662E2jjqUlT1dRQ/viewform)
+- December 19, 2025 – Nomination slate posted for community review
+- January 9, 2026 – Deadline for community comments on the slate
+
+### [Nominate a keynote speaker!](https://docs.google.com/forms/d/e/1FAIpQLSchUjaUlZw9n05kinPrYOohqukURIJrK6y662E2jjqUlT1dRQ/viewform)
diff --git a/content/posts/2025-12-04-Fatemeh-Elixir-BioHackathon-experience.md b/content/posts/2025-12-04-Fatemeh-Elixir-BioHackathon-experience.md
new file mode 100644
index 000000000..dcad00dc0
--- /dev/null
+++ b/content/posts/2025-12-04-Fatemeh-Elixir-BioHackathon-experience.md
@@ -0,0 +1,77 @@
+---
+author: Fatemeh Mirzadeh Sarcheshmeh
+date: 2025-12-04
+category:
+ - community
+ - event-fellowship
+ - travel-fellowship
+cover:
+ image: /img/2025/2025-11-03-Fatemeh-cover-image.png
+ alt: "Group photo of BioHackathon Europe 2025 participants"
+tag:
+ - travel-fellowship
+title: "Elixir BioHackathon Experience"
+url: /2025/12/04/2025-12-04-Fatemeh-Elixir-BioHackathon-experience/
+---
+
+The Open Bioinformatics Foundation (OBF) Event Fellowship program aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Fatemeh Mirzade, a PhD researcher at the University of Antwerp, was awarded an OBF Event Fellowship to attend the BioHackathon Europe 2025 ([https://biohackathon-europe.org/2025](https://biohackathon-europe.org/)).
+
+
+# My BioHackathon Experience: Contributing to Open Science in Proteomics
+
+From the 3rd to 7th of November 2025, I had an incredible opportunity that shaped my early PhD journey: participating in BioHackathon Europe 2025 as part of **Project #29 on proteomics quality control**. Thanks to the Open Bioinformatics Foundation (OBF) Event Fellowship, I joined a team of bioinformaticians and proteomics researchers working to solve a critical challenge in our field.
+
+🔗 Project #29 repository: https://github.com/MS-Quality-Hub/biohackathon2025
+🔗 OBF on GitHub: https://github.com/OBF
+
+## Why I Joined
+As someone just starting their PhD, I was both nervous and excited to dive into this collaborative coding event. Our project aimed to build automated quality control frameworks for public proteomics repositories like PRIDE, which contains over 31,000 datasets. The problem? Without standardized quality metrics, researchers can't confidently reuse existing data, essentially flying blind when trying to assess if a dataset is suitable for their analysis.
+
+## My Contribution: Making Sense of Quality Metrics
+I was assigned to create a formal taxonomy for QC metrics in mass spectrometry. When I first looked at the existing PSI-MS Controlled Vocabulary, I was overwhelmed. There were metrics scattered everywhere, categorized in ways that mixed fundamentally different information together.
+
+Working with the team, I helped develop a **seven-dimensional classification system** that describes each metric along orthogonal axes:
+- workflow stage
+- analytical dimension
+- information dependency
+- measurement scope
+- acquisition strategy
+- quality interpretation
+- metric value type
+
+
+
+I compiled and classified **94 metrics** from scientific literature, covering everything from chromatographic performance to identification confidence. For each one, I documented PSI-MS accession numbers, wrote descriptions, specified units, and noted applicability to different acquisition workflows. The work was tedious but deeply educational. By the end, I understood what “quality” actually means in proteomics.
+
+## What Open Source Contribution Feels Like
+This was my first real experience contributing to open-source infrastructure that will be used globally. The spreadsheet I created is now feeding directly into updates to the PSI-MS Controlled Vocabulary. The team used my work to add new relationship types to the ontology, enabling tools to automatically understand what each metric means.
+
+What struck me most was the collaborative nature of open science. I watched established researchers patiently explain concepts, saw consensus emerge through respectful debate, and learned that asking “stupid” questions often reveals important assumptions.
+
+Meanwhile, other team members built incredible tools:
+- an **mzQC export function for pMultiQC**
+- an **ID-free QC calculator using pyOpenMS**
+- a **web-based validator** for our classification system
+
+These weren’t just internal prototypes but contributions to the broader proteomics ecosystem.
+
+## Beyond Technical Skills
+Yes, I learned about mzQC formats, PSI-MS ontologies, and GitHub workflows. But the most valuable learning was about how open science actually functions. I experienced the generosity of researchers who take time to mentor newcomers, learned that technical decisions involve tradeoffs between elegance and practicality, and discovered that it's okay to feel out of your depth because that's where real learning happens.
+
+Coming in as a fresh PhD student, I felt intimidated by fast-moving technical discussions and unfamiliar acronyms. But that initial disorientation became exactly what made the experience valuable. I'm leaving not just with new technical knowledge but with lasting connections to a community committed to collaborative infrastructure development.
+
+## Why This Matters
+We're building something that will help researchers worldwide make better use of public proteomics data. Imagine filtering datasets by quality before downloading terabytes, training machine learning models on curated high-quality data, or conducting meta-analyses that properly account for technical variation. That's the future we're working toward.
+
+This hackathon showed me what open science looks like in practice: people from different backgrounds coming together to tackle shared challenges, contributing their expertise freely, and building infrastructure that lifts the entire field.
+
+I'm grateful to the Open Bioinformatics Foundation for making my participation possible and excited to continue contributing throughout my PhD.
+
+## Want to Explore More?
+
+❖ **Full story on Medium:**
+https://medium.com/@fatemehmirzadehsarcheshmeh/building-the-future-of-proteomics-quality-control-my-experience-at-biohackathon-europe-2025-8487191e170f
+
+❖ **Project repo:** https://github.com/MS-Quality-Hub/biohackathon2025
+
+❖ **OBF GitHub:** https://github.com/OBF
diff --git a/content/posts/2025-12-18-keynote-nominees-call-for-comments.md b/content/posts/2025-12-18-keynote-nominees-call-for-comments.md
new file mode 100644
index 000000000..d68d31540
--- /dev/null
+++ b/content/posts/2025-12-18-keynote-nominees-call-for-comments.md
@@ -0,0 +1,57 @@
+---
+author: "Monica Munoz-Torres and Jason Williams"
+date: "2025-12-18"
+category:
+ - community
+ - conference
+ - bosc
+
+tag:
+ - community
+ - conference
+ - bosc
+ - ismb
+
+title: "Call for Comments on BOSC 2026 Keynote Speaker Candidates"
+url: /2025/12/18/2026-keynote-community-comment/
+
+---
+
+
+
+We thank our community for the excellent keynote speaker suggestions for [BOSC 2026](/events/bosc).
+The next phase of our selection process invites you to share any concerns about the suitability of the nominated individuals.
+Our [invited speaker selection process and criteria](https://github.com/OBF/bosc_materials/blob/master/invited-speaker-process.md) outline the factors we consider when selecting speakers for BOSC 2026, including characteristics that will exclude a speaker.
+
+Please use **[this anonymous form](https://docs.google.com/forms/d/e/1FAIpQLSe3hUXZ5BQv2-I7DpL-SdEovAVh6Bq9wWgs93FMx5LylAC_Eg/viewform)** to submit any concerns,
+including as much detail as you are comfortable providing, by **Friday, January 9th, 2026**.
+
+### This year’s nominees are:
+
+- Katy Börner
+- Anne Carpenter
+- Ishwar Chandramouliswaran
+- Kyunghyun Cho
+- Francis Collins
+- Medha Devare
+- Casey Greene
+- Eric Green
+- Susan Gregurick
+- Lukas Heumos
+- Mikhail Kolmogorov
+- Heng Li
+- Thomas Leitner
+- Marcia McNutt
+- Alondra Nelson
+- Sandra Orchard
+- Francis Oullette
+- Cyril Pommier
+- John Quackenbush
+- Heidi Sofia
+- Paul Thomas
+- Kirstie Whitaker
+- Maryam Zaringhalam
+
+The BOSC Organizing Committee will extend invitations for keynote speakers using the community-nominated list after the comment period closes.
+Since the Committee cannot guarantee a speaker's acceptance, they may need to consider individuals not on the original list without repeating the entire nomination process.
+However, the Committee remains open to community input if a speaker is believed not to meet the established standards.
diff --git a/content/posts/2026-02-02-David-Mwaura-AIBBC2025.md b/content/posts/2026-02-02-David-Mwaura-AIBBC2025.md
new file mode 100644
index 000000000..96a40b2cc
--- /dev/null
+++ b/content/posts/2026-02-02-David-Mwaura-AIBBC2025.md
@@ -0,0 +1,40 @@
+---
+author: "David-Kiragu-Mwaura"
+date: 2026-02-23
+category:
+ - community
+ - event-fellowship
+ - travel-fellowship
+tag:
+ - community
+ - event-fellowship
+ - travel-fellowship
+
+title: "Bridging Learning Gaps Through Open-Source Tools"
+url: /2026/02/23/2026-02-23-David-Mwaura-AIBBC2025/
+---
+
+The [Open Bioinformatics Foundation (OBF) Event Fellowship program](/travel-awards) aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. David Kiragu Mwaura,_an Assistant Research Scientist at the Kenya Institute of Primate Research, was awarded an OBF Event Fellowship to attend the [2025 AIBBC conference](https://www.aibbc-society.org/).
+
+
+
+ ## Introduction
+My desire to share my masters’ research output in a real world demonstration had finally come to fruition. This was achieved by securing a competitive travel grant from the **Open Bioinformatics Foundation Event Fellowship**. Leaving the chilly landscapes of Glasgow, Scotland for the warm, tropical weather in my home country, Kenya, I was honored to attend the [2025 African International Biotechnology and Biomedical Conference](https://www.aibbc-society.org/), where scientists from around the world gather to exchange ideas that directly address Africa’s needs.
+
+## Poster Presentation
+My simple and urgent plan was to showcase that open-source educational tools are practical, fair, high-impact solutions and not just an alternative means to the huge learning gap created by expensive proprietary software, especially in resource-constrained environments like Africa. My core contribution was to demonstrate how freely available platforms, particularly R Shiny, can revolutionize learning. My poster, **"BRIDGING TECHNOLOGY AND GENETIC EDUCATION: AN OPEN SOURCE SHINY APPLICATION FOR TEACHING PATERNITY ANALYSIS"**, served as the definitive proof of concept.
+
+Standing proudly beside my poster, I highlighted the complexity of teaching kinship inference and presented our solution, [DadApp](https://github.com/KIRAGU-MWAURA/DadApp_Shiny_Web_App), the open source R shiny tool. I shared the successful results from the Kenya Institute of Primate Research (KIPRE) pilot study that described the increase of interest and confidence upon using DadApp as an active learning tool. The results were uniquely compelling to the audience which sparked the discussion among lecturers and researchers from many institutions across Africa, who recognized the immense value of such open source tools. They saw an accessible, validated tool that could be replicated and scaled here in Africa where technology is gradually accessible.
+
+
+
+However, what stood out was how diverse my audience was: Some asked what Open Source is and why it matters in the Biotechnology and Biomedical fields? Whereas some audience members were advanced to ask what license is the Shiny App released under and if it allows commercial use, modification and/or redistribution? The diverse audience validated the continuous need for sensitizing about the importance of Open Source tools and Open Science in general. One of the most satisfying highlights was having a Professor from one of the leading universities in Kenya appreciating the content of the poster and commenting that such Open Source tools are the future as they can help in enhancing flexibility in curriculum design. He further added that lecturers and those passionate in capacity development can tailor such tools to course goals especially in lessons that are mathematically and coding intensive.
+
+## Final Thoughts
+The AIBBC conference was a humbling experience because for the first time I got to see something that was once a thoughtful concept became a product that was exciting and appreciated by my peers to advanced scientists and lecturers from different scientific backgrounds. However, my greatest achievement was showing that advanced learning does not have to rely on expensive softwares but can also be achieved with an open source Shiny App like DadApp. Students/participants can utilize such open source tools to explore data, visualize results, and understand scientific principles that once felt out of reach. The sparked conversations, encouragement and collaborative opportunities ignited a strong desire amongst the audience to champion genuine scientific equity, and a recognition that every scientist has a role in bringing that future of Open Science to life.
+
+Looking back, the bridge from Glasgow to Kenya became one of ideas, innovation, and global learning. I hope the experience leaves a lasting impact on both myself and the audience long after the conference.
+
+ ‘When knowledge travels freely, learning knows no borders.’
+
+---
diff --git a/content/posts/2026-02-03-Rafal-Milodrowski-BioHackathon-Europe-2025.md b/content/posts/2026-02-03-Rafal-Milodrowski-BioHackathon-Europe-2025.md
new file mode 100644
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--- /dev/null
+++ b/content/posts/2026-02-03-Rafal-Milodrowski-BioHackathon-Europe-2025.md
@@ -0,0 +1,73 @@
+---
+author: milodrowski
+date: 2026-02-04
+
+category:
+ - community
+ - event-fellowship
+ - travel-fellowship
+tag:
+ - community
+ - event-fellowship
+ - travel-fellowship
+
+title: "BioHackathon Europe 2025: BUSCO genes, lakeside hacking, and open workflows"
+url: /2026/02/03/2026-02-03-Rafal-Milodrowski-BioHackathon-Europe-2025/
+---
+
+The Open Bioinformatics Foundation (OBF) Event Fellowship program aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. I was awarded an OBF Event Fellowship to attend [BioHackathon Europe 2025](https://biohackathon-europe.org), held 3–7 November at the Esplanade Resort & Spa in Bad Saarow, near Berlin, Germany.
+I am a PhD student at the Jagiellonian University in Kraków, working with insect genomes and large-scale comparative datasets. [BUSCO](https://busco.ezlab.org) is part of my everyday toolkit, so spending a week contributing to a BUSCO-based phylogenomics workflow with an international team felt like a perfect fit. The fellowship covered my travel costs and made it possible for me to fully participate in the hackathon.
+
+
+## A hackathon by the lake
+
+BioHackathon Europe took over a lakeside hotel that turned into a giant shared office for a week: meeting rooms full of laptops and whiteboards, and a steady flow of coffee and conversations. Mornings started with a short plenary, followed by focused hacking sessions in the project rooms. Evenings were more relaxed, with social activities, ad‑hoc debugging sessions, and lots of informal discussions about tools, data and careers.
+
+
+
+## Project #03: benchmarking BUSCO genes for phylogenomics
+
+I joined project #03, “Automatic workflow for benchmarking BUSCO genes for phylogenomics”. BUSCO lineage datasets are widely used to assess genome completeness and to extract putatively single-copy orthologs for phylogenetic analyses. However, once you look across many genomes at once, especially in groups with whole‑genome duplications, it quickly becomes clear that many BUSCO loci are not truly single copy. Our project aims to make this complexity visible and manageable.
+The goal for the week was to turn existing scripts and a prototype workflow into a robust Snakemake pipeline that starts from BUSCO output and ends with phylogenomic trees. The workflow includes steps for multiple‑sequence alignment and trimming, gene‑tree inference, detection of in‑ and out‑paralogs, and construction of concatenated supermatrices and species trees that explicitly account for paralogy.
+
+
+
+
+## My role: testing and debugging
+
+Coming from a background of running Snakemake pipelines on HPC systems, I focused on the “does this actually run for a new user?” side of the project. A surprising amount of hackathon time can disappear into environment issues, so as a team we invested early in getting a clean, reproducible setup with conda and Snakemake with clearly pinned software versions.
+My main contribution was to run the pipeline on a curated set of genomes and report back where things broke or behaved unexpectedly. This included checking intermediate outputs (alignments, gene trees, paralog reports), tracking down missing dependencies, and helping to standardise file naming conventions for genome FASTA files and BUSCO output directories. These details may sound minor, but they are crucial when scaling up to dozens or hundreds of genomes.
+
+
+
+## Community and mid‑week reporting
+
+A highlight of the week was the mid‑week reporting session, where each project prepared a short poster and gave lightning updates. Walking around the room, it was impressive to see the variety of topics being tackled in parallel: workflows, training materials, AI‑readiness, data standards and more. Presenting our BUSCO project forced us to summarise why this workflow matters, not just how it works.
+The poster session also helped to connect with people from other projects who use BUSCO or phylogenomics in their own work. Several visitors were interested in applying the workflow to their clades, and their questions helped us clarify which configuration options and outputs will be most useful for future users.
+
+
+
+## Take‑home messages
+
+The week left me with a few key lessons:
+- **Reproducible workflows are a collective effort.** Agreeing on file naming, pinning software versions and writing documentation takes time, but doing it together during a hackathon pays off immediately.
+- **“Single‑copy” genes are often more complicated than they look.** The preliminary results we explored during the week highlight just how common paralogy is, even in supposedly universal BUSCO sets.
+- **Hackathons are great for collaboration across time zones.** Our work in Bad Saarow connected with contributions from an Australian outpost of the project, with progress passed back and forth through shared repositories and notes.
+- **Open tools lower the entry barrier.** By investing in a polished, documented workflow instead of a one‑off analysis, we make it easier for others to reuse and extend our work.
+- **Pipelines live and grow in the open.** The BUSCO phylogenomics pipeline we worked on is being developed in the open as the “buscophy” workflow on [GitHub](https://github.com/tbrown91/biohackathon-projects-2025/tree/main/03-automatic-workflow-for-benchmarking/buscophy). It takes BUSCO output from many genomes, aligns and trims the corresponding genes, builds gene trees, flags in- and out-paralogs, and then builds concatenated supermatrices and summary species trees from the filtered genes. Having all of this encoded in one reproducible pipeline means others can rerun exactly the same analysis, adapt it to their own taxa, or extend it with new methods.
+
+
+## What comes next
+
+The work we began at BioHackathon Europe 2025 will continue as the team refines the workflow, runs it on additional clades and prepares it for broader release. For my own research, I am excited to apply the BUSCO phylogenomics pipeline to insect genomes and to compare patterns of paralogy across groups with very different genome architectures. I expect this will directly improve the robustness of the phylogenies I use in my PhD.
+
+
+
+---
+
+## Acknowledgements
+
+I am very grateful to the Open Bioinformatics Foundation for the Event Fellowship that made my participation in BioHackathon Europe 2025 possible, and to the organisers from ELIXIR for creating such a welcoming environment. I would also like to thank the BUSCO phylogenomics project leads and all my teammates for their patience, good humour and willingness to explain things one more time when the logs got confusing. Finally, I appreciate the support of my home institution and colleagues in Kraków, who made it easier for me to step away from local duties for a week of focused hacking.
+Thank you, OBF!
+
+---
diff --git a/content/posts/2026-03-04-BOSC-registration-support.md b/content/posts/2026-03-04-BOSC-registration-support.md
new file mode 100644
index 000000000..9bd69275f
--- /dev/null
+++ b/content/posts/2026-03-04-BOSC-registration-support.md
@@ -0,0 +1,80 @@
+---
+author: nlharris
+category:
+ - bosc
+ - ismb
+ - community
+cover:
+ alt: Participants in CoFest 2025
+ image: /img/2025/bosc2025-img/CoFest%20-%203%20people%20working%20at%20table.jpeg
+
+date: "2026-03-04T02:30:32+00:00"
+draft: false
+tag:
+ - bosc
+ - ismb
+ - conferences
+
+title: "Financial support options for attending BOSC 2026"
+url: /posts/financial-support-BOSC2026/
+
+---
+
+BOSC is part of the big [ISMB 2026](https://www.iscb.org/ismb2026/home) conference, so you need to register for ISMB to participate in BOSC.
+
+We recognize that the high price of travel and registration can be a barrier.
+Below are some ways to apply for financial assistance to attend ISMB / BOSC.
+
+
+{{< columns >}}
+
+
+
+{{< column >}}
+
+## OBF Event Fellowships
+
+The Open Bioinformatics Foundation (OBF)'s
+[Event Fellowships](/event-awards/) are aimed at increasing diverse participation at events promoting open science
+in the bioinformatics and biological research communities...such as BOSC.
+
+Awards are made three times a year; the next **deadline is April 1, 2026** (note that this is earlier than the ISMB submission deadline of April 9).
+
+{{< endcolumns >}}
+
+
+## BOSC Registration Fee Support
+
+
+
+Authors who [submit their work to BOSC](/events/bosc-2026/submit/) can request ISMB registration fee support on the abstract submission form (these requests are not seen by reviewers). This initiative is funded by [sponsorships](/events/sponsors/).
+
+Only presenting authors whose abstracts are accepted for talk or poster presentation are eligible for this fee support, and not all requests will be granted.
+
+Requests from early-career applicants and people from underrepresented geographical areas will be given priority.
+Applicants will be notified about whether their request was granted shortly after abstract acceptance notifications go out in early May.
+
+
+## ISCB Conference Fellowships
+
+{{< columns >}}
+
+
+
+{{< column >}}
+
+The ISCB (the organization that runs the ISMB conference) offers a limited number of [conference fellowships](https://www.iscb.org/ismb2026/general-info/conference-fellowships) that cover the registration fee to help students and postdocs to present their work at ISMB.
+
+These fellowships are only open to those who have a **Proceeding, Talk, or Poster (not late poster) accepted for presentation at ISMB**.
+The application will be sent automatically to eligible people on May 5.
+The number of awards is limited; not all eligible applicants will receive awards.
+Please consult the [ISMB page](https://www.iscb.org/ismb2026/general-info/conference-fellowships) for more information.
+
+{{< endcolumns >}}
+
+## Apply to be Event Staff at ISMB
+
+
+
+You can [apply to work at ISMB 2026](https://www.iscb.org/ismb2026/general-info/apply-to-be-event-staff) for approximately 20-24 hours in exchange for free registration and time-based pay.
+(When you're not working, you can attend talks.) The **application deadline is May 1, 2026**.
diff --git a/content/posts/2026-03-05-Event-Awards.md b/content/posts/2026-03-05-Event-Awards.md
new file mode 100644
index 000000000..44f387b38
--- /dev/null
+++ b/content/posts/2026-03-05-Event-Awards.md
@@ -0,0 +1,47 @@
+---
+author: hzahroh
+date: 2026-03-05 # format is YYYY-MM-DD
+
+category:
+ - community
+ - event-fellowship
+ - travel-fellowship
+
+
+tag:
+ - community
+ - event-fellowship
+ - travel-fellowship
+
+title: Call for the first 2026 round of the OBF Event Fellowship & overview of the awards made in 2025
+url: /2026/03/05/event-fellowship-2026-1/
+---
+
+---
+The call for applications for **round 1** of the [OBF Event Fellowship](https://www.open-bio.org/event-awards/) for 2026 is now open. **The deadline for this round is 1 April 2026\.** You can submit your application through [this Google Form](https://forms.gle/maZEJzCF4rifEJgz5). We have provided a Word template to help you draft the application locally before filling out the form – [make a copy of this template](https://forms.gle/maZEJzCF4rifEJgz5).
+
+
+The Open Bioinformatics Foundation (OBF)'s Event Fellowship program is aimed at increasing diverse participation at events promoting open science in the bioinformatics and biological research communities. Awards are made three times a year; the next deadline is April 1, 2026. (For those who want to apply for [BOSC](/events/bosc/), note that this is earlier than the BOSC/ISMB submission deadline of April 9.)
+
+We invite applications from candidates seeking financial support to attend relevant scientific events between May 2026 to April 2027\. ***These events include conferences, workshops, code fests, hackathons, training courses, collaborative sprints, informal meet-ups or other skill-building and networking events***. For more details, please read our [OBF Event Fellowship policy document](https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md).
+
+### Overview of the overall 2025 rounds of OBF Event Fellowship
+
+The [Open Bioinformatics Foundation (OBF) Event Fellowship program](https://www.open-bio.org/event-awards/) is now in its 9th year. Since 2023, we have three application rounds per year with the following deadlines: 1 April, 1 August, and 1 December.
+
+We changed the OBF event fellowship policy to say that the event that the applicant is applying to must be **high-quality and not predatory**. We also **require** the applicants and awardees write the application and blog draft themselves, and prohibit the use of AI/LLMs for this. These changes are now integrated in [travel_fellowship.md](https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md) and the [OBF Event Fellowship application form](https://forms.gle/xKBJqC9L5U2SAEKV8).
+
+Looking back at 2025, we received numerous applications, and **nine applicants were selected** from three rounds across 2025 to support their participation in various events. All OBF Event Fellowship awardees are required to write blog posts after their events; two of the people who were selected for awards in 2025 have not yet attended their events.
+**Seven of them have written blog posts** sharing their experiences at events that promote open science and open source bioinformatics, with the support of the OBF Event Fellowship. You can read their posts here:
+
+1. Ruby Krasnow: [2025 ESIIL Innovation Summit: Collaborative and Open Environmental Data Science in Boulder](https://www.open-bio.org/2025/11/03/2025-11-03-Krasnow-ESIIL-Summit/)
+2. Tayyaba Alvi: [ISMB 2025: A Week of Learning, Teaching, and Connecting in Liverpool](https://www.open-bio.org/2025/08/25/2025-08-25-Tayyaba-Alvi-ISMB2025/)
+3. Muhamad Haries Ramdhani: [ISMB/ECCB 2025: Liverpool, LLMs and Lessons in Open Science](https://www.open-bio.org/2025/09/04/2025-09-04-muhamad-haries-ramdhani-ismb-eccb-2025/)
+4. Fatemeh Mirzadeh Sarcheshmeh: [Elixir BioHackathon Experience](https://www.open-bio.org/2025/12/04/2025-12-04-Fatemeh-Elixir-BioHackathon-experience/)
+5. Hetvi Jethwani: [BioHackathon Europe 2025: A Week full of Brainstorming, Coding & Collaboration](https://www.open-bio.org/2025/12/02/2025-12-02-Hetvi-J-BioHackathon-Europe-2025/)
+6. Rafał Miłodrowski: [BioHackathon Europe 2025: BUSCO genes, lakeside hacking, and open workflows](https://www.open-bio.org/2026/02/03/2026-02-03-Rafal-Milodrowski-BioHackathon-Europe-2025/)
+7. David Kiragu Mwaura: [Bridging Learning Gaps Through Open-Source Tools](https://www.open-bio.org/2026/02/23/2026-02-23-David-Mwaura-AIBBC2025/)
+
+Congratulations to all of our awardees! We are delighted to help support their participation in open-source-related events with OBF Event Fellowships, and we wish them all the best for their future work.
+
+**Please share this post and [apply for the fellowship](https://forms.gle/D31zSs558aRwj2ig9) before 1 April 2026\.**
diff --git a/content/posts/2026-03-30-open-source-in-the-age-of-AI.md b/content/posts/2026-03-30-open-source-in-the-age-of-AI.md
new file mode 100644
index 000000000..0418b5f48
--- /dev/null
+++ b/content/posts/2026-03-30-open-source-in-the-age-of-AI.md
@@ -0,0 +1,44 @@
+---
+author: nlharris
+category:
+ - bosc
+ - ismb
+ - community
+date: "2026-03-30T02:30:32+00:00"
+draft: false
+tag:
+ - bosc
+ - ismb
+ - conferences
+
+title: "Open Source in the Age of AI"
+url: /posts/Open-Source-in-the-Age-of-AI/
+
+---
+
+At BOSC 2026, we want to talk about the elephant in the open-source room: **Is generative AI an advantage or a hindrance to open source?**
+
+
+We invite abstracts on this topic. Some might be selected to give talks at BOSC (which will be part of ISMB 2026).
+We may also invite some of the chosen speakers to participate in a panel. The [submission deadline](/events/bosc-2026/submit/) is April 9.
+
+For example, here are some possible topics (but don't feel restricted to these):
+
+- Reuse: how can we encourage and facilitate reuse of tools and frameworks when AI makes it easy to code things up from scratch?
+- Evaluating open source projects: AI tools can generate thousands of lines of code in seconds. The most costly process is now verifying that code for scientific accuracy (https://arxiv.org/abs/2507.09089). What are some good approaches to address this?
+- Contribution guidelines: balancing scale and utility of AI-assisted development with community-building
+ - How should an open source project assess pull requests from AI agents?
+ - Are zero-tolerance bans on submissions generated using AI reasonable? (e.g., https://medium.com/@livewyer/ai-disruption-to-open-source-software-oss-377f10be2d8a)
+ - How can humans and AI agents best work together?
+- Attribution and credit:
+ - How should we recognize contributions in an age of AI-assisted commits?
+ - Transparency: Should there be mandatory requirements to disclose AI use, including models and prompts used?
+ - Human ownership: should authors always remain legally and ethically accountable for the outputs of their code?
+ - Licensing: do open source licenses still mean anything when coding agents can translate or reimplement code?
+- Sustainability: who does the long-term hard work of maintaining open source projects when AI does the "easy" work?
+- Credit for training data: part of what AI proposes is reusing existing human-coded work without crediting it. Can there be a way to fairly credit the contribution of an open source project to the (often non open-source) models?
+- When AI is the user: should open source projects be designed for machine consumers?
+- The deadly feedback loop: models are trained on what they produce. Does this really work?
+- Open data in the AI era: balancing access with protection from misuse
+
+We look forward to seeing your thoughts on these topics! Please be sure to [submit your abstract](/events/bosc-2026/submit/) by April 9 if you want to be considered for a talk.
diff --git a/content/posts/2026-05-13-CoFest-2026.md b/content/posts/2026-05-13-CoFest-2026.md
new file mode 100644
index 000000000..a36c7d66e
--- /dev/null
+++ b/content/posts/2026-05-13-CoFest-2026.md
@@ -0,0 +1,35 @@
+---
+author: nlharris
+category:
+ - bosc
+ - ismb
+ - community
+date: "2026-05-13T02:30:32+00:00"
+draft: false
+tag:
+ - bosc
+ - ismb
+ - conferences
+
+title: "CollaborationFest 2026"
+url: /posts/CollaborationFest-2026/
+---
+
+
+The OBF/BOSC CollaborationFest (aka CoFest) is a collaborative event where participants get to work together on code, documentation, training materials, challenging analysis problems, use cases, and more.
+Participants can bring their own project ideas or pitch in on others’ projects.
+
+BOSC has organized CoFests every year before or after ISMB since 2010. This year, CoFest will take place after ISMB 2026 on **Friday, July 17 and Saturday, July 18** (9am-5pm each day).
+The location is in central Washington, D.C. (not far from the ISMB location); the exact address will be shared with those who register.
+There will be limited opportunities for virtual participation; videoconferencing is not guaranteed but participants will be able to interact on Slack.
+
+CoFest is free, but registration is mandatory, and space is limited. To sign up:
+1. Add yourself to [this spreadsheet](https://docs.google.com/spreadsheets/d/1HvB9nHCBiCrSLWR9BNG5ypMecEbn7MOOnWIZxagQwRo/edit) to help us gauge interest, coordinate topic groups and logistics
+2. Add your project ideas to [this document](https://docs.google.com/document/d/1x7h4Tx3Y8IrcDSkSs_LylVFzQhjNKmQpwAbizQnyxYQ/edit?tab=t.0) if you have something in mind
+3. Join the #cofest2026 channel in the [OBF Slack](https://join.slack.com/t/obf-bosc/shared_invite/zt-3va3bz5qa-hR9nKXHXO9GmrkddIpJXcQ) for discussion before/during/after CoFest!
+
+We're excited to see you in July at BOSC@ISMB and hope you’ll stick around for CoFest right after.
+
+For more information on CoFest (including updates about planned projects and activities), please visit our [CoFest page](https://www.open-bio.org/events/bosc-2026/collaborationfest/).
+
+Big thanks to [Computercraft](https://computercraft-usa.com/) for providing the meeting space, and to [Seqera](https://seqera.io/), whose sponsorship is helping cover the cost of lunches!
diff --git a/content/posts/2026-06-17-Francesco-Micocci-BITS2026-hackathon.md b/content/posts/2026-06-17-Francesco-Micocci-BITS2026-hackathon.md
new file mode 100644
index 000000000..7904059a5
--- /dev/null
+++ b/content/posts/2026-06-17-Francesco-Micocci-BITS2026-hackathon.md
@@ -0,0 +1,68 @@
+---
+author: "Francesco Maria Antonio Micocci"
+date: 2026-06-26 # format is YYYY-MM-DD
+category:
+ - community
+ - event-fellowship
+ - travel-fellowship
+cover:
+ image: /static/img/2026/2026-06-17-Micocci-Francesco-poster.jpg
+ alt: "Francesco Maria Antonio Micocci presenting the JupyDo poster at the BITS2026 conference"
+
+tag:
+ - community
+ - event-fellowship
+ - travel-fellowship
+
+title: "Undergraduate to Best Poster Awardee: My experience at BITS2026 and BioHackathon"
+url: /2026/06/17/2026-06-17-francesco-micocci-bits2026/
+---
+
+**_The_** [**_Open Bioinformatics Foundation (OBF) Event Fellowship program_**](/travel-awards) **_aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. [Francesco Maria Antonio Micocci](https://github.com/Vehx35),_** _**a Undergraduate Student at**_ _**University Of Turin**_, **_was awarded an OBF Event Fellowship to attend_** _**the**_ **_[BITS2026 Conference](https://bioinformatics.it/bits2026)_** _**and**_ **_[BioHackathon2026](https://younginfolife.github.io/events/2026-biohackathon)_**.
+
+
+
+Attending a conference for the first time and as an undergraduate student can be really intimidating. Finding yourself in rooms filled with affirmed researchers and topics you’ve not studied before.
+That was exactly the situation I found myself in at the recent Biohackathon and BITS2026 in the beautiful city of Padova.
+
+I want to thank the Open Bioinformatics Foundation (OBF) for giving me the opportunity to participate in these events, without their support I wouldn't have been able to embark on this experience.
+
+
+## The BioHackathon
+
+As soon as I arrived in the city and after a rapid lunch, I found myself catapulted right into the action. After the groups were formed by the organizers, we got access to the GitHub repository. As an undergraduate, looking at the assigned tasks was a mix of excitement and panic.
+Quickly I came to realize that most of what we had to do I had only little knowledge of.
+While I felt like I couldn't be of much help to the rest of the group, I got to learn a lot from the other members that didn’t leave me out even when I was clearly having difficulties.
+
+
+## The Conference
+
+After the Hackathon, on the second day the conference finally started.
+To be really honest, the various talk sessions were packed with advanced topics that were lightyears ahead of my actual knowledge. But while the technical details went mostly over my head, listening to the speakers gave me an idea of where the field of bioinformatics is heading. Instead of feeling discouraged, it was actually motivating. Seeing how some of the knowledge I already possess is used in real life applications gave me a boost.
+
+
+## The Poster Session: The turning point
+
+While I felt a bit out of place during the oral sessions, now it was time for the poster session.
+That was my chance to share our work and get feedback from the community.
+At first, I was quite nervous, but soon people came to read our poster and had a chat about it, then all the nervousness faded away.
+It was amazing to explain our project and to receive feedback from experienced researchers.
+This fantastic experience ended then with wonderful news. We won the best poster award!
+Getting this recognition completed this experience in the best possible way. I couldn’t really believe it!
+For an undergraduate like me getting an award like this and seeing people actually appreciating my work felt unreal.
+*You can view and download the full award-winning poster on [Zenodo](https://zenodo.org/records/20763335).*
+
+
+## Not only Science
+
+This experience was not only about science.
+The social moments have been one of the best sides of this conference. Whether it was discussing projects over a coffee during breaks, having a laugh during dinners, or enjoying a drink with people, I always felt welcomed in the community.
+
+
+## Conclusion: A message to other Undergraduate students
+
+Looking back at this whole experience, I think it taught me that you don’t need to know everything to be part of the bioinformatics and open source world. All you need is curiosity and the willingness to learn.
+
+Once again, I want to express my gratitude to OBF for making all of this possible.
+If you are an undergraduate student thinking about applying for an OBF travel grant to attend these events: don’t hesitate, do it.
+You could get an opportunity to learn, meet incredible people that you wouldn't experience otherwise, and you might also walk away with a win you didn’t expect coming!
diff --git a/content/posts/2026-06-24-Event-Awards.md b/content/posts/2026-06-24-Event-Awards.md
new file mode 100644
index 000000000..77fa6ed9b
--- /dev/null
+++ b/content/posts/2026-06-24-Event-Awards.md
@@ -0,0 +1,46 @@
+---
+author: ckibet
+date: 2026-06-24 # format is YYYY-MM-DD
+
+category:
+ - community
+ - event-fellowship
+ - travel-fellowship
+
+
+tag:
+ - community
+ - event-fellowship
+ - travel-fellowship
+
+title: Call for the second 2026 round of the OBF Event Fellowship & overview of the first round of 2026.
+url: /2026/06/24/event-fellowship-2026-2/
+---
+
+---
+The call for applications for round 2 of the[ OBF Event Fellowship](https://www.open-bio.org/event-awards/) for 2026 is now open. The deadline for this round is 1 August 2026. You can submit your application through[ this Google Form](https://forms.gle/D31zSs558aRwj2ig9). We have provided a Word template to help you draft the application locally before filling out the form --[ make a copy of this template](https://docs.google.com/document/d/11Uiw3pVWHPhv-5_Zbnkd9EqS2J3dXWm_xqt3n6V2m4Y/edit?usp=sharing).
+
+
+The OBF Event Fellowship program aims to increase diverse participation at events that promote open-source bioinformatics and/or open science. We invite applications from candidates seeking financial support to attend relevant scientific events between September 2026 to August 2027. These events include conferences, workshops, code fests, hackathons, training courses, collaborative sprints, informal meet-ups or other skill-building and networking events. For more details, please read our [OBF Event Fellowship policy document](https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md).
+
+
+
+The[ Open Bioinformatics Foundation (OBF) Event Fellowship program](https://www.open-bio.org/event-awards/) is now in its 9th year. Since 2023, we have had three application rounds per year with the following deadlines: 1 April, 1 August, and 1 December.
+
+Looking back at the first round of 2026, we received 40 applications, and six applicants were selected to support their participation in various events.
+
+1. Francesco Maria Antonio Micocci: BITS 2026 & BioHackathon 2026, 26-29 May 2026
+
+2. Aditya Karna: Bioinformatics Open Source Conference (BOSC 2026), July 14-15, 2026
+
+3. Lee Jia Wei: Bioinformatics Open Source Conference (BOSC 2026), July 14-15, 2026
+
+4. Anastasia Bratulin: 34th Conference on Intelligent Systems for Molecular Biology, July 12-16, 2026
+
+5. Jeremy Fan: Bioinformatics Open Source Conference (BOSC 2026), July 14-15, 2026
+
+6. Neha Arora: Bioinformatics Open Source Conference (BOSC 2026), July 14-15, 2026
+
+Congratulations to all of our awardees! We are delighted to help support their participation in open-source-related events with OBF Event Fellowships, and we wish them all the best for their future work.
+
+**Please share this post and [apply for the fellowship](https://www.open-bio.org/event-awards/) before 1 August 2026.**
diff --git a/content/posts/5-tips-to-promote-water-cooler-effects-at-informal-discussion-sessions.md b/content/posts/5-tips-to-promote-water-cooler-effects-at-informal-discussion-sessions.md
index 96fe88e0f..d736789a5 100644
--- a/content/posts/5-tips-to-promote-water-cooler-effects-at-informal-discussion-sessions.md
+++ b/content/posts/5-tips-to-promote-water-cooler-effects-at-informal-discussion-sessions.md
@@ -38,23 +38,23 @@ As a community manager, informal discussion sessions are hands-down my favourite
>
> — Malvika Sharan (@MalvikaSharan) [July 24, 2019](https://twitter.com/MalvikaSharan/status/1154007583730126848?ref_src=twsrc%5Etfw)
-Here are my **top 5 tips for facilitating BoFs** or similar discussion sessions that promote the informal and unplanned aspects of the water cooler effect.
+Here are my **top 5 tips for facilitating BoFs** or similar discussion sessions that promote the informal and unplanned aspects of the water cooler effect.
1\. **Set the ground rules**
-Start your session by welcoming everyone and highlighting the main points of your organization’s/conference’s Code of Conduct. By choosing an inclusive discussion format (see [this post by The Instruction Section, ACRL](https://acrl.ala.org/IS/is-committees-2/committees-task-forces/discussion-group-steering/possible-discussion-format-options/) for ideas) we can provide a platform for our attendees to participate equitably. It is also useful to introduce a few simple tips for effective discussions, for example, by inviting volunteers to take different roles such as notetaker, timekeeper, or chair in different groups to ensure that everyone’s voice is heard and noted (see [this role card by Ada Initiative](https://files.adainitiative.org/wiki_binaries/role_cards.pdf)).
+Start your session by welcoming everyone and highlighting the main points of your organization’s/conference’s Code of Conduct. By choosing an inclusive discussion format (see [this post by The Instruction Section, ACRL](https://acrl.ala.org/IS/is-committees-2/committees-task-forces/discussion-group-steering/possible-discussion-format-options/) for ideas) we can provide a platform for our attendees to participate equitably. It is also useful to introduce a few simple tips for effective discussions, for example, by inviting volunteers to take different roles such as notetaker, timekeeper, or chair in different groups to ensure that everyone’s voice is heard and noted (see [this role card by Ada Initiative](https://files.adainitiative.org/wiki_binaries/role_cards.pdf)).
**2\. Get everyone on the same page**
-State the objective of your sessions clearly so that your participants know what to expect. You shouldn’t assume that participants will know the specific details essential to discuss the topic (we can always ask!), therefore, you can take the first few minutes to briefly introduce the topic and the main terminologies. It’s important to clarify what they will and will not discuss in your session.
+State the objective of your sessions clearly so that your participants know what to expect. You shouldn’t assume that participants will know the specific details essential to discuss the topic (we can always ask!), therefore, you can take the first few minutes to briefly introduce the topic and the main terminologies. It’s important to clarify what they will and will not discuss in your session.
**3\. Manage your time effectively**
-Be thoughtful and appreciative of people’s time that they invest in your sessions. Conferences can be stressful. Listening to talks, taking down notes, and getting introduced to new topics while coping with the busy schedule, new venues, and jet-lag can be both mentally and physically exhausting. Therefore informal sessions should not demand too much effort from our attendees and should allow them to decompress. To make everyone’s time count, you can share a clear agenda and divide your session into short rounds. When a session is attended by a large number of participants, it’s more effective to split them into smaller groups where they can discuss different aspects of the given topic. We should also encourage people to switch groups to maximize their chances for personal interactions. As facilitators, we should minimize our own contribution but shouldn't hesitate to bring the focus back to the topic when the discussions derail.
+Be thoughtful and appreciative of people’s time that they invest in your sessions. Conferences can be stressful. Listening to talks, taking down notes, and getting introduced to new topics while coping with the busy schedule, new venues, and jet-lag can be both mentally and physically exhausting. Therefore informal sessions should not demand too much effort from our attendees and should allow them to decompress. To make everyone’s time count, you can share a clear agenda and divide your session into short rounds. When a session is attended by a large number of participants, it’s more effective to split them into smaller groups where they can discuss different aspects of the given topic. We should also encourage people to switch groups to maximize their chances for personal interactions. As facilitators, we should minimize our own contribution but shouldn't hesitate to bring the focus back to the topic when the discussions derail.
**4\. Make it truly collaborative**
-Short sessions are great for brainstorming and generating new ideas. To ensure that these ideas don’t get lost after the session is over, there should be possibilities for your participants to collaboratively explore the topic and take notes. Each group can be provided with pens, sticky notes, flip charts, and/or whiteboards to facilitate note-taking or drawing concept maps. Online documents such as Etherpad, google docs and GitHub are generally used for sharing details of the sessions, offering a place for everyone to exchange their contact information, store their notes, add questions, and refer back to after the session is over. These online tools can be distracting if not balanced well with in-person collaborative activities (see this excellent [post on facilitating discussions](https://uwaterloo.ca/centre-for-teaching-excellence/teaching-resources/teaching-tips/alternatives-lecturing/discussions/facilitating-effective-discussions) by University of Waterloo). Each group discussion can be guided by a set of questions or scenarios and the chair of each group can be asked to share the outcome of their discussion with everyone.
+Short sessions are great for brainstorming and generating new ideas. To ensure that these ideas don’t get lost after the session is over, there should be possibilities for your participants to collaboratively explore the topic and take notes. Each group can be provided with pens, sticky notes, flip charts, and/or whiteboards to facilitate note-taking or drawing concept maps. Online documents such as Etherpad, google docs and GitHub are generally used for sharing details of the sessions, offering a place for everyone to exchange their contact information, store their notes, add questions, and refer back to after the session is over. These online tools can be distracting if not balanced well with in-person collaborative activities (see this excellent [post on facilitating discussions](https://uwaterloo.ca/centre-for-teaching-excellence/teaching-resources/teaching-tips/alternatives-lecturing/discussions/facilitating-effective-discussions) by University of Waterloo). Each group discussion can be guided by a set of questions or scenarios and the chair of each group can be asked to share the outcome of their discussion with everyone.
**5\. Communicate your next steps**
diff --git a/content/posts/ISMB-CollaborationFest-2025.md b/content/posts/ISMB-CollaborationFest-2025.md
index 4d4f2de49..bb162eae6 100644
--- a/content/posts/ISMB-CollaborationFest-2025.md
+++ b/content/posts/ISMB-CollaborationFest-2025.md
@@ -22,9 +22,9 @@ url: /2025/02/26/ISMB-CollaborationFest-2025
[CollaborationFest 2025](/events/bosc/collaborationfest/) will be a two-day collaborative work event at which participants work together to contribute code, documentation, training materials, and challenging analysis problems and use cases. Bring your own project ideas or come ready to collaborate with others on their projects!
-[](/events/bosc/collaborationfest/)
-
-BOSC has held CollaborationFests (aka CoFests) every year before or after ISMB since 2010. This year, we decided to hold the CollaborationFest as part of ISMB/ECCB and open it to all registered ISMB/ECCB participants. It will take place during the last two days of ISMB/ECCB.
+[](/events/bosc/collaborationfest/)
+
+BOSC has held CollaborationFests (aka CoFests) every year before or after ISMB since 2010. This year, we decided to hold the CollaborationFest as part of ISMB/ECCB and open it to all registered ISMB/ECCB participants. It will take place during the last two days of ISMB/ECCB.
[ISMB CollaborationFest 2025](/events/bosc/collaborationfest/) is co-organized by volunteers from four COSIs:
- Bioinformatics Open Source Conference (BOSC)
diff --git a/content/posts/YYYY-MM-DD-event-fellowship-blog-template.md b/content/posts/YYYY-MM-DD-event-fellowship-blog-template.md
index 559c9a77c..a1b77e5d6 100644
--- a/content/posts/YYYY-MM-DD-event-fellowship-blog-template.md
+++ b/content/posts/YYYY-MM-DD-event-fellowship-blog-template.md
@@ -1,8 +1,8 @@
---
-author: yourusername
+author: "Your name as you'd like it to be shown on the website"
date: 2025-05-20 # format is YYYY-MM-DD
draft: true
-category:
+category:
- community
- event-fellowship
- travel-fellowship
@@ -37,7 +37,7 @@ If you don’t have a GitHub account, create one at https://github.com/signup
### 2. Fork the OBF Website Repository
-Go to the OBF website repository:
+Go to the OBF website repository:
https://github.com/OBF/OBF.github.io
Click the **"Fork"** button (top right) to create a copy under your GitHub account.
@@ -50,8 +50,8 @@ In your forked repository:
1. Navigate to `content/posts/`
2. Click **"Add file" → "Create new file"**
-3. Name your file based on the date using the format:
- `YYYY-MM-DD-your-name-blog-title.md`
+3. Name your file based on the date using the format:
+ `YYYY-MM-DD-your-name-blog-title.md`
_Example:_ `2025-04-29-your-name-nfcore-nextflow-hackathon.md`
4. View template raw, and Copy and paste all the contents of this template into the new file.
@@ -61,9 +61,11 @@ In your forked repository:
### 4. Upload Your Images
-1. Navigate to the folder: `static/img/YYYY/` for the current year
-2. Click **"Add file" → "Upload files"**
-3. Upload your image(s) here using the format YYYY-MM-DD-image-name.jpg
+1. Resize your images if needed to at most 1024 pixels high/wide
+ (to keep the download size reasonable so the page loads quicky).
+2. Navigate to the folder: `static/img/YYYY/` for the current year
+3. Click **"Add file" → "Upload files"**
+4. Upload your image(s) here using the format YYYY-MM-DD-image-name.jpg
To insert images in your blog post, use the following format (without the static prefix):
@@ -79,7 +81,7 @@ Once your edits are complete:
1. Go to your fork’s main page on GitHub
2. Click **"Contribute" → "Open pull request"**
-3. Make sure it targets the `main` branch of
+3. Make sure it targets the `main` branch of
https://github.com/OBF/OBF.github.io
4. Use the title: `New blog post: [your title] by [your name]`
5. Click **"Create pull request"**
@@ -116,6 +118,8 @@ Describe the sessions, people, activities, or discoveries that stood out, emphas
- Or numbered lists
- Or paragraphs with images and links
+(Keep this section brief! You're not writing a grant proposal!)
+
### Add Images
Upload your images to `static/img/YYYY/` for the current year.
@@ -124,10 +128,12 @@ Then use the following without the static prefix:
```markdown
```
+#### Add an image to your first paragraph
-Example:
-
-
+Due to a quirk in the way our web templating system is set up, you need to include an image in the opening paragraph in order to have it show up on the [Posts page](https://www.open-bio.org/blog/).
+You can put a good image (ideally, one that shows you at the conference, and is more wide than tall) at the end of the canned text about the OBF Event Fellowship,
+on the next line but with no blank line in between.
+See, for example, https://github.com/OBF/OBF.github.io/blob/main/content/posts/2025-08-25-Tayyaba-Alvi-ISMB2025.md.
### Add Links
@@ -139,7 +145,7 @@ Example: [OBF Event Fellowship](https://www.open-bio.org/event-awards/)
### Add Code Blocks
-Use fenced blocks:
+There's probably no need to add code blocks to a blog post, but if you do, use fenced blocks:
\`\`\`bash
nextflow run awesome-workflow.nf
@@ -147,7 +153,7 @@ nextflow run awesome-workflow.nf
### Add Videos
-Embed a video with a simple link or screenshot and description.
+You can embed a video with a simple link or screenshot and description.
Example:
@@ -165,9 +171,7 @@ What did you learn? Who did you connect with? How will you promote open science
Thank your funders, mentors, collaborators, or community members.
-> "Thank you OBF Event Fellowship for supporting my travel to [Event Name]!"
-
---
-Ready to Submit?
+Ready to Submit?
Follow the pull request steps above under “ How to Submit Your Blog Post”
diff --git a/content/posts/biojava-3-0-4-released.md b/content/posts/biojava-3-0-4-released.md
index c007b9702..f074cbb53 100644
--- a/content/posts/biojava-3-0-4-released.md
+++ b/content/posts/biojava-3-0-4-released.md
@@ -11,14 +11,14 @@ title: BioJava 3.0.4 released
url: /2012/05/23/biojava-3-0-4-released/
---
-BioJava 3.0.4 has been released and is available from
-[http://www.biojava.org/wiki/BioJava:Download](http://www.biojava.org/wiki/BioJava:Download) as well as from the
+BioJava 3.0.4 has been released and is available from
+[http://www.biojava.org/wiki/BioJava:Download](http://www.biojava.org/wiki/BioJava:Download) as well as from the
BioJava maven repository at [http://www.biojava.org/download/maven/](http://www.biojava.org/download/maven/) .
-\- This is mainly a bug fix release addressing issues with the protein
+\- This is mainly a bug fix release addressing issues with the protein
structure and disorder modules
-\- One new feature: SCOP data can now be accessed from either the
+\- One new feature: SCOP data can now be accessed from either the
[original SCOP](http://scop.mrc-lmb.cam.ac.uk/) site in the UK (v. 1.75) or [from Berkeley](http://scop.berkeley.edu/) (v. 1.75A) .
diff --git a/content/posts/bioperl-list-summary-january-2003.md b/content/posts/bioperl-list-summary-january-2003.md
index ced752c66..1294e0969 100644
--- a/content/posts/bioperl-list-summary-january-2003.md
+++ b/content/posts/bioperl-list-summary-january-2003.md
@@ -61,7 +61,7 @@ http://makeashorterlink.com/?S17521DA3
# Questions
-- **Searching the mailing list archives**
+- **Searching the mailing list archives**
This seemed like an appropriate topic to put at the top of my list.
The Bioperl-l mailing list isn't exactly as high-traffic as
@@ -91,7 +91,7 @@ http://makeashorterlink.com/?S17521DA3
http://bioperl.org/pipermail/bioperl-l/
```
-- **Bioperl 1.2 builds under cygwin**
+- **Bioperl 1.2 builds under cygwin**
John Nash reports that he was able to build the 1.2 distribution
under cygwin once MakeMaker issues were overcome (in his case by
@@ -102,7 +102,7 @@ http://makeashorterlink.com/?S17521DA3
http://makeashorterlink.com/?M27643DA3
```
-- **Getting/untarring the 1.2 distribution**
+- **Getting/untarring the 1.2 distribution**
Some people had trouble either FTPing the 1.2 distribution, or with
successfully untarring the tarball. These problems seemed to have
@@ -113,7 +113,7 @@ http://makeashorterlink.com/?S17521DA3
http://www.bioperl.org/ftp/DIST/bioperl-1.2.tar.gz
```
-- **man pages with bioperl-1.2**
+- **man pages with bioperl-1.2**
People may have noticed that the "make" process for bioperl-1.2 does
not generate nor install man pages. Ewan Birney explains, "In 1.2 we
@@ -126,7 +126,7 @@ http://makeashorterlink.com/?S17521DA3
http://makeashorterlink.com/?F10761DA3
```
-- **Converting ABI trace to Phred format**
+- **Converting ABI trace to Phred format**
When asked why an ABI trace file read via SeqIO::abi didn't generate a
Bio::Seq::SeqWithQuality (a sequence with associated quality values),
@@ -138,7 +138,7 @@ http://makeashorterlink.com/?S17521DA3
http://makeashorterlink.com/?H2C954DA3
```
-- **biocorba status**
+- **biocorba status**
When asked about the status of the biocorba project, Jason Stajich
replied, "We have working bindings in java,perl,python and bridges to
@@ -152,7 +152,7 @@ http://makeashorterlink.com/?S17521DA3
http://makeashorterlink.com/?G57A42DA3
```
-- **DNA Smith-Waterman**
+- **DNA Smith-Waterman**
Yee Man has reimplemented the classic Smith-Waterman algorithm, with
algorithmic improvements as suggested by Gotoh (affine gaps) and Myers
@@ -174,7 +174,7 @@ http://makeashorterlink.com/?S17521DA3
http://makeashorterlink.com/?M12B23DA3
```
-- **using AUTOLOAD for get/set accessors**
+- **using AUTOLOAD for get/set accessors**
The BioPerl code is full of explicitly coded accessor methods; often
we are asked why we don't use more code-efficient methods of
@@ -192,7 +192,7 @@ http://makeashorterlink.com/?S17521DA3
http://makeashorterlink.com/?Z22C32DA3
```
-- **Bio:Seq no longer a RangeI (bug in Bio::Graphics::Panel)**
+- **Bio:Seq no longer a RangeI (bug in Bio::Graphics::Panel)**
Much to the consternation of Lincoln Stein (and his legions of
Bio::Graphics users), BioPerl 1.2 introduced a change to Bio::Seq in
@@ -216,7 +216,7 @@ http://makeashorterlink.com/?S17521DA3
http://makeashorterlink.com/?S3AC21DA3
```
-- **complement(join(e1, e2)) vs. join(complement(e1), `complement(e2))`**
+- **complement(join(e1, e2)) vs. join(complement(e1), `complement(e2))`**
Periodically, people ask "Is it possible to have bioperl output
features in Genbank format of the form
@@ -232,7 +232,7 @@ http://makeashorterlink.com/?S17521DA3
http://makeashorterlink.com/?H2CC16DA3
```
-- **GenBank `bond()` FT operator**
+- **GenBank `bond()` FT operator**
Recent GenBank files have begun to exhibit a new feature location
operator, "bond", to identify dicysteine bonds in proteins and mRNA
@@ -250,7 +250,7 @@ http://makeashorterlink.com/?S17521DA3
# Changes/Additions
-- **SearchIO now has megablast parser**
+- **SearchIO now has megablast parser**
Jason Stajich writes, "The oft requested megablast parser has now been
implemented in SearchIO". This should be available in the upcoming
@@ -260,7 +260,7 @@ http://makeashorterlink.com/?S17521DA3
http://makeashorterlink.com/?O29D62DA3
```
-- **bl2seq parser needs to know report type to get strand right**
+- **bl2seq parser needs to know report type to get strand right**
No matter how hard he tried, Dave Arenillas couldn't retrieve HSP
strand information from a bl2seq (BLAST two sequences against each
@@ -273,7 +273,7 @@ http://makeashorterlink.com/?S17521DA3
http://makeashorterlink.com/?M2ED52DA3
```
-- **bioperl.rpm in biolinux.org distribution**
+- **bioperl.rpm in biolinux.org distribution**
Marc Logghe reports that "A couple of friends of mine have started up
www.biolinux.org \[ ... and\] are offering a number of rpm packages for
@@ -290,7 +290,7 @@ http://makeashorterlink.com/?S17521DA3
http://makeashorterlink.com/?S16E22DA3
```
-- **example scripts reorganization for installation as "production" code**
+- **example scripts reorganization for installation as "production" code**
Spurred on by an earlier conversation regarding the perl scripts
scattered between examples/ and scripts/, Brian Osborne has taken up
@@ -305,7 +305,7 @@ http://makeashorterlink.com/?S17521DA3
http://makeashorterlink.com/?R29E32DA3
```
-- **Bio::Seq::SequenceTrace**
+- **Bio::Seq::SequenceTrace**
Chad Matsalla has added a Bio::Seq::SequenceTrace object, to "mimic
the information available in a scf 'Sequence Chromatogram File"'. It
@@ -317,7 +317,7 @@ http://makeashorterlink.com/?S17521DA3
http://makeashorterlink.com/?R3AE25DA3
```
-- **MLAGAN/LAGAN support**
+- **MLAGAN/LAGAN support**
Stephen Montgomery has supplied both MLAGAN and LAGAN wrappers and
parsers (the Lagan Tookit is a set of alignment programs for
@@ -331,14 +331,14 @@ http://makeashorterlink.com/?S17521DA3
# Fixes
-- **SeqIO/scf.pm bug**
+- **SeqIO/scf.pm bug**
Tony Cox "finally got around to checking in a fix for the SeqIO/scf
module when it has to deal with 8-bit encoded trace data". It's not
yet clear where this fix stands with Chad Matsalla's rewrite of
Bio/SeqIO/scf.pm
-- **Bio::Tools::Run::WrapperBase.pm missing from 1.2**
+- **Bio::Tools::Run::WrapperBase.pm missing from 1.2**
Because of some code migration between bioperl subprojects,
Bio/Tools/Run/WrapperBase.pm went missing in the 1.2 release, causing
@@ -349,7 +349,7 @@ http://makeashorterlink.com/?S17521DA3
http://makeashorterlink.com/?B20015EA3
```
-- **bug fixes in Blast HSP tiling code**
+- **bug fixes in Blast HSP tiling code**
After finding that for certain BLAST reports the "blast" and
"psiblast" SearchIO parsers gave mildly differing values for
@@ -366,7 +366,7 @@ http://makeashorterlink.com/?S17521DA3
# Proposals
-- **Project ideas for the aspiring biohacker**
+- **Project ideas for the aspiring biohacker**
Periodically, we're asked "I'd like to get involved, do you have any
project ideas a newbie could work on?". Jason Stajich shot out a few
@@ -377,7 +377,7 @@ http://makeashorterlink.com/?S17521DA3
http://makeashorterlink.com/?D28022EA3
```
-- **Bio::Perl namespace export groups**
+- **Bio::Perl namespace export groups**
The Bio::Perl module is a top-level, "novice" interface to a few small
tidbits of BioPerl functionality. Many first-time users appreciate
diff --git a/content/posts/biopython-1-78-released.md b/content/posts/biopython-1-78-released.md
index b8509dd29..3736a5799 100644
--- a/content/posts/biopython-1-78-released.md
+++ b/content/posts/biopython-1-78-released.md
@@ -20,7 +20,7 @@ The main change is that `Bio.Alphabet` is no longer used. In some cases you will
`Bio.SeqIO.parse()` is faster with "fastq" format due to small improvements in the `Bio.SeqIO.QualityIO` module.
-The `SeqFeature` object's `.extract()` method can now be used for
+The `SeqFeature` object's `.extract()` method can now be used for
trans-spliced locations via an optional dictionary of references.
As in recent releases, more of our code is now explicitly available under either our original " _Biopython License Agreement_", or the very similar but more commonly used " _3-Clause BSD License_". See the `LICENSE.rst` file for more details.
diff --git a/content/posts/biopython-1-79-released.md b/content/posts/biopython-1-79-released.md
index 40178dd37..62095f556 100644
--- a/content/posts/biopython-1-79-released.md
+++ b/content/posts/biopython-1-79-released.md
@@ -36,11 +36,11 @@ Additionally, a number of small bugs and typos have been fixed with further addi
Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:
-\- Damien Goutte-Gattat
-\- Gert Hulselmans
-\- João Rodrigues
-\- Markus Piotrowski
-\- Sergio Valqui
-\- Suyash Gupta
-\- Vini Salazar (first contribution)
+\- Damien Goutte-Gattat
+\- Gert Hulselmans
+\- João Rodrigues
+\- Markus Piotrowski
+\- Sergio Valqui
+\- Suyash Gupta
+\- Vini Salazar (first contribution)
\- Leighton Pritchard
diff --git a/content/posts/bioruby-1-4-3-released.md b/content/posts/bioruby-1-4-3-released.md
index 4c005c4c5..e6e8a3951 100644
--- a/content/posts/bioruby-1-4-3-released.md
+++ b/content/posts/bioruby-1-4-3-released.md
@@ -28,15 +28,15 @@ Here is a brief summary of changes.
In addition, many changes have been made, including incompatible changes. For more information, see [RELEASE\_NOTES.rdoc](https://github.com/bioruby/bioruby/blob/1.4.3/RELEASE_NOTES.rdoc) and [ChangeLog](https://github.com/bioruby/bioruby/blob/1.4.3/ChangeLog).
-The archive is available at: [http://bioruby.org/archive/bioruby-1.4.3.tar.gz](http://bioruby.org/archive/bioruby-1.4.3.tar.gz)
+The archive is available at: [http://bioruby.org/archive/bioruby-1.4.3.tar.gz](http://bioruby.org/archive/bioruby-1.4.3.tar.gz)
Gem file is also available at: [http://bioruby.org/archive/gems/bio-1.4.3.gem](http://bioruby.org/archive/gems/bio-1.4.3.gem)
-We also put RubyGems pacakge at RubyGems.org and RubyForge. You can easily install by using RubyGems. First, check the version number by using search command:
+We also put RubyGems pacakge at RubyGems.org and RubyForge. You can easily install by using RubyGems. First, check the version number by using search command:
-% gem search --remote bio
+% gem search --remote bio
-and find “bio (1.4.3)” in the list. Then,
+and find “bio (1.4.3)” in the list. Then,
% sudo gem install bio
diff --git a/content/posts/bosc-2014-keynote-competition.md b/content/posts/bosc-2014-keynote-competition.md
index 0fa6e9dc9..182fcf409 100644
--- a/content/posts/bosc-2014-keynote-competition.md
+++ b/content/posts/bosc-2014-keynote-competition.md
@@ -23,8 +23,8 @@ url: /2013/12/13/bosc-2014-keynote-competition/
---
We're pleased to officially confirm that one of the two keynote speakers for the 15th annual Bioinformatics Open Source Conference ( [BOSC 2014](/wiki/BOSC_2014)) will be C. Titus Brown, as he announced on Twitter recently:
-> [Titus Brown (@ctitusbrown):](https://twitter.com/ctitusbrown/)
-[](https://twitter.com/ctitusbrown/) Excited to be a keynote speaker at BOSC 2014! My title: "A History of Bioinformatics (in the year 2039)" - plenty of room for mischief ;)
+> [Titus Brown (@ctitusbrown):](https://twitter.com/ctitusbrown/)
+[](https://twitter.com/ctitusbrown/) Excited to be a keynote speaker at BOSC 2014! My title: "A History of Bioinformatics (in the year 2039)" - plenty of room for mischief ;)
[https://twitter.com/ctitusbrown/status/410934403565490176](https://twitter.com/ctitusbrown/status/410934403565490176)
In recognition of the growing use of Twitter and social media within science as a way of connecting across geographical divides, we're announcing a Twitter competition to guess who is scheduled to give the second keynote at BOSC 2014 in Boston.
diff --git a/content/posts/bosc-finishes-and-i-weep-as-i-miss-it-already.md b/content/posts/bosc-finishes-and-i-weep-as-i-miss-it-already.md
index 8c3c84825..6b226874b 100644
--- a/content/posts/bosc-finishes-and-i-weep-as-i-miss-it-already.md
+++ b/content/posts/bosc-finishes-and-i-weep-as-i-miss-it-already.md
@@ -80,7 +80,7 @@ pretending that I actually know something about philosophical thinking further
then watching Kevin Spacey play a philosophy professor in a movie on the
plane, here's how the talks have been going:
-**You're my PAL. Heh. Heh. -- Matthew Goode**
+**You're my PAL. Heh. Heh. -- Matthew Goode**
Let's say you have to do phylogenies. Lots of us do. I can faithfully say as a
current study of phylogenetic techniques that these analyses might be the
@@ -98,7 +98,7 @@ substitution models and all those good things. Beautiful. My highest
recommendation. Four stars. I recommend the oyster platter with sea clams in
mint garlic sauce. Tasty.
-**Generic Model Organisms and their Database -- Suzanna Lewis**
+**Generic Model Organisms and their Database -- Suzanna Lewis**
Continuing on a food theme (damn, when is lunch?), let's say you take a dash
of collaboration, a pinch of model organisms (geez, these cheesy recipe
@@ -127,12 +127,12 @@ open source, code, and then take six months off traveling around the world on
a sailboat you built yourself when you are "working" on developing this
database. I think I'm gonna sail my boat to Puerto Rico.
-**Biopython -- me**
+**Biopython -- me**
This was the worst talk I've ever seen. This speaker is complete bollocks. I
would have walked out if I wasn't up there giving the talk.
-**Lightning Talks -- lots of people**
+**Lightning Talks -- lots of people**
Come on these go every five minutes. The only good way to describe them is
with stream of consciousness. Plus I've been reading lots of Joyce, so what
@@ -184,7 +184,7 @@ Python. PyPop. Nice. It uses dataflows and goes back and forth with Excel.
Once again, we know what it's like to work with laboratory biologists
completely in love with Excel. Here's the URL for those of you who would be
searching just like me:
-[http://allele5.biol.berkeley.edu/pypop/](http://allele5.biol.berkeley.edu/pypop/)
+[http://allele5.biol.berkeley.edu/pypop/](http://allele5.biol.berkeley.edu/pypop/)
The really nice thing about BOSC this year is that there is lots of room for
people to make contributions "on-the-fly." A really nice example of this type
diff --git a/content/posts/call-for-obf-travel-fellowship-is-open-until-1-december-2019.md b/content/posts/call-for-obf-travel-fellowship-is-open-until-1-december-2019.md
index cbdb7a613..c7e0dab4e 100644
--- a/content/posts/call-for-obf-travel-fellowship-is-open-until-1-december-2019.md
+++ b/content/posts/call-for-obf-travel-fellowship-is-open-until-1-december-2019.md
@@ -25,4 +25,4 @@ Applications are particularly encouraged from members from historically underrep
Since 2018, OBF has offered this fellowship to **12 awardees** to defray or subsidize their travel-related cost of up to **$1000 each**. You can read their blog posts in [OBF blog](/category/travel-fellowship/) where they have shared their experiences from attending different events as OBF travel fellows.
-In 2020, there will be two application calls that will close on 1 March and 1 September 2020. \[ **NOTE**: This was later changed to 1 April and 1 October.\] Please read more details on the [fellowship program](https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md) and feel free to contact the committee by writing an email to [board@open-bio.org](mailto:board@open-bio.org).
+In 2020, there will be two application calls that will close on 1 March and 1 September 2020. \[ **NOTE**: This was later changed to 1 April and 1 October.\] Please read more details on the [fellowship program](https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md) and feel free to contact the committee by writing an email to [board@open-bio.org](mailto:board@open-bio.org).
diff --git a/content/posts/cordon-bleu-bioinformatics.md b/content/posts/cordon-bleu-bioinformatics.md
index 367a6a47a..bd2e8a0f0 100644
--- a/content/posts/cordon-bleu-bioinformatics.md
+++ b/content/posts/cordon-bleu-bioinformatics.md
@@ -14,19 +14,19 @@ title: Cordon Bleu Bioinformatics
url: /2019/08/25/cordon-bleu-bioinformatics/
---
-I attended the Bioinformatics Open Source Conference ( [BOSC](/events/bosc/) 2019) organized this year along with [ISMB/ECCB](https://www.iscb.org/ismbeccb2019) in Basel, Switzerland from July 21st-25th. BOSC 2019 was in multiple ways a lot of 'firsts' for me. I was attending my first ISMB/ECCB. It also happened to be my first time in Europe. It was the first time I was putting faces and voices to a lot of names. Like in most of the conferences these days, I met a lot of Twitter-verse friends for the very first time. And above all, this was my first ever BOSC. I was funded in part by the Open Bioinformatics Foundation’s [Travel Award](/travel-awards/) and ISMB/ECCB’s Travel Fellowship. My travel and the learnings I summarize here would have been impossible without both.
+I attended the Bioinformatics Open Source Conference ( [BOSC](/events/bosc/) 2019) organized this year along with [ISMB/ECCB](https://www.iscb.org/ismbeccb2019) in Basel, Switzerland from July 21st-25th. BOSC 2019 was in multiple ways a lot of 'firsts' for me. I was attending my first ISMB/ECCB. It also happened to be my first time in Europe. It was the first time I was putting faces and voices to a lot of names. Like in most of the conferences these days, I met a lot of Twitter-verse friends for the very first time. And above all, this was my first ever BOSC. I was funded in part by the Open Bioinformatics Foundation’s [Travel Award](/travel-awards/) and ISMB/ECCB’s Travel Fellowship. My travel and the learnings I summarize here would have been impossible without both.
Nomi Harris introducing the 20th BOSC 2019 (Couldn't capture Nomi at this angle)
### **BOSC and me**
-I had been trying to go to BOSC for around three years. I submitted three abstracts over the three years which were all accepted for a lightning talk. However, a lack of funding made it impossible for me to make it to BOSC 2016 and BOSC 2018. I submitted my abstract for a poster and talk about [pysradb](https://github.com/saketkc/pysradb) that was selected for a lightning talk (a short five-minute talk) and a poster.
+I had been trying to go to BOSC for around three years. I submitted three abstracts over the three years which were all accepted for a lightning talk. However, a lack of funding made it impossible for me to make it to BOSC 2016 and BOSC 2018. I submitted my abstract for a poster and talk about [pysradb](https://github.com/saketkc/pysradb) that was selected for a lightning talk (a short five-minute talk) and a poster.
-### **ISMB/ECCB Single Cell Workshop**
+### **ISMB/ECCB Single Cell Workshop**
I arrived in Switzerland on July 19th, two days earlier than the official start date of the meeting and a day earlier than the Tutorial tracks.
-OBF’s Travel award not only covered my ISMB registration but was also generous enough to cover the registration costs for Tutorial(s). ISMB/ECCB 2019 had multiple tutorial tracks spanning the fields of interpretation of deep learning in biology, computational drug discovery, statistical methods for single-cell RNA-seq, biological data visualization, biomarker discovery and tools for reproducible analysis. I decided to attend the tutorial on statistical methods for single-cell RNA-seq primarily to get an overview of the single-cell world, which is not very distant from my current research interest of deciphering translation regulation. The [tutorial](https://github.com/rhondabacher/ISMB2019_SingleCellTutorial) was very comprehensive and gave an overview of the technology, its nuances and the methods developed to tackle them. I expected it to be a bit more methods oriented, but it is difficult to have the best of everything for a diverse audience.
+OBF’s Travel award not only covered my ISMB registration but was also generous enough to cover the registration costs for Tutorial(s). ISMB/ECCB 2019 had multiple tutorial tracks spanning the fields of interpretation of deep learning in biology, computational drug discovery, statistical methods for single-cell RNA-seq, biological data visualization, biomarker discovery and tools for reproducible analysis. I decided to attend the tutorial on statistical methods for single-cell RNA-seq primarily to get an overview of the single-cell world, which is not very distant from my current research interest of deciphering translation regulation. The [tutorial](https://github.com/rhondabacher/ISMB2019_SingleCellTutorial) was very comprehensive and gave an overview of the technology, its nuances and the methods developed to tackle them. I expected it to be a bit more methods oriented, but it is difficult to have the best of everything for a diverse audience.
### **Keynotes at ISMB**/ECCB
@@ -67,7 +67,7 @@ https://twitter.com/morgantaschuk/status/1154326308203257857
I need to mention my fellow OBF Travel awardee Dr. Aziz Khan's efforts at building [ECRcentral](https://ecrcentral.org/) that helps early-stage researches find and discuss funding opportunities besides providing them a platform to share their experiences and mentor peers. As an early stage researcher myself, I have found the resources there extremely useful.
-Finally, a project that I will keep a lookout on is [Biotite](https://www.biotite-python.org/) by Patrick Kunzmann designed as a comprehensive and efficient computational molecular biology library. But we already have [Biopython](https://biopython.org)? Well, yes and no. Extensive usage of numpy and cythonization results in reduced runtimes.
+Finally, a project that I will keep a lookout on is [Biotite](https://www.biotite-python.org/) by Patrick Kunzmann designed as a comprehensive and efficient computational molecular biology library. But we already have [Biopython](https://biopython.org)? Well, yes and no. Extensive usage of numpy and cythonization results in reduced runtimes.
Biotite and Biopython: Open source wins
@@ -75,27 +75,27 @@ Finally, a project that I will keep a lookout on is [Biotite](https://www.biotit
**My lightning talk at BOSC**
-My schedule before leaving for ISMB/ECCB 2019 from Los Angeles was jam-packed. I did the grave mistake of overestimating my ability to make a presentation for a 5-minute lightning talk. You just have to talk for 5 minutes, but then you have **only** five minutes. My presentation was only complete the night before my actual talk and would not have been possible without the feedback of Meghna Verma, a PhD candidate at Virginia Tech. I met her also for the first time at ISMB. I had a lightning talk on Day 1 where I talked about [pysradb](https://f1000research.com/articles/8-532), which I built over the last year to help me in my Ph.D. project. In the future, I plan to not overestimate my abilities, they are not worth the potential ill-effects they can have.
+My schedule before leaving for ISMB/ECCB 2019 from Los Angeles was jam-packed. I did the grave mistake of overestimating my ability to make a presentation for a 5-minute lightning talk. You just have to talk for 5 minutes, but then you have **only** five minutes. My presentation was only complete the night before my actual talk and would not have been possible without the feedback of Meghna Verma, a PhD candidate at Virginia Tech. I met her also for the first time at ISMB. I had a lightning talk on Day 1 where I talked about [pysradb](https://f1000research.com/articles/8-532), which I built over the last year to help me in my Ph.D. project. In the future, I plan to not overestimate my abilities, they are not worth the potential ill-effects they can have.
https://twitter.com/yoyehudi/status/1153969142665502720?ref\_src=twsrc%5Etfw
-I also had a poster on pysradb on the day of my lightning talk. I got a lot of visitors and a bunch of feedback. I hope pysradb also gets more contributors in the days to come!
+I also had a poster on pysradb on the day of my lightning talk. I got a lot of visitors and a bunch of feedback. I hope pysradb also gets more contributors in the days to come!
P-01: pysradb poster
-### **Applying for BOSC Travel Award**
+### **Applying for BOSC Travel Award**
-If you are thinking of traveling to any event promoting open-source bioinformatics software development and open science in the biological research community, OBF covers up to USD 1000 and it is possible to request a higher amount. The [application process](/travel-awards/) is one of the smoothest I have ever come across!
+If you are thinking of traveling to any event promoting open-source bioinformatics software development and open science in the biological research community, OBF covers up to USD 1000 and it is possible to request a higher amount. The [application process](/travel-awards/) is one of the smoothest I have ever come across!
Application Deadlines: April 15, August 15, December 15 every year.
-### **Applying for ISMB Travel Fellowship**
+### **Applying for ISMB Travel Fellowship**
ISCB also provides Travel Fellowships that can come in handy if your original source of funding is not sufficient. Switzerland travel was a bit expensive, so I had applied for a travel fellowship once I got an acceptance. If you are submitting to ISMB in the future, you will receive instructions via email if you want to apply for a Travel Fellowship. Both the OBF and ISMB applications are very easy to fill out.
### **Cordon Bleu?**
-Though more often associated with a [dish](https://en.wikipedia.org/wiki/Cordon_bleu_(dish)), I chose the title of this post as such for the high quality of talks at ISMB/ECCB and BOSC. I learned a lot in the span of five days and look forward to participating in the future as well. Again, I can’t thank enough the Open Bioinformatics Foundation and ISMB/ECCB for making this cordon bleu experience possible.
+Though more often associated with a [dish](https://en.wikipedia.org/wiki/Cordon_bleu_(dish)), I chose the title of this post as such for the high quality of talks at ISMB/ECCB and BOSC. I learned a lot in the span of five days and look forward to participating in the future as well. Again, I can’t thank enough the Open Bioinformatics Foundation and ISMB/ECCB for making this cordon bleu experience possible.
Cordon Bleu - the dish
diff --git a/content/posts/dos-and-don-ts-for-computational-training.md b/content/posts/dos-and-don-ts-for-computational-training.md
index 71b4a5850..286907613 100644
--- a/content/posts/dos-and-don-ts-for-computational-training.md
+++ b/content/posts/dos-and-don-ts-for-computational-training.md
@@ -25,9 +25,9 @@ This was my first CCMcr19 and first Carpentry event. I was curious to know more
I joined the computational world a few years ago, after moving from “wet” to “dry” lab. Shortly after the transition, I started delivering computational training and naturally, as a novice trainer, my main focus was on the material in terms of what to cover, how relevant it is, in what order do I present it and so on.
-When I faced my first classroom, I quickly realized that prepping the material and doing my research was the easy part. Instead, I found myself thinking of the other factors that contribute to the participants' learning experience such as; how do I address and interact with them, how do I account for their very diverse demographics such as gender, age and language.
+When I faced my first classroom, I quickly realized that prepping the material and doing my research was the easy part. Instead, I found myself thinking of the other factors that contribute to the participants' learning experience such as; how do I address and interact with them, how do I account for their very diverse demographics such as gender, age and language.
-Diversity and Inclusion CCMcr19
+Diversity and Inclusion CCMcr19
Ms. Brönte
Our classrooms today are not what they used to be 10 years ago. Participants come from all over the world and all walks of life, in other words, very diverse. This is especially true in computational training. For instance, bioinformatics training events in EMBL-EBI have two different types of attendees, one of which is made of plastic; [robot avatars](https://www.ebi.ac.uk/about/news/announcements/bioinformatics-training-with-robot-avatars) allowing students to participate virtually without having to be physically there.
@@ -84,10 +84,10 @@ We also discussed breaks during sessions, such as;
**“Brain Breaks”**, a mental break of 1-3 minutes each hour of the session, to help participants to re-energize, re-focus and relax, allowing people to reflect or clear their minds.
-## Since we are focused on computational teaching, it didn’t go amiss to include advice on technological solutions to facilitate training sessions while catering for different abilities and needs.
+## Since we are focused on computational teaching, it didn’t go amiss to include advice on technological solutions to facilitate training sessions while catering for different abilities and needs.
Check out the list of Do's and Don'ts in computational training and please feel free to share your tips and advice on [GitHub](https://github.com/selgebali/CCMcr19_dos).
-#### Sara El-Gebali
-Email: selgebali@gmail.com
-Twitter: @yalahowy
-GitHub: @selgebali
+#### Sara El-Gebali
+Email: selgebali@gmail.com
+Twitter: @yalahowy
+GitHub: @selgebali
diff --git a/content/posts/eight-incredible-gsoc-students-for-the-obf-this-year.md b/content/posts/eight-incredible-gsoc-students-for-the-obf-this-year.md
index 95054120f..3de620973 100644
--- a/content/posts/eight-incredible-gsoc-students-for-the-obf-this-year.md
+++ b/content/posts/eight-incredible-gsoc-students-for-the-obf-this-year.md
@@ -20,7 +20,7 @@ Every year the OBF applies to participate as a mentoring organisation for [Googl
## Enabling and prototyping JavaScript visualization in QT-based viewer TOPPView
-**Student:** Dhanmoni Nath
+**Student:** Dhanmoni Nath
**Mentors:** Julianus Pfeuffer, Timo Sachsenberg
OpenMS’ TOPPView tool is used for mass-spectrometry data analysis. However, TOPPView is lacking some often requested high-level summary views of results that are produced by OpenMS’ other tools. Although we have other open-source libraries that provide this feature, they are written in JavaScript, and re-implementing them in C++ to integrate into TOPPView would be tedious.
@@ -31,10 +31,10 @@ This project aims to solve this problem by enabling JavaScript visualizations in
## GtfBase - A curated resource of multispecies genomic regions
-**Student:** Tanishq Gupta
+**Student:** Tanishq Gupta
**Mentors:** Saket Choudhary, Amal Thomas
-Each genome has some common features: exons that make the mRNA, CDS, and UTRs. There are a lot of resources available that provide access to these features in the form of General Transfer Format (GTF) files.
+Each genome has some common features: exons that make the mRNA, CDS, and UTRs. There are a lot of resources available that provide access to these features in the form of General Transfer Format (GTF) files.
While GTF files are by themselves comprehensive, a lot of analysis is focused on individual features and these analyses often rely on a BED file, a more focused variant of GTFs. Though it is trivial to obtain a BED file from GTF, currently there are no resources that provide ready access to BED files.
We have a collection of scripts currently available as part of gencode\_regions repository: [https://github.com/saketkc/gencode\_regions](https://github.com/saketkc/gencode_regions) that tries to address this gap. For GSoC2021, our goal is to generalize these scripts into a usable tool that can be used to generate BED files for a variety of use cases and serve as a readily updated database of BED files that will keep in sync with ENSEMBL’s GTF releases.
@@ -43,7 +43,7 @@ We have a collection of scripts currently available as part of gencode\_regions
## Developing WellcomeML further for the visualisation of academic research data
-**Student:** Federica Trevisan
+**Student:** Federica Trevisan
**Mentors**: Jeff Uren, Elizabeth Gallagher, Antonio Campello
WellcomeML is a python library with functions that use machine learning for reading, processing, embedding, extracting entities and classifying academic text data like publications, grants, and other documents. However, the visualisation modules of WellcomeML are scarce and the need of developing further visualisation features for the library has emerged.
@@ -56,7 +56,7 @@ The aim of this GSoC project is then to standardize the way the results are pres
## Development of a user interface to visualise VEP data using neXtProt tools
-**Student:** Shrey Sachdeva
+**Student:** Shrey Sachdeva
**Mentors:** Kasun Samarasinghe, Lydie Lane
Several open source tools, such as the Ensembl Variant Effect Predictor (VEP), have been developed to predict the structural and functional effects of variants.
@@ -67,7 +67,7 @@ The VEP tool has a number of plugins, including a neXtProt plugin that was relea
## Implementations of AVX-512 functions
-**Student:** Kunwar Maheep Singh
+**Student:** Kunwar Maheep Singh
**Mentors:** Evan Nemerson, Jun Aruga
SIMD instruction intrinsics provide users with extreme control over vectorization of code, but the problem with using them is that they are not very portable. This is because different vendors provide their own API’s to match the instruction sets implemented in their hardware. e.g. MMX, SSE2, AVX-512, etc. on Intel x86, Altivec and VSX on PowerPC, and NEON, MVE, and SVE/SVE2 on ARM.
@@ -82,21 +82,21 @@ The aim of this project is to implement multiple families of AVX-512 intrinsics
## Implementation of NEON functions in SIMDe
-**Student:** Atharva Nimbalkar
+**Student:** Atharva Nimbalkar
**Mentors:** Evan Nemerson, Zhi An Ng
SIMD stands for Single Instruction Multiple Data. It’s a class of parallel computers that performs the same instruction on multiple data points simultaneously. SIMD can be very advantageous to multimedia applications.
SIMDe is a library that provides portable implementations of SIMD Intrinsics on hardware that don’t natively support them, while still taking advantage of SIMD when possible. It allows you to call NEON functions on x86, or SSE functions on ARM, etc.
-This project aims to add portable implementations of many more NEON functions
+This project aims to add portable implementations of many more NEON functions
in SIMDe. Along with native fallbacks for other popular architectures, which would allow NEON SIMD intrinsics to be used on WASM, AVX-512 etc.
[https://summerofcode.withgoogle.com/projects/#4927690232037376](https://summerofcode.withgoogle.com/projects/#4927690232037376)
## Design and implementation of Code is Science front-end using ReactJS
-**Student**: Isaac Miti
+**Student**: Isaac Miti
**Mentors**: Yo Yehudi, João Paulo Tiz
The Code is science website is currently built using vanilla HTML, CSS and JavaScript with Ruby as part of its backend. The current frontend needs to be redesigned and updated.
@@ -107,7 +107,7 @@ This project aims to design and develop the code is science frontend using React
## Data streaming in scientific workflows, implementation for Toil
-**Student:** Mihai Popescu
+**Student:** Mihai Popescu
**Mentors:** Michael R. Crusoe, Lon Blauvelt
Toil is an open-source Python workflow engine that lets people write data analysis pipelines in Python, CWL, and WDL. Toil has support for common workflow language (CWL), an open standard for describing analysis workflows.
diff --git a/content/posts/festus-nyasimi-journey-to-the-ismb-bosc-2022-conference.md b/content/posts/festus-nyasimi-journey-to-the-ismb-bosc-2022-conference.md
index 437033f08..ea72b0f45 100644
--- a/content/posts/festus-nyasimi-journey-to-the-ismb-bosc-2022-conference.md
+++ b/content/posts/festus-nyasimi-journey-to-the-ismb-bosc-2022-conference.md
@@ -24,10 +24,10 @@ I looked into it immediately, and I was lucky to find the late abstract submissi
In the happy moment, the rush to plan for the conference set in; this included travel, accommodation and misc stuff. The rest of the team and I worked on the presentation alongside our training activities; this is one amazing team. Considering we are a young and growing community mostly running training through volunteering and small grants to cater for the training, we had to find a source of funding to cater for the conference fee and that’s where the OBF Event fellowship showed up perfectly. Honestly, I least expected this but I didn’t discount myself and gave it a shot; I always tell myself, _“ **if I don’t knock, I will never know the answer**”._
-Fast forward, here I am at the conference; I got to attend some sessions i.e. BioInfo Core, NetBio, Varl, MLCSB and Educational COSI, where I learnt many new skills in Bioinformatics the BOSC track started. Some of the things I learned I will propose to the organizing team we develop tutorials for the community to learn from. The opening day of BOSC was the peak of the conference for me; I had an opportunity to learn more about open-source software, how to efficiently contribute to ongoing projects and how to help communities grow. I also had a chance to join the GA4GH VRS hackathon at the conference. I had a good opportunity to represent the BHKI community on what we are doing and received great responses from attendees who visited my poster. The light was shining on our community; I hope the spotlight will be on and attract more collaborators to help us achieve our mission of a collaborative and inclusive hub.
+Fast forward, here I am at the conference; I got to attend some sessions i.e. BioInfo Core, NetBio, Varl, MLCSB and Educational COSI, where I learnt many new skills in Bioinformatics the BOSC track started. Some of the things I learned I will propose to the organizing team we develop tutorials for the community to learn from. The opening day of BOSC was the peak of the conference for me; I had an opportunity to learn more about open-source software, how to efficiently contribute to ongoing projects and how to help communities grow. I also had a chance to join the GA4GH VRS hackathon at the conference. I had a good opportunity to represent the BHKI community on what we are doing and received great responses from attendees who visited my poster. The light was shining on our community; I hope the spotlight will be on and attract more collaborators to help us achieve our mission of a collaborative and inclusive hub.
-
-Some of the cool people I meet at BOSC: _panelist Jenea Adams and keynote speaker Jason Williams_.
+
+Some of the cool people I meet at BOSC: _panelist Jenea Adams and keynote speaker Jason Williams_.
I learned how to advocate for our community to grow well towards achieving Diversity, Equity and Inclusion (DEI) goals; these are necessary for a strong, welcoming and collaborative community. Interacting with attendees at the conference provided me with an opportunity to learn more about leadership and how to be a good leader from a different perspective. I look forward to keeping in touch with other communities to grow further collaborations, especially in community empowerment.
diff --git a/content/posts/following-up-from-bosc-s-obf-birds-of-a-feather-meeting.md b/content/posts/following-up-from-bosc-s-obf-birds-of-a-feather-meeting.md
index 03d647be9..c3c40348a 100644
--- a/content/posts/following-up-from-bosc-s-obf-birds-of-a-feather-meeting.md
+++ b/content/posts/following-up-from-bosc-s-obf-birds-of-a-feather-meeting.md
@@ -48,11 +48,11 @@ After reading all this, if you’re interested in helping out with any of the id
- Leaving a comment on this post!
- Tweet to [@obf\_news](https://twitter.com/obf_news)
-Also - please don’t forget to [**join the OBF**](/wiki/Membership) if you haven’t already. Any BOSC attendee automatically qualifies for membership, and even if you haven’t attended BOSC before, if you’re reading this post there’s a good chance you’ll fulfil the requirements anyway. [Details are in the form!](/wiki/Membership)
-{{< gallery cols="1" >}}
+Also - please don’t forget to [**join the OBF**](/wiki/Membership) if you haven’t already. Any BOSC attendee automatically qualifies for membership, and even if you haven’t attended BOSC before, if you’re reading this post there’s a good chance you’ll fulfil the requirements anyway. [Details are in the form!](/wiki/Membership)
+{{< gallery cols="1" >}}
{{< figure src="/wp-content/uploads/2018/07/OBF-BoF-2018-25.jpg" title="OBF-BoF-2018 - 25" alt="OBF-BoF-2018 - 25" >}}
{{< figure src="/wp-content/uploads/2018/07/OBF-BoF-2018-31.jpg" title="OBF-BoF-2018 - 31" alt="OBF-BoF-2018 - 31" >}}
-{{< figure src="/wp-content/uploads/2018/07/OBF-BoF-2018-22-e1531151626641.jpg" title="Hilmar, Peter, and Yo" alt="Hilmar, Peter, and Yo" >}}
-{{< /gallery >}}
+{{< figure src="/wp-content/uploads/2018/07/OBF-BoF-2018-22-e1531151626641.jpg" title="Hilmar, Peter, and Yo" alt="Hilmar, Peter, and Yo" >}}
+{{< /gallery >}}
diff --git a/content/posts/global-community-biosummit-2019-mit.md b/content/posts/global-community-biosummit-2019-mit.md
index 634001058..125c1beb2 100644
--- a/content/posts/global-community-biosummit-2019-mit.md
+++ b/content/posts/global-community-biosummit-2019-mit.md
@@ -14,8 +14,8 @@ title: Global Community Biosummit 2019 @MIT
url: /2019/12/17/global-community-biosummit-2019-mit/
---
-
-_The [Open Bioinformatics Foundation (OBF)](https://www.open-bio.org) sponsors a Travel Fellowship program aimed at increasing diverse participation at events promoting Open Source bioinformatics software development and open science in the biological research community. Arunav Konwar's participation at_ [Global Community Biosummit (GCBS),](https://www.biosummit.org/) _2019 was supported by this fellowship. Find more information [here.](/travel-awards/)_
+
+_The [Open Bioinformatics Foundation (OBF)](https://www.open-bio.org) sponsors a Travel Fellowship program aimed at increasing diverse participation at events promoting Open Source bioinformatics software development and open science in the biological research community. Arunav Konwar's participation at_ [Global Community Biosummit (GCBS),](https://www.biosummit.org/) _2019 was supported by this fellowship. Find more information [here.](/travel-awards/)_
diff --git a/content/posts/goodbye-mediawiki-hello-new-website.md b/content/posts/goodbye-mediawiki-hello-new-website.md
index 69f86195f..711723392 100644
--- a/content/posts/goodbye-mediawiki-hello-new-website.md
+++ b/content/posts/goodbye-mediawiki-hello-new-website.md
@@ -19,17 +19,17 @@ Above: the old BOSC page. Below: the [new one](/events/bosc/).
-If you’ve been around the OBF and BOSC community, you’re probably familiar with our slightly rusty old site, which ran on [MediaWiki](https://www.mediawiki.org/wiki/MediaWiki), the same open source software that runs [Wikipedia](https://en.wikipedia.org/wiki/Main_Page). While they’re both awesome tools, [we decided it was time for a refresh](/2018/11/19/updates-are-coming/).
+If you’ve been around the OBF and BOSC community, you’re probably familiar with our slightly rusty old site, which ran on [MediaWiki](https://www.mediawiki.org/wiki/MediaWiki), the same open source software that runs [Wikipedia](https://en.wikipedia.org/wiki/Main_Page). While they’re both awesome tools, [we decided it was time for a refresh](/2018/11/19/updates-are-coming/).
-Over the last few months, our [Outreachy](https://www.outreachy.org/alums/) Intern [Deepashree Deshmukh](https://github.com/kushinauwu/) designed and implemented the [new OBF website](/)(with supervision by OBF Board member Yo Yehudi). The goal was an attractive and easily-updatable site that can function as a community-oriented hub. Did we accomplish that? Your feedback on the [new site](/) is welcome!
+Over the last few months, our [Outreachy](https://www.outreachy.org/alums/) Intern [Deepashree Deshmukh](https://github.com/kushinauwu/) designed and implemented the [new OBF website](/)(with supervision by OBF Board member Yo Yehudi). The goal was an attractive and easily-updatable site that can function as a community-oriented hub. Did we accomplish that? Your feedback on the [new site](/) is welcome!
**What’s going to happen to the old OBF and BOSC websites?**
-The two old sites - the old wiki / main site at [/wiki](/wiki) and the blog at [http://news.obf.org](http://news.obf.org) \- will stick around for a while, but they won’t be updated any more. One of our goals was to make sure not to break any of our old links - some of them have been around for years. You’ll probably notice a banner at the top of the old pages, pointing towards the new site. Longer term, we’re hoping to redirect all our old URLs directly to their equivalents on the new website.
+The two old sites - the old wiki / main site at [/wiki](/wiki) and the blog at [http://news.obf.org](http://news.obf.org) \- will stick around for a while, but they won’t be updated any more. One of our goals was to make sure not to break any of our old links - some of them have been around for years. You’ll probably notice a banner at the top of the old pages, pointing towards the new site. Longer term, we’re hoping to redirect all our old URLs directly to their equivalents on the new website.
**What to do if you spot any bugs or strange things**
-We’ve spent a lot of time testing, updating content, tweaking things, and squashing bugs - but no site is ever perfect so it’s possible (probable?!) we’ve missed things. If you spot broken links, layout problems, browser compatibility issues, or anything else, please let us know. If you have a GitHub account, you can [log an issue directly](https://github.com/OBF/homepage/issues/new), or if it’s easier drop by our [gitter homepage chat](https://gitter.im/OBF/homepage) and let us know there. You’re also welcome to pick the issue up if you know how to fix it!
+We’ve spent a lot of time testing, updating content, tweaking things, and squashing bugs - but no site is ever perfect so it’s possible (probable?!) we’ve missed things. If you spot broken links, layout problems, browser compatibility issues, or anything else, please let us know. If you have a GitHub account, you can [log an issue directly](https://github.com/OBF/homepage/issues/new), or if it’s easier drop by our [gitter homepage chat](https://gitter.im/OBF/homepage) and let us know there. You’re also welcome to pick the issue up if you know how to fix it!
**Acknowledgements**
diff --git a/content/posts/google-summer-of-code-2021-we-need-your-project-ideas.md b/content/posts/google-summer-of-code-2021-we-need-your-project-ideas.md
index d39cefae4..058e234eb 100644
--- a/content/posts/google-summer-of-code-2021-we-need-your-project-ideas.md
+++ b/content/posts/google-summer-of-code-2021-we-need-your-project-ideas.md
@@ -16,12 +16,12 @@ TL;DR: Please send ideas for half-sized projects (1.5 months, not 3 months) **by
Longer version:
-**New mailing list: please subscribe!**
+**New mailing list: please subscribe!**
A few notes for this year: from here on we'll be using Google Groups rather than the old OBF GSoC lists or direct to private mailing address. This will make moderation easier.
If you're interested in mentoring this year, I'd recommend signing up to these two lists for now - we'll mostly use the mentors list until (if) we're accepted as an organisation, and the general list will become more active once (if) we have any students.
-[https://groups.google.com/g/obf-gsoc-general](https://groups.google.com/g/obf-gsoc-general) [https://groups.google.com/g/obf-gsoc-mentors](https://groups.google.com/g/obf-gsoc-mentors)
+[https://groups.google.com/g/obf-gsoc-general](https://groups.google.com/g/obf-gsoc-general) [https://groups.google.com/g/obf-gsoc-mentors](https://groups.google.com/g/obf-gsoc-mentors)
**No further emails will be sent to the old OBF GSoC mailing lists or to individual email addresses.**
**Code of Conduct**: The OBF is in the process of drafting a code of conduct, which will soon be presented to the OBF membership to (hopefully) vote to adopt it. Please take a few minutes to preview it here: [https://github.com/OBF/obf-docs/pull/78/files](https://github.com/OBF/obf-docs/pull/78/files) \- while it's not officially ratified yet, it would be good to run this year's GSoC with this CoC's intent behind our behaviour.
@@ -30,11 +30,11 @@ If you're interested in mentoring this year, I'd recommend signing up to these t
Please add your project ideas to this list by THURSDAY 18 FEBRUARY (using suggest mode). [https://docs.google.com/document/d/1kPf-fLDmjoVGf7TvbOB6H12pC\_s\_y\_5TUGiKAxre64M/edit?usp=sharing](https://docs.google.com/document/d/1kPf-fLDmjoVGf7TvbOB6H12pC_s_y_5TUGiKAxre64M/edit?usp=sharing) \- you can add ideas after this if needed, but we need as many fully fleshed ideas as possible already online for the organisation review phase.
-These are the project ideas from last year for inspiration: [/events/gsoc/gsoc-project-ideas/](/events/gsoc/gsoc-project-ideas/)
+These are the project ideas from last year for inspiration: [/events/gsoc/gsoc-project-ideas/](/events/gsoc/gsoc-project-ideas/)
**We're all pretty tired**
- Make sure you have 2-3 mentors for every project idea to cover in case of something coming up (such as covid related downtime, whether illness, caring, or anything else).
- If you're interested in helping us with org admin duties, we'd love to have you on board and are willing to provide you support and mentoring while you learn how to do it. Email [obf-gsoc-admins@googlegroups.com](mailto:obf-gsoc-admins@googlegroups.com) to discuss it.
-**Finally - any questions?
+**Finally - any questions?
** If you have any questions please email either the mentor group ( [obf-gsoc-mentors@googlegroups.com](mailto:obf-gsoc-mentors@googlegroups.com)) or the admin group ( [obf-gsoc-admins@googlegroups.com](mailto:obf-gsoc-admins@googlegroups.com)). You can also book a quick chat with me if that's easier: [https://calendly.com/yo-yehudi-manchester/gsoc-chat?month=2021-02](https://calendly.com/yo-yehudi-manchester/gsoc-chat?month=2021-02)
diff --git a/content/posts/google-summer-of-code-2022-time-for-project-ideas.md b/content/posts/google-summer-of-code-2022-time-for-project-ideas.md
index eda82a7b7..b5234445b 100644
--- a/content/posts/google-summer-of-code-2022-time-for-project-ideas.md
+++ b/content/posts/google-summer-of-code-2022-time-for-project-ideas.md
@@ -15,7 +15,7 @@ Hi everyone!
My name is Melissa and I’m happy to be collaborating with OBF as lead GSoC admin this year along with support from Yo Yehudi. I had a great (virtual) time at BOSC 2021 as an Outreachy intern and am glad to be supporting another internship program this year.
-It’s time to start coming up with GSoC project ideas again! Below is some info that should help with that.
+It’s time to start coming up with GSoC project ideas again! Below is some info that should help with that.
diff --git a/content/posts/iscbacademy-webinar-feb-22-yo-yehudi.md b/content/posts/iscbacademy-webinar-feb-22-yo-yehudi.md
index a27bac40c..4b27f52cc 100644
--- a/content/posts/iscbacademy-webinar-feb-22-yo-yehudi.md
+++ b/content/posts/iscbacademy-webinar-feb-22-yo-yehudi.md
@@ -18,11 +18,11 @@ title: 'ISCBacademy webinar Feb 22: Yo Yehudi'
url: /2022/01/20/iscbacademy-webinar-feb-22-yo-yehudi/
---
-Date & Time: Tuesday, February 22, 2022, 15:00 UTC / 11am EDT
+Date & Time: Tuesday, February 22, 2022, 15:00 UTC / 11am EDT
-Location: online webinar hosted by ISCB
+Location: online webinar hosted by ISCB
-Speaker: Yo Yehudi, Open Life Science (former OBF board member and Google Summer of Code admin & mentor)
+Speaker: Yo Yehudi, Open Life Science (former OBF board member and Google Summer of Code admin & mentor)
Topic: Growing open source communities with internships
@@ -36,11 +36,11 @@ One effective way to grow your community can be via internships. Programs such a
This webinar will cover the ins and outs of participating in internship programs like this, from the perspective of a mentoring organisation. Topics will include:
-1\. Getting started with internship programs - finding mentors and defining a set of projects
+1\. Getting started with internship programs - finding mentors and defining a set of projects
-2\. Time commitments for mentors, before the application period and after interns are selected.
+2\. Time commitments for mentors, before the application period and after interns are selected.
-3\. Funding for internship programs! (It's not as tricky as you may fear - others handle this bit!)
+3\. Funding for internship programs! (It's not as tricky as you may fear - others handle this bit!)
4\. Keeping interns engaged during the program and bringing them in as long-term contributors afterwards.
diff --git a/content/posts/iscbacademy-webinar-on-patient-led-research.md b/content/posts/iscbacademy-webinar-on-patient-led-research.md
index 1f970588b..17d6f02c1 100644
--- a/content/posts/iscbacademy-webinar-on-patient-led-research.md
+++ b/content/posts/iscbacademy-webinar-on-patient-led-research.md
@@ -17,9 +17,9 @@ title: ISCBacademy webinar on Patient-Led Research
url: /2023/03/07/iscbacademy-webinar-on-patient-led-research/
---
-Date and Time: Tuesday, March 14, 11am EDT/ 15:00 (not 16:00!) UTC
-Location: [Online webinar](https://iscb.junolive.co/Nucleus/live/mainstage/iscbacademycosi79) hosted by ISCB and free to the public. (Video now available at [https://youtu.be/M2vAotWKd\_Q](https://youtu.be/M2vAotWKd_Q))
-Speaker: Hannah Wei, co-founder and technologist at the Patient-Led Research Collaborative
+Date and Time: Tuesday, March 14, 11am EDT/ 15:00 (not 16:00!) UTC
+Location: [Online webinar](https://iscb.junolive.co/Nucleus/live/mainstage/iscbacademycosi79) hosted by ISCB and free to the public. (Video now available at [https://youtu.be/M2vAotWKd\_Q](https://youtu.be/M2vAotWKd_Q))
+Speaker: Hannah Wei, co-founder and technologist at the Patient-Led Research Collaborative
Topic: Re-Thinking the Patient's Role in a Learning Health System: Lessons from the Patient-Led Research Collaborative
> The ISCB, which runs the annual ISMB conference, is offering a series of [ISCBacademy webinars](https://www.iscb.org/iscbacademy) hosted by the Communities of Special Interest (COSIs), which include BOSC/OBF. These webinars are now open to the public; you'll just need to create an ISCB Nucleus account to [register for the webinar](https://iscb.junolive.co/Nucleus/live/mainstage/iscbacademycosi79).
diff --git a/content/posts/iscbacademy-webinar-open-sourcing-ourselves-together-mad-price-ball.md b/content/posts/iscbacademy-webinar-open-sourcing-ourselves-together-mad-price-ball.md
index ad36adb7e..8864f8c4c 100644
--- a/content/posts/iscbacademy-webinar-open-sourcing-ourselves-together-mad-price-ball.md
+++ b/content/posts/iscbacademy-webinar-open-sourcing-ourselves-together-mad-price-ball.md
@@ -23,7 +23,7 @@ The first BOSC/OBF ISCBacademy COSI webinar will take place on Tuesday, Septembe
### Open Sourcing Ourselves - Together
-Mad Price Ball (Open Humans Foundation)
+Mad Price Ball (Open Humans Foundation)
September 14, 2021 at 15:00 UTC / 11:00AM EDT
diff --git a/content/posts/meet-our-new-travel-fellowship-review-chair-farah-zaib-khan.md b/content/posts/meet-our-new-travel-fellowship-review-chair-farah-zaib-khan.md
index f054caab4..b486ba2dc 100644
--- a/content/posts/meet-our-new-travel-fellowship-review-chair-farah-zaib-khan.md
+++ b/content/posts/meet-our-new-travel-fellowship-review-chair-farah-zaib-khan.md
@@ -16,7 +16,7 @@ url: /2019/01/09/meet-our-new-travel-fellowship-review-chair-farah-zaib-khan/
---
Farah presents _CWLProv_ at GCCBOSC 2018
-The [next round of our OBF Travel Fellowships just ended](https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md) on the 15th of December! This round we have introduced a Review Chair coming from the midst of our community that will help us in reviewing the applications. The role will be filled by Farah Zaib Khan, one of our OBF Travel Fellowship alumni. Farah has successfully applied for the Fellowship twice before. Thanks in part to this support, she has become a central community member both of the Bioinformatics Open Source Conference and the Open Bioinformatics Foundation itself.
+The [next round of our OBF Travel Fellowships just ended](https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md) on the 15th of December! This round we have introduced a Review Chair coming from the midst of our community that will help us in reviewing the applications. The role will be filled by Farah Zaib Khan, one of our OBF Travel Fellowship alumni. Farah has successfully applied for the Fellowship twice before. Thanks in part to this support, she has become a central community member both of the Bioinformatics Open Source Conference and the Open Bioinformatics Foundation itself.
Farah recently completed her PhD at The University of Melbourne, Australia. The OBF travel fellowship helped her interact with the Bioinformatics community during BOSC 2017 and GCCBOSC 2018 where she actively participated in the Codefests and other activities to shape her PhD work. Her PhD research is about the provenance and interoperability of bioinformatics workflows. The funding and support provided by OBF is acknowledged in the article recently [submitted by her for publication](http://dx.doi.org/10.5281/zenodo.1966881).
diff --git a/content/posts/minutes-2005-bosc-meeting.md b/content/posts/minutes-2005-bosc-meeting.md
index 5f1239ba9..3132f8272 100644
--- a/content/posts/minutes-2005-bosc-meeting.md
+++ b/content/posts/minutes-2005-bosc-meeting.md
@@ -8,7 +8,7 @@ title: Minutes:2005 BOSC Meeting
url: /2005/06/23/minutes2005-bosc-meeting/
---
-**Venue:** Renaissance Center in Detroit, on the first floor next to the Starbucks.
+**Venue:** Renaissance Center in Detroit, on the first floor next to the Starbucks.
**Date:** June 23, 2005, 16:15.
#### **Call to order:**
@@ -71,8 +71,8 @@ Travel to Brazil is expensive and out of the way. Not everyone on the Board is s
A general lament on how we're a bunch of white men and we should encourage more diversity. For that matter, we're rather close knit, which is good, but it doesn't help bring in enough new people to lead projects, help with BOSC, be on the Board, etc.
-_Chris:_ Move to adjourn.
-_Jason:_ Seconded.
+_Chris:_ Move to adjourn.
+_Jason:_ Seconded.
Motion passed by unanimous consent.
Closed at 18:15. A two hour meeting.
diff --git a/content/posts/minutes-2007-bosc-meeting.md b/content/posts/minutes-2007-bosc-meeting.md
index e0f7df3d6..6472c8553 100644
--- a/content/posts/minutes-2007-bosc-meeting.md
+++ b/content/posts/minutes-2007-bosc-meeting.md
@@ -8,8 +8,8 @@ title: Minutes:2007 BOSC Meeting
url: /2007/07/21/minutes2007-bosc-meeting/
---
-**Venue:** Cafe Prückl, Vienna
-**Date:** 7/21/2007, 5.30pm
+**Venue:** Cafe Prückl, Vienna
+**Date:** 7/21/2007, 5.30pm
**Attending:** Jason Stajich (OBF President), Hilmar Lapp (OBF Parliamentarian), Darin London, Kam Dahlquist
### BOSC
diff --git a/content/posts/minutes-2011-confcall.md b/content/posts/minutes-2011-confcall.md
index a179abf2f..517f5b95c 100644
--- a/content/posts/minutes-2011-confcall.md
+++ b/content/posts/minutes-2011-confcall.md
@@ -130,24 +130,24 @@ Adjourned at 1.03pm. Board elections could not be held as planned due to loss of
Prepared by Rob Buels, who served as organization administrator for the OBF.
-> We had 6 students this year, the same number as last year. I had hoped we might grow the program somewhat over last year's numbers, but the number and quality of applications turned out approximately the same. However, the solicitations for student applications went out quite a bit later this year than last year. I think us having a similar applicant pool despite the late solicitations may point to there being a latent potential to grow the program next year, if I make sure to be more on top of the schedule, which I intend to do.
+> We had 6 students this year, the same number as last year. I had hoped we might grow the program somewhat over last year's numbers, but the number and quality of applications turned out approximately the same. However, the solicitations for student applications went out quite a bit later this year than last year. I think us having a similar applicant pool despite the late solicitations may point to there being a latent potential to grow the program next year, if I make sure to be more on top of the schedule, which I intend to do.
As for this year's 6 students, they were quite a good group. Pasted from the [OBF GSoC page](/wiki/Google_Summer_of_Code), the 6 student projects were:
>
-> BioPython
+> BioPython
-> Justinas Vygintas Daugmaudis, Michele dos Santos da Silva (2 students), mentored by Thomas Hamelryck and Eric Talevich
+> Justinas Vygintas Daugmaudis, Michele dos Santos da Silva (2 students), mentored by Thomas Hamelryck and Eric Talevich
Mocapy++Biopython: from data to probabilistic models of biomolecules BioPython Integration and Mocapy++ Plugin System
>
-> BioJava
+> BioJava
Chuan Hock Koh, mentored by Peter Troshin, Andreas Prlic, and Jay Vyas: Amino Acid Physico-Chemical Properties Calculation
>
-> BioRuby
+> BioRuby
Michał Koziarski, mentored by Raoul J.P. Bonnal and Francesco Strozzi: Represent bio-objects and related information with images
>
-> BioPerl
+> BioPerl
Sheena Scroggins, mentored by Robert Buels and Chris Fields: Major BioPerl reorganization
>
-> BioPython
+> BioPython
Mikael Eric Trellet, mentored by João Rodrigues and Eric Talevich: Interface analysis module for BioPython
>
> Happily, all of the students accomplished their project objectives and were eligible for full stipend payments from Google. This is a bit better than last year, when we had one student who failed to complete the program.
diff --git a/content/posts/minutes-2013-apr-confcall.md b/content/posts/minutes-2013-apr-confcall.md
index f1bb48085..621f1f494 100644
--- a/content/posts/minutes-2013-apr-confcall.md
+++ b/content/posts/minutes-2013-apr-confcall.md
@@ -10,8 +10,8 @@ url: /2013/12/09/minutes2013-apr-confcall/
---
### Agenda
-**Venue:** to be held by conference call on April 9, 2013, 1.30pm EDT (17:30 UTC)
-Dial-in Number: 1-605-475-5950 (Midwest)
+**Venue:** to be held by conference call on April 9, 2013, 1.30pm EDT (17:30 UTC)
+Dial-in Number: 1-605-475-5950 (Midwest)
Participant Access Code: 279610
1. Old business
diff --git a/content/posts/minutes-2013-dec-confcall.md b/content/posts/minutes-2013-dec-confcall.md
index 45abdc6af..d3d50be67 100644
--- a/content/posts/minutes-2013-dec-confcall.md
+++ b/content/posts/minutes-2013-dec-confcall.md
@@ -10,8 +10,8 @@ url: /2013/12/12/minutes2013-dec-confcall/
---
### Agenda
-**Venue:** to be held by conference call on Dec 12, 2013, 12pm EDT (17:00 UTC)
-Dial-in Number: 1-605-475-5950 (US Midwest)
+**Venue:** to be held by conference call on Dec 12, 2013, 12pm EDT (17:00 UTC)
+Dial-in Number: 1-605-475-5950 (US Midwest)
Participant Access Code: 279610
1. Old business
diff --git a/content/posts/minutes-2014-nov-confcall.md b/content/posts/minutes-2014-nov-confcall.md
index a216973af..8f0aade98 100644
--- a/content/posts/minutes-2014-nov-confcall.md
+++ b/content/posts/minutes-2014-nov-confcall.md
@@ -10,7 +10,7 @@ url: /2014/11/18/minutes2014-nov-confcall/
---
### Agenda
-**Venue:** to be held by conference call on Nov 18, 2014, 12.30pm EST (17:30 UTC)
+**Venue:** to be held by conference call on Nov 18, 2014, 12.30pm EST (17:30 UTC)
Dial-in Information: +1-857-216-2939 PIN: 62534 [http://www.uberconference.com/hlapp](http://www.uberconference.com/hlapp)
1. Old business
diff --git a/content/posts/minutes-2015-may-confcall.md b/content/posts/minutes-2015-may-confcall.md
index 666bc6824..91f20767e 100644
--- a/content/posts/minutes-2015-may-confcall.md
+++ b/content/posts/minutes-2015-may-confcall.md
@@ -10,7 +10,7 @@ url: /2015/05/12/minutes2015-may-confcall/
---
### Agenda
-**Venue:** to be held by conference call on May 12, 2015, 1pm EDT (17:00 UTC, 18:00 BST, 19:00 CEST, 10am PDT)
+**Venue:** to be held by conference call on May 12, 2015, 1pm EDT (17:00 UTC, 18:00 BST, 19:00 CEST, 10am PDT)
Dial-in Information: +1-857-216-2939 PIN: 62534 [http://www.uberconference.com/hlapp](http://www.uberconference.com/hlapp)
1. Old business
diff --git a/content/posts/minutes-2016-oct-confcall.md b/content/posts/minutes-2016-oct-confcall.md
index 93891c67c..c0206b856 100644
--- a/content/posts/minutes-2016-oct-confcall.md
+++ b/content/posts/minutes-2016-oct-confcall.md
@@ -10,7 +10,7 @@ url: /2016/10/04/minutes2016-oct-confcall/
---
### Agenda
-**Venue:** To be held by conference call on Oct 4, 2016, 12.30pm EDT (16:30 UTC, 17:30 BST, 18:30 CEST, 9.30am PDT)
+**Venue:** To be held by conference call on Oct 4, 2016, 12.30pm EDT (16:30 UTC, 17:30 BST, 18:30 CEST, 9.30am PDT)
**Dial-in Information:** +1-857-216-2939 PIN: 62534 [http://www.uberconference.com/hlapp](http://www.uberconference.com/hlapp)
1. Old business
diff --git a/content/posts/minutes-2018-mar-confcall.md b/content/posts/minutes-2018-mar-confcall.md
index ea1a4963c..94a13f7b3 100644
--- a/content/posts/minutes-2018-mar-confcall.md
+++ b/content/posts/minutes-2018-mar-confcall.md
@@ -16,7 +16,7 @@ url: /2018/03/16/minutes2018-mar-confcall/
## Agenda
-**Venue:** To be held by conference call on March 16, 2018, 11.00am EDT (15:00 UTC, 16:00 CET, 8.00am PDT). _Note that at the time of the meeting, the US will have switched already to DST, whereas Europe will not, so the time zone difference is an hour less than it would normally be._
+**Venue:** To be held by conference call on March 16, 2018, 11.00am EDT (15:00 UTC, 16:00 CET, 8.00am PDT). _Note that at the time of the meeting, the US will have switched already to DST, whereas Europe will not, so the time zone difference is an hour less than it would normally be._
**Dial-in Information:** +1-857-216-2939 PIN: 62534 [http://www.uberconference.com/hlapp](http://www.uberconference.com/hlapp)
1. Old business
diff --git a/content/posts/minutes-2019-bosc.md b/content/posts/minutes-2019-bosc.md
index 122c04dc7..3781c9ce1 100644
--- a/content/posts/minutes-2019-bosc.md
+++ b/content/posts/minutes-2019-bosc.md
@@ -12,8 +12,8 @@ The July 2019 Open Bioinformatics Foundation Public Board Meeting was held in pe
## Date, Location and Dial-In
-Date and time: July 25, 12:45pm CEST
-Venue: Congress Center Basel, Switzerland, in the Dehli Room (ground floor, same room as BOSC)
+Date and time: July 25, 12:45pm CEST
+Venue: Congress Center Basel, Switzerland, in the Dehli Room (ground floor, same room as BOSC)
Dial-In for participating remotely: _expired_
## Agenda
diff --git a/content/posts/minutes-of-2002-bosc-meeting.md b/content/posts/minutes-of-2002-bosc-meeting.md
index 5b051f6b2..e29fc4564 100644
--- a/content/posts/minutes-of-2002-bosc-meeting.md
+++ b/content/posts/minutes-of-2002-bosc-meeting.md
@@ -14,20 +14,20 @@ Edmonton, Alberta, Canada
### Call to order
-Board members present: Hilmar, Chris, Ewan, Steven, Andrew
+Board members present: Hilmar, Chris, Ewan, Steven, Andrew
### Recognition of observers (about 21)
-This meeting was open to the the public. I don't know all of the people who commented, hence the question marks.
+This meeting was open to the the public. I don't know all of the people who commented, hence the question marks.
### Review of schedule by Ewan
-Steven - asked about money owed us from Hidelberg meeting
-Chris - says it's about 20-30 commercial people
-Decided to follow up on that money - assigned to Chris (AI)
-Steven - asked about audit
-Chris, financials Jan. to Jan. year; report out next year
-Action item: Chris to find an accountant to audit
+Steven - asked about money owed us from Hidelberg meeting
+Chris - says it's about 20-30 commercial people
+Decided to follow up on that money - assigned to Chris (AI)
+Steven - asked about audit
+Chris, financials Jan. to Jan. year; report out next year
+Action item: Chris to find an accountant to audit
### BOSC 2003, lead by Ewan
@@ -37,130 +37,128 @@ Action item: Chris to find an accountant to audit
straw vote showed enthusiastic support for BOSC 2003
-Lincoln suggested survey of attendees tomorrow
-?? suggested too small for standalone conference
-Martin - price to Oz not bad
-Chris - but subjective impression of distance
-??? \- will be better Asia/Pacific input
-Janet - A/P can help grow the community
-Ewan - build a travel fund?
-??? \- give concrete examples of other conference sites when doing the survey
-ORA would be too expensive and submerged
-RECOMB in April in Berlin
-Thomas - reemphasized the international / worldwide aspect of the conference
-Lincoln - web meetings cut in half when moved to OZ
+Lincoln suggested survey of attendees tomorrow
+?? suggested too small for standalone conference
+Martin - price to Oz not bad
+Chris - but subjective impression of distance
+??? \- will be better Asia/Pacific input
+Janet - A/P can help grow the community
+Ewan - build a travel fund?
+??? \- give concrete examples of other conference sites when doing the survey
+ORA would be too expensive and submerged
+RECOMB in April in Berlin
+Thomas - reemphasized the international / worldwide aspect of the conference
+Lincoln - web meetings cut in half when moved to OZ
Chris - worried about losing people for next year, re costs, esp. if using professional organization
### Organizing BOSC 2003, lead by Ewan
-Request for volunteers - all declined
-Request for suggestions of volunteers
-Ewan volunteered Elia Stupka
-Elia tentatively agreed this morning
-Doreen said she would help, but not organize
-Motion: Ewan nominated Elia as organizer.
-Andrew seconded
-Motion passsed by unanimous consent
-Motion: Ewan nominated Doreen as "BOSC 2004 organizer in waiting"
-Chris seconded
+Request for volunteers - all declined
+Request for suggestions of volunteers
+Ewan volunteered Elia Stupka
+Elia tentatively agreed this morning
+Doreen said she would help, but not organize
+Motion: Ewan nominated Elia as organizer.
+Andrew seconded
+Motion passsed by unanimous consent
+Motion: Ewan nominated Doreen as "BOSC 2004 organizer in waiting"
+Chris seconded
Motion passsed by unanimous consent
### 2003 Hackathon, lead by Ewan
-Belief that hackathon helped in intergroup cohesiveness and should be repeated
-Andrew: What about funding?
-Chris: I3C, through Brian Gilman, may fund the hackathon
-Cost between 30 to 50 grand
-Jason: What influence will I3C have on the funding /
-what will they get out of it?
-Ewan: Sponser should not have influence on the scedule.
-May pick some attendees, write press.
-Hilmar: What about government funding?
-Ewan: Overhead is prohibitive compared to corporate sponsership. Steven: Could redirect gov't funding through a university (as was done for ISMB, using San Diego)
-Matthew: hackathon a great idea
-Lincoln: we should be able to get corporate sponsership pretty easily - great press
-??? \- didn't get much output / documentation / etc
-Ewan: we should invite documenters
-Hilmar: What about a 'doc-athon'?
-Ewan: doc people may find the social interactions of a hackathon more useful
-Motion: Create a hackathon committee with Ewan as chair. Main goals are to identify funding sources and site for hackathon.
-Chris seconded.
-Motion passsed by unanimous consent
-Misc., lead by Ewan
-Chris: Interest earned by idle cash
-Motion: Chris Investigate ways to make interest in no-risk way to make interest.
-Ewan seconded.
+Belief that hackathon helped in intergroup cohesiveness and should be repeated
+Andrew: What about funding?
+Chris: I3C, through Brian Gilman, may fund the hackathon
+Cost between 30 to 50 grand
+Jason: What influence will I3C have on the funding /
+what will they get out of it?
+Ewan: Sponser should not have influence on the scedule.
+May pick some attendees, write press.
+Hilmar: What about government funding?
+Ewan: Overhead is prohibitive compared to corporate sponsership. Steven: Could redirect gov't funding through a university (as was done for ISMB, using San Diego)
+Matthew: hackathon a great idea
+Lincoln: we should be able to get corporate sponsership pretty easily - great press
+??? \- didn't get much output / documentation / etc
+Ewan: we should invite documenters
+Hilmar: What about a 'doc-athon'?
+Ewan: doc people may find the social interactions of a hackathon more useful
+Motion: Create a hackathon committee with Ewan as chair. Main goals are to identify funding sources and site for hackathon.
+Chris seconded.
+Motion passsed by unanimous consent
+Misc., lead by Ewan
+Chris: Interest earned by idle cash
+Motion: Chris Investigate ways to make interest in no-risk way to make interest.
+Ewan seconded.
Motion passsed by unanimous consent
### OBF Branding
-Should we work on a logo?
-Tentative yes.
-Idea is to get community input for logo and get a professional organization to cleaned up. Also work on unifying web pages, etc.
-Hilmar: Why?
-Chris: Help present a more professional image
-Ewan: Likes O\|B\|F
-Andrew agrees.
-Motion by Steven that Chris can spend up to $2,000 on the branding project, with further discussion to occur.
-Ewan seconded.
+Should we work on a logo?
+Tentative yes.
+Idea is to get community input for logo and get a professional organization to cleaned up. Also work on unifying web pages, etc.
+Hilmar: Why?
+Chris: Help present a more professional image
+Ewan: Likes O\|B\|F
+Andrew agrees.
+Motion by Steven that Chris can spend up to $2,000 on the branding project, with further discussion to occur.
+Ewan seconded.
Motion passsed by unanimous consent
### Digital certificates
-BioJava wants to sign jar files. May want secure web connections May want multiple certificates, eg, one for the different projects.
-Lincoln: certificates for web different than for jar and has its own costs. Agreed that we can ignore secure web connections. Chris: jar signing costs a few $100 a year
+BioJava wants to sign jar files. May want secure web connections May want multiple certificates, eg, one for the different projects.
+Lincoln: certificates for web different than for jar and has its own costs. Agreed that we can ignore secure web connections. Chris: jar signing costs a few $100 a year
Matthew: who has signing authority?
#### Virus scanning of inbound and outbound mail.
-Ewan: Authorize Chris to look into virus scanning and digital certificates, report costs and benefits, and allow a vote on expenses over email.
-Andrew seconds.
-Motion passed by unanimous consent
-Steven:relevant NIH grants, like conference grants we are a "rounding error" compared to most conferences but grant administration has overhead. Another grant: PAs, as for software development should we investigate that? Probably no, but proposing the idea
-Andrew: what is a PA?
-Program announcement, interested in area, expect to spend money, doesn't guarantee funding, but encourages.
-Lincoln: some can be recurring
-Doreen: funds for technical writer or other non-developer Chris: OBF lacks in administration; what's the overhead? Lincoln (and Steven): would need to admin through a site (like CSHL) with experience in admin'ing these sorts of grants. Ewan: We direct and support groups which get the PA funding, rather than go through us. Is that feasible?
-Lincoln: Study sections are mostly concerned about the likelihood of success, so shouldn't be a problem
-Decided that Steven would encourage others to work with the OBF, but not really look for it outselves, unless it was really adventagous
-No need for a motion.
-More enthusiastic about the NIH grant
- Steven: we should provide more funding to speakers
-Ewan suggested that Doreen look into funding, esp. long term (5 year funding) from NIH
-Chris offered to help
-Steven:Do we need a response to the ISCB open source statement found in .... ? Some statements are quite wrong, in the view of many open source people.
-Ewan: OBF stay away from policy influence as an organization Andrew: why bother?
-Steven: what about a simple statement in the minutes?
-Johann: Win (and others) pointed out corrections before it was published, and it still went through.
-Janet: would it interfere with our associations with ICMB? Lincoln: we should be a more vocal source
-Ewan: but we are a support organization, not leading the direction. Uncomfortable with setting the direction. Lincoln: this is a clarification of our policy
-Lincoln: should there be a response? No, theirs is a reponse to ours. First, check our statement to see if we agree with it.
-Ewan: reads statement aloud. Ewan and Andrew are still comfortable. Some questions about wording. Steven clarified. Chris: we should mention this to people tomorrow, esp. those who are members, to reponse individually
-Lincoln: document will be used as leverage to funding agencies to justify research proposal. Eg, "this isthe ISCB approved level 3 development model". Used for policy decisions. Jason: as members we should be offended, but OBF? not sure. Andrew: I haven't read this document yet.
-Ewan: Stay away from "journalistic ping-pong"
-Steven: vote was close. Be polite, but make our point(as ISCB members) known.
-???: could argument from a technical level be used for leverage.
-Ewan and Lincoln: no
-Matthew: statement should say what open source means
-Motion by Ewan to modify statement to point to the opensource.org definition of "open source" and to confer later to clarify our position.
-Steven seconded.
+Ewan: Authorize Chris to look into virus scanning and digital certificates, report costs and benefits, and allow a vote on expenses over email.
+Andrew seconds.
+Motion passed by unanimous consent
+Steven:relevant NIH grants, like conference grants we are a "rounding error" compared to most conferences but grant administration has overhead. Another grant: PAs, as for software development should we investigate that? Probably no, but proposing the idea
+Andrew: what is a PA?
+Program announcement, interested in area, expect to spend money, doesn't guarantee funding, but encourages.
+Lincoln: some can be recurring
+Doreen: funds for technical writer or other non-developer Chris: OBF lacks in administration; what's the overhead? Lincoln (and Steven): would need to admin through a site (like CSHL) with experience in admin'ing these sorts of grants. Ewan: We direct and support groups which get the PA funding, rather than go through us. Is that feasible?
+Lincoln: Study sections are mostly concerned about the likelihood of success, so shouldn't be a problem
+Decided that Steven would encourage others to work with the OBF, but not really look for it outselves, unless it was really adventagous
+No need for a motion.
+More enthusiastic about the NIH grant
+ Steven: we should provide more funding to speakers
+Ewan suggested that Doreen look into funding, esp. long term (5 year funding) from NIH
+Chris offered to help
+Steven:Do we need a response to the ISCB open source statement found in .... ? Some statements are quite wrong, in the view of many open source people.
+Ewan: OBF stay away from policy influence as an organization Andrew: why bother?
+Steven: what about a simple statement in the minutes?
+Johann: Win (and others) pointed out corrections before it was published, and it still went through.
+Janet: would it interfere with our associations with ICMB? Lincoln: we should be a more vocal source
+Ewan: but we are a support organization, not leading the direction. Uncomfortable with setting the direction. Lincoln: this is a clarification of our policy
+Lincoln: should there be a response? No, theirs is a reponse to ours. First, check our statement to see if we agree with it.
+Ewan: reads statement aloud. Ewan and Andrew are still comfortable. Some questions about wording. Steven clarified. Chris: we should mention this to people tomorrow, esp. those who are members, to reponse individually
+Lincoln: document will be used as leverage to funding agencies to justify research proposal. Eg, "this isthe ISCB approved level 3 development model". Used for policy decisions. Jason: as members we should be offended, but OBF? not sure. Andrew: I haven't read this document yet.
+Ewan: Stay away from "journalistic ping-pong"
+Steven: vote was close. Be polite, but make our point(as ISCB members) known.
+???: could argument from a technical level be used for leverage.
+Ewan and Lincoln: no
+Matthew: statement should say what open source means
+Motion by Ewan to modify statement to point to the opensource.org definition of "open source" and to confer later to clarify our position.
+Steven seconded.
Motion passsed by unanimous consent
-Vote to accept minutes of last meeting. Unanimous consent.
+Vote to accept minutes of last meeting. Unanimous consent.
Make meeting minutes available. Question about making comments from people publically available. No one objected nor wanted to be anonymous.
-Mark Wilkinson wanted to assign BioMOBY copyright to OBF Consensus is that we see no problems with that
-??? what about moving services to collab.net / sourceforge-style installation
-Ewan: suggest talking with Chris about that; don't yet need board involvement
-Lincoln: keep our own hardware. Yep.
-Steven: want to make publications at least as available as the software.
-Ewan: declined to accept that topic -- getting late
-Hilmar: How do we handle nominations for new board members? Expanding the board?
-Chris: we have some templates already which we could use
-Chris: call for suggestions (eg, from church groups and other non-profits organization
-Action item: Hilmar will look into this
-Chris proposed we adjurn.
-Ewan seconded.
+Mark Wilkinson wanted to assign BioMOBY copyright to OBF Consensus is that we see no problems with that
+??? what about moving services to collab.net / sourceforge-style installation
+Ewan: suggest talking with Chris about that; don't yet need board involvement
+Lincoln: keep our own hardware. Yep.
+Steven: want to make publications at least as available as the software.
+Ewan: declined to accept that topic -- getting late
+Hilmar: How do we handle nominations for new board members? Expanding the board?
+Chris: we have some templates already which we could use
+Chris: call for suggestions (eg, from church groups and other non-profits organization
+Action item: Hilmar will look into this
+Chris proposed we adjurn.
+Ewan seconded.
Motion passed by unanimous consent.
-
-
diff --git a/content/posts/o-b-f-in-google-summer-of-code.md b/content/posts/o-b-f-in-google-summer-of-code.md
index f79268aec..d14871222 100644
--- a/content/posts/o-b-f-in-google-summer-of-code.md
+++ b/content/posts/o-b-f-in-google-summer-of-code.md
@@ -30,7 +30,7 @@ url: /2010/03/21/obf-in-google-summer-of-code/
---
The Open Bioinformatics Foundation has been accepted as a mentoring organization for this summer's Google Summer of Code. Our list of project ideas and mentors is linked from the [O\|B\|F GSoC page](http://open-bio.org/wiki/Google_Summer_of_Code "O|B|F GSoC").
-Student applications must be submitted to Google by **April 9, 2010,** see the [official GSoC 2010 FAQ](http://socghop.appspot.com/document/show/gsoc_program/google/gsoc2010/faqs). That is less than three weeks away!
+Student applications must be submitted to Google by **April 9, 2010,** see the [official GSoC 2010 FAQ](http://socghop.appspot.com/document/show/gsoc_program/google/gsoc2010/faqs). That is less than three weeks away!
Students, have a look at that wiki page, contact the project you're interested in working with, and get rolling on that application post-haste. A good GSoC application takes quite a bit of thought and effort to put together. **Students are encouraged to get help from mentors to put together a good application.**
diff --git a/content/posts/obf-public-board-meeting-2023-12-19-11am-est.md b/content/posts/obf-public-board-meeting-2023-12-19-11am-est.md
index c18524da5..acae71ffb 100644
--- a/content/posts/obf-public-board-meeting-2023-12-19-11am-est.md
+++ b/content/posts/obf-public-board-meeting-2023-12-19-11am-est.md
@@ -31,5 +31,3 @@ url: /2023/12/04/obf-public-board-meeting-2023-12-19/
- This will be an electronic ballot of the current board members
#### After the meeting, the meeting minutes will be made available in the [obf-docs GitHub repository](https://github.com/OBF/obf-docs/tree/master/minutes) as a pull request.
-
-
diff --git a/content/posts/obf-travel-fellowships-update-in-light-of-the-coronavirus-covid-19.md b/content/posts/obf-travel-fellowships-update-in-light-of-the-coronavirus-covid-19.md
index 104927487..38cd4269c 100644
--- a/content/posts/obf-travel-fellowships-update-in-light-of-the-coronavirus-covid-19.md
+++ b/content/posts/obf-travel-fellowships-update-in-light-of-the-coronavirus-covid-19.md
@@ -13,19 +13,19 @@ title: "OBF travel fellowships update in light of the Coronavirus (COVID-19) \u
url: "/2020/03/13/obf-travel-fellowships-update-in-light-of-the-coronavirus-covid-19-\uFEFF/"
---
-In light of the current outbreak, we urge everyone to avoid travelling if possible, in order to slow the rate at which the virus spreads to vulnerable people. You may have read that the [BCC (BOSC+Galaxy) committee is delaying registration whilst considering the best options](https://bcc2020.github.io/blog/postponement).
+In light of the current outbreak, we urge everyone to avoid travelling if possible, in order to slow the rate at which the virus spreads to vulnerable people. You may have read that the [BCC (BOSC+Galaxy) committee is delaying registration whilst considering the best options](https://bcc2020.github.io/blog/postponement).
With the next [travel fellowship deadline](/travel-awards/) approaching on April 1st, we are issuing slightly different advice regarding the types of applications we’d like to see, compared to previous years.
## Let’s go remote
-Given how many conferences are (quite sensibly) being cancelled at the moment, we would like to help facilitate remote conferences where possible. We are open to creative ideas for ways to increase diversity and representation for remote conferences.
+Given how many conferences are (quite sensibly) being cancelled at the moment, we would like to help facilitate remote conferences where possible. We are open to creative ideas for ways to increase diversity and representation for remote conferences.
-As an example, this might mean that instead of spending your fellowship on a hotel and travel, your fellowship budget might cover a headset, webcam, remote conference fee, and access to high-speed internet for the duration of the conference. This is not an exhaustive list of things we are willing to consider covering - you may have better ideas for ways to manage safe virus-free conference participation and we’d love to hear them and/or see your application for a fellowship. Like before, fellowships are open to people anywhere in the world, so long as they’re for open+bio related events.
+As an example, this might mean that instead of spending your fellowship on a hotel and travel, your fellowship budget might cover a headset, webcam, remote conference fee, and access to high-speed internet for the duration of the conference. This is not an exhaustive list of things we are willing to consider covering - you may have better ideas for ways to manage safe virus-free conference participation and we’d love to hear them and/or see your application for a fellowship. Like before, fellowships are open to people anywhere in the world, so long as they’re for open+bio related events.
## Still planning to attend something in person?
-We have the following tips if you do wish to request an in-person conference related fellowship:
+We have the following tips if you do wish to request an in-person conference related fellowship:
- Please make sure to budget for travel insurance. This is a requirement for any fellowships to be granted - but be aware that many travel insurance policies may not cover cancellations due to events such as pandemics.
- Applications to attend conferences with dates a long time in the future, e.g. late 2020 or early 2021, may be better candidates for travel fellowships than conferences that are scheduled in the near future, though of course we don’t know when the outbreak will be contained and travel will become safe.
diff --git a/content/posts/open-source-and-open-minds-a-memorable-experience-tbnss-2024.md b/content/posts/open-source-and-open-minds-a-memorable-experience-tbnss-2024.md
index aa04d7318..6996af9a7 100644
--- a/content/posts/open-source-and-open-minds-a-memorable-experience-tbnss-2024.md
+++ b/content/posts/open-source-and-open-minds-a-memorable-experience-tbnss-2024.md
@@ -17,7 +17,7 @@ _The_ [_Open Bioinformatics Foundation (OBF) Event Fellowship program_](/travel-
In September 2024, I had the wonderful opportunity to attend the [Transatlantic Behavioral Neuroscience Summer School 2024 (TBNSS 2024)](https://nenckiopenlab.org/tbnss2024/) conducted in Mikolajki, Poland, from September 9th to 20th 2024 by the Nencki Open Lab, Nencki Institute of Experimental Biology PAS, Poland. First and foremost, this was made possible by the travel fellowship granted to me by the Open Bioinformatics Foundation, for which I am extremely grateful.
-
+
_Organizers and participants of TBNSS 2024_
The summer school was a particularly enriching experience for me because it was my first summer school. It introduced me to the wonderful world of open science and also to a great community of researchers and friends. The interactions and discussions that ensued provided invaluable insights into neuroscience research and, importantly, about the incorporation of open source tools.
@@ -48,4 +48,4 @@ _``_
_Keerthana presenting her project at TBNSS 2024_
-The overall learning experience at the school was one of a kind and a maiden one for me. It has initiated me into the world of open science and has opened up a plethora of applications for my own research. The school has successfully managed to bring about participation of early-life researchers from underprivileged/under-represented countries and that is the highlight of this endeavour of TBNSS 2024. On a personal note, I have gained immensely in terms of knowledge enhancement and also made a whole lot of beautiful memories and very special friends at the school. My special thanks to the organizers of TBNSS 2024 for being such wonderful mentors and initiating someone with very little experience with coding into the world of open source software. I am happy that with these connections, I have just begun on a lifelong journey of learning and contributing to open-science. I hope this community continues to grow and I can continue to contribute to it.
+The overall learning experience at the school was one of a kind and a maiden one for me. It has initiated me into the world of open science and has opened up a plethora of applications for my own research. The school has successfully managed to bring about participation of early-life researchers from underprivileged/under-represented countries and that is the highlight of this endeavour of TBNSS 2024. On a personal note, I have gained immensely in terms of knowledge enhancement and also made a whole lot of beautiful memories and very special friends at the school. My special thanks to the organizers of TBNSS 2024 for being such wonderful mentors and initiating someone with very little experience with coding into the world of open source software. I am happy that with these connections, I have just begun on a lifelong journey of learning and contributing to open-science. I hope this community continues to grow and I can continue to contribute to it.
diff --git a/content/posts/ruth-nanjala-my-experience-attending-and-participating-at-the-ichg-2023-conference-hosted-in-the-mother-city.md b/content/posts/ruth-nanjala-my-experience-attending-and-participating-at-the-ichg-2023-conference-hosted-in-the-mother-city.md
index ffc9d4beb..88affa734 100644
--- a/content/posts/ruth-nanjala-my-experience-attending-and-participating-at-the-ichg-2023-conference-hosted-in-the-mother-city.md
+++ b/content/posts/ruth-nanjala-my-experience-attending-and-participating-at-the-ichg-2023-conference-hosted-in-the-mother-city.md
@@ -23,7 +23,7 @@ url: /2023/03/21/ruth-nanjala-experience-at-the-ichg-2023-conference/
**_The_** [**_Open Bioinformatics Foundation (OBF) Event Fellowship program_**](/travel-awards) **_aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Ruth Nanjala, a DPhil student in Cellular and Molecular Medicine at the University of Oxford, was awarded an OBF Event Fellowship to attend the_** [**_International Congress of Human Genetics (ICHG) 2023_**](https://www.ichg2023.com) **_conference._**
-Earlier in 2022, I received the Open Bioinformatics Foundation (OBF) Event Fellowship for participating and promoting open science at the American Society of Human Genetics (ASHG) 2022 conference in Los Angeles. However, I could not travel to ASHG due to unavoidable circumstances. Fortunately, OBF gave me a second chance by facilitating my travel to the International Congress of Human Genetics (ICHG) 2023 conference hosted at home (Africa is considered the cradle of humankind) between the 22nd and 26th of February.
+Earlier in 2022, I received the Open Bioinformatics Foundation (OBF) Event Fellowship for participating and promoting open science at the American Society of Human Genetics (ASHG) 2022 conference in Los Angeles. However, I could not travel to ASHG due to unavoidable circumstances. Fortunately, OBF gave me a second chance by facilitating my travel to the International Congress of Human Genetics (ICHG) 2023 conference hosted at home (Africa is considered the cradle of humankind) between the 22nd and 26th of February.
@@ -32,23 +32,23 @@ Earlier in 2022, I received the Open Bioinformatics Foundation (OBF) Event Fello
My research focused on evaluating different programs, reference panels, and genotyping arrays used to predict HLA alleles from the highly polymorphic human Major Histocompatibility Complex region. The workflow was written using the open-source software, Nextflow and published on GitHub https://github.com/nanjalaruth/MHC-Imputation-Accuracy. For those interested in learning more, the preprint can be accessed at the link: [https://pubmed.ncbi.nlm.nih.gov/36747714/.](https://pubmed.ncbi.nlm.nih.gov/36747714/.)
-Aside from presenting a poster of my work, I was able to attend and engage in other conference sessions. Below, I highlight take-home messages from each day:
+Aside from presenting a poster of my work, I was able to attend and engage in other conference sessions. Below, I highlight take-home messages from each day:
-**Day 1**
+**Day 1**
The keynote on Genomics and anthropology set the tone for the day as insights were shared on human settlement patterns and migration patterns in Africa. The continent is widely considered the birthplace of modern humans. During this day, Prof. Nicola Mulder proposed the setup of a network of Genomic Centres of Excellence in Africa with the aim of reducing the access gap for genomic technologies.
-**Day 2**
+**Day 2**
Karoline Kuchenbaecker from University College London showed that diversity in genetic investigations promotes gene prioritization, causal inference, precise mapping, and locus identification. Andrew Morris from the University of Manchester demonstrated the effectiveness of heterogeneous populations for Genome-Wide Association Studies discovery and application.
-**Day 3**
+**Day 3**
A captivating session was chaired by Athena, which focused on overcoming obstacles to studying diversity in global genetics. The session presenters, Adebowale, Krystal, and Lerato pointed out strategies that can be adopted to improve diversity.
-**Day 4**
+**Day 4**
An interesting session was on the “Southern African Population structure, Admixture and Adaptation,” as I got insights on the changes in skin color in southern Africa, Khoisan gene flow and its significance for genetic research, and the intricate patterns of mixing and population migrations during the Bantu expansion.
The conference was then closed by the ICHG conference team led by Prof. Michele Ramsay, who handed over the planning for the next conference in 2026 to the Mexico team.
-
+
**_Image: Aerial view of Cape Town. Table Mountain (left), Lion’s head (right)_**
diff --git a/content/posts/seeking-community-volunteers-nomination-open-for-obf-board-election-2021.md b/content/posts/seeking-community-volunteers-nomination-open-for-obf-board-election-2021.md
index 363a7dc42..7f52f2d48 100644
--- a/content/posts/seeking-community-volunteers-nomination-open-for-obf-board-election-2021.md
+++ b/content/posts/seeking-community-volunteers-nomination-open-for-obf-board-election-2021.md
@@ -19,11 +19,11 @@ _TL;DR: Nominate candidates or yourself for the OBF board via this [form](https:
OBF is committed to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community. The roles and functions of OBF have evolved over the last 20 years, and currently include:
-\- hosting and sponsoring the annual events, Bioinformatics Open Source Conference
-\- running open source events like CodeFests and Google Summer of Code (GSoC)
-\- offering Event fellowships to promote diversity of underrepresented community members at open source events
-\- onboarding and supporting OBF member projects by providing financial management support (e.g., reimbursements and payments and advertising)
-\- maintaining OBF website, social media and newsletter for information dissemination
+\- hosting and sponsoring the annual events, Bioinformatics Open Source Conference
+\- running open source events like CodeFests and Google Summer of Code (GSoC)
+\- offering Event fellowships to promote diversity of underrepresented community members at open source events
+\- onboarding and supporting OBF member projects by providing financial management support (e.g., reimbursements and payments and advertising)
+\- maintaining OBF website, social media and newsletter for information dissemination
\- advocating through policy and public statements
OBF board members are elected through public nomination and voting. As board member Yo Yehudi (see [this post](/2021/02/12/title-would-you-like-to-make-a-difference-in-grassroots-open-bioinformatics/)) reaches the end of her term, we are reflecting on the need to recruit new and more diverse board members.
@@ -40,27 +40,27 @@ In addition to the projects mentioned earlier, we are grateful to the members of
These tasks could not have been accomplished without the support of our community members. If you would like to be involved in OBF but don’t want to nominate yourself for a position on the Board, we would be delighted talk to you about how you could get involved with these or other projects:
-\- [Curate and edit our quarterly (approximately) newsletter](https://github.com/obf/newsletter), time commitment approximately 4 hours per issue
-\- Help maintain and update our website: [https://www.open-bio.org](https://www.open-bio.org) (WordPress, HTML, CSS skills)
-\- Help manage our social channels (such as [Twitter](https://twitter.com/obf_news))
-\- [Become a GSoC](/events/gsoc/) mentor or organisation admin
+\- [Curate and edit our quarterly (approximately) newsletter](https://github.com/obf/newsletter), time commitment approximately 4 hours per issue
+\- Help maintain and update our website: [https://www.open-bio.org](https://www.open-bio.org) (WordPress, HTML, CSS skills)
+\- Help manage our social channels (such as [Twitter](https://twitter.com/obf_news))
+\- [Become a GSoC](/events/gsoc/) mentor or organisation admin
\- Volunteer at the Bioinformatics Open Source Conference
We appreciate that many of these roles may be new to you and we would offer mentorship and support if it is your first time occupying this type of position - please don’t feel that inexperience should stop you from applying!
OBF also offers support for individuals and groups to promote open source practices and build bioinformatics skills. Here are a few opportunities that you can benefit from:
-\- [Apply for the OBF Event fellowship](/event-awards), 2 deadlines on 1 April and 1 October 2021
-\- [Become an OBF member to participate in the community](/membership)
-\- Apply to become an affiliate project by discussing with the board ( [see currently affiliated projects](/projects/#affiliated-projects))
+\- [Apply for the OBF Event fellowship](/event-awards), 2 deadlines on 1 April and 1 October 2021
+\- [Become an OBF member to participate in the community](/membership)
+\- Apply to become an affiliate project by discussing with the board ( [see currently affiliated projects](/projects/#affiliated-projects))
\- Apply for the OBF Grassroots Event Sponsorship (will be announced soon)
We would also love to hear your ideas for how you could help boost OBF’s commitments to:
-\- representing interests of bioinformatics and open source communities from developing countries
-\- onboarding member projects from low and middle-income backgrounds
-\- supporting individuals and communities who are contributing to policy development
-\- boosting grassroots projects that can benefit from OBF’s support
+\- representing interests of bioinformatics and open source communities from developing countries
+\- onboarding member projects from low and middle-income backgrounds
+\- supporting individuals and communities who are contributing to policy development
+\- boosting grassroots projects that can benefit from OBF’s support
\- spreading awareness of OBF Event Fellowship and affiliation programs
Sound interesting? If so, please get in touch with the board by emailing [board@open-bio.org](mailto:board@open-bio.org). If you want more information, or want to talk to one of us about being on the board or in the OBF community in general, see the [OBF Board page](/board/) for contact information.
diff --git a/content/posts/students-selected-for-gsoc.md b/content/posts/students-selected-for-gsoc.md
index aebb726c5..0b4f7af7f 100644
--- a/content/posts/students-selected-for-gsoc.md
+++ b/content/posts/students-selected-for-gsoc.md
@@ -22,20 +22,20 @@ I'm very pleased and excited to announce that the Open Bioinformatics Foundation
The accepted students, their projects, and their mentors (in alphabetical order):
-- **[Wibowo Arindrarto](http://bow.web.id/blog/tag/gsoc/)**:
-_SearchIO Implementation in Biopython_
+- **[Wibowo Arindrarto](http://bow.web.id/blog/tag/gsoc/)**:
+_SearchIO Implementation in Biopython_
mentored by Peter Cock
-- **[Lenna Peterson](http://arklenna.tumblr.com/tagged/gsoc2012)**:
-_Diff My DNA: Development of a Genomic Variant Toolkit for Biopython_
+- **[Lenna Peterson](http://arklenna.tumblr.com/tagged/gsoc2012)**:
+_Diff My DNA: Development of a Genomic Variant Toolkit for Biopython_
mentored by Brad Chapman, Reece Hart, James Casbon
-- **[Marjan Povolni](http://blog.mpthecoder.com/tagged/gsoc)**:
-_The worlds fastest parallelized GFF3/GTF parser in D, and an interfacing biogem plugin for Ruby_
+- **[Marjan Povolni](http://blog.mpthecoder.com/tagged/gsoc)**:
+_The worlds fastest parallelized GFF3/GTF parser in D, and an interfacing biogem plugin for Ruby_
mentored by Pjotr Prins, Francesco Strozzi, Raoul Bonnal
-- **[Artem Tarasov](http://lomereiter.wordpress.com/tag/gsoc/)**:
-_Fast parallelized GFF3/GTF parser in C++, with Ruby FFI bindings_
+- **[Artem Tarasov](http://lomereiter.wordpress.com/tag/gsoc/)**:
+_Fast parallelized GFF3/GTF parser in C++, with Ruby FFI bindings_
mentored by Pjotr Prins, Francesco Strozzi, Raoul Bonnal
-- **[Clayton Wheeler](http://csw.github.com/bioruby-maf/)**:
-_Multiple Alignment Format parser for BioRuby_
+- **[Clayton Wheeler](http://csw.github.com/bioruby-maf/)**:
+_Multiple Alignment Format parser for BioRuby_
mentored by Francesco Strozzi and Raoul Bonnal
As in every year, we received many great applications and ideas. However, funding and mentor resources are limited, and we were not able to accept as many as we would have liked. Our deepest thanks to all the students who applied: we sincerely appreciate the time and effort you put into your applications, and hope you will still consider being a part of the OBF's open source projects, even without Google funding. I speak for myself and all of the mentors who read and scored applications when I say that we were truly honored by the number and quality of the applications we received.
@@ -44,5 +44,5 @@ For the accepted students: congratulations! You have risen to the top of a very
Best regards,
-Robert Buels
+Robert Buels
OBF GSoC 2012 Organization Administrator
diff --git a/content/posts/they-let-me-into-australia-and-this-is-what-i-saw.md b/content/posts/they-let-me-into-australia-and-this-is-what-i-saw.md
index 268fb028d..4bfa638ca 100644
--- a/content/posts/they-let-me-into-australia-and-this-is-what-i-saw.md
+++ b/content/posts/they-let-me-into-australia-and-this-is-what-i-saw.md
@@ -57,7 +57,7 @@ up immediately as a threat to myself and others. Come on, friends, I am
completely harmless. And this is what I've seen so far in the land down under
at the number one meeting in the entire world of open-source biology folks.
-**Python and Systems Biology -- Michiel de Hoon**
+**Python and Systems Biology -- Michiel de Hoon**
Cool graphics with python. So let's say we've got one hundred million
expression data and we want to make a gene regulatory network from them. To
@@ -79,7 +79,7 @@ all in Python. Always Python. Sweet. Of course, also sweet open-source since
you can get the code and documentation and tutorials about how to get started
programming with Python. We want to help you help yourself.
-**Eukaryotic Linear Motifs and Disorder -- Rune Linding**
+**Eukaryotic Linear Motifs and Disorder -- Rune Linding**
This one day I'm walking along, minding my own business, whistling gently the
tune to my favorite Frank Sinatra song, and I run into this protein. Bam,
@@ -101,7 +101,7 @@ There is a nice database to search and classify proteins using these methods,
which is what this talk is all about. As with all good things it's developed
in Python using Biopython. Bonus.
-**Sort of like close to Lectin Domains -- Alex Zelensky**
+**Sort of like close to Lectin Domains -- Alex Zelensky**
This domain completely rules. It has more then 2000 references in GenPept and
tons of ligands and groups and types all over vertebrates. So, we have got to
@@ -123,7 +123,7 @@ develop an on-line database of these motifs completely sorted out. Beautiful,
MySQL, BioPerl. Life is good and I'm gonna make that lunch date; give Claudia
a call to let her know.
-**Nice popular terms like Web Services -- Martin Senger**
+**Nice popular terms like Web Services -- Martin Senger**
If you ever accidentally forget to uncheck one of those "send me as many mails
as possible" boxes while filling out a form to download Java from the good
diff --git a/content/posts/travel-award-recipients-for-april-2019.md b/content/posts/travel-award-recipients-for-april-2019.md
index 701bafee8..62911cabe 100644
--- a/content/posts/travel-award-recipients-for-april-2019.md
+++ b/content/posts/travel-award-recipients-for-april-2019.md
@@ -25,4 +25,4 @@ Congratulations to our April 2019 recipients:
· **Vid Ayer** will attend [BOSC 2019](/events/bosc/) and plans to conduct a Bird Of Feathers (BOF) session on Research Data Management. Having completed her Software Carpentry training, Vid has been actively mentoring and inspiring fellow women researchers to be more involved in open source software development.
-The next deadline for [travel awards](/travel-awards/) is August 15, 2019. You can apply to travel to participate in any event that develops or promotes open source development and open science in the biological research community. The program is aimed at increasing diverse participation at such events.
+The next deadline for [travel awards](/travel-awards/) is August 15, 2019. You can apply to travel to participate in any event that develops or promotes open source development and open science in the biological research community. The program is aimed at increasing diverse participation at such events.
diff --git a/content/posts/travel-award-recipients-for-december-2018.md b/content/posts/travel-award-recipients-for-december-2018.md
index c9822b247..4100e0386 100644
--- a/content/posts/travel-award-recipients-for-december-2018.md
+++ b/content/posts/travel-award-recipients-for-december-2018.md
@@ -12,16 +12,16 @@ title: Travel award recipients for December 2018
url: /2019/02/13/travel-award-recipients-for-december-2018/
---
-We had a great round of OBF travel fellowship candidates in our last round of applications, and after review we extended offers to three deserving applicants: Malvika Sharan, Lindsay Rutter, and Sarker Kamruzzaman. They’ve all accepted the award, and we’re looking forward to hearing about their experiences!
+We had a great round of OBF travel fellowship candidates in our last round of applications, and after review we extended offers to three deserving applicants: Malvika Sharan, Lindsay Rutter, and Sarker Kamruzzaman. They’ve all accepted the award, and we’re looking forward to hearing about their experiences!
-Congratulations to our December 2018 recipients:
+Congratulations to our December 2018 recipients:
-**Malvika Sharan** will be attending [BOSC](/wiki/BOSC_2019) at [ISMB 2019](https://www.iscb.org/ismbeccb2019) in Basel this July. Abstract submissions have only just opened, but she intends to submit an abstract expanding on the idea “Inclusiveness in Open Science” that she spoke about last year ( [slides](https://speakerdeck.com/malvikasharan/inclusiveness-in-open-science)). She’s been active in the BOSC community for several years, participating in abstract review and BoF organisation, and she plans to continue this for 2019.
+**Malvika Sharan** will be attending [BOSC](/wiki/BOSC_2019) at [ISMB 2019](https://www.iscb.org/ismbeccb2019) in Basel this July. Abstract submissions have only just opened, but she intends to submit an abstract expanding on the idea “Inclusiveness in Open Science” that she spoke about last year ( [slides](https://speakerdeck.com/malvikasharan/inclusiveness-in-open-science)). She’s been active in the BOSC community for several years, participating in abstract review and BoF organisation, and she plans to continue this for 2019.
-**Lindsay Rutter** attended the [Plant and Animal Genome Conference](http://www.intlpag.org/2019/) to give an invited workshop talk for the “ _Big Data: Manage your data before your data kills you_” session. Her software " [bigPint](https://lindsayrutter.github.io/bigPint/)" allows biologists to visualize genomics data, especially RNA-sequencing data, and was recently submitted and accepted to [Bioconductor](https://bioconductor.org/packages/devel/bioc/html/bigPint.html).
+**Lindsay Rutter** attended the [Plant and Animal Genome Conference](http://www.intlpag.org/2019/) to give an invited workshop talk for the “ _Big Data: Manage your data before your data kills you_” session. Her software " [bigPint](https://lindsayrutter.github.io/bigPint/)" allows biologists to visualize genomics data, especially RNA-sequencing data, and was recently submitted and accepted to [Bioconductor](https://bioconductor.org/packages/devel/bioc/html/bigPint.html).
-**Sarker Kamruzzaman** will be attending the [2019 U.S. Semantic Technologies Symposium](http://www.us2ts.org/) in March. He’ll be presenting a tutorial " [On the Role of Data Semantics for Explainable AI](http://us2ts.org/2019/posts/program-session-iii.html)" as well as a poster. The conference is meant to bring together specialists in many different fields, including natural sciences, so they can benefit from emerging semantic web technologies.
+**Sarker Kamruzzaman** will be attending the [2019 U.S. Semantic Technologies Symposium](http://www.us2ts.org/) in March. He’ll be presenting a tutorial " [On the Role of Data Semantics for Explainable AI](http://us2ts.org/2019/posts/program-session-iii.html)" as well as a poster. The conference is meant to bring together specialists in many different fields, including natural sciences, so they can benefit from emerging semantic web technologies.
Watch this space for blog posts from each of the awardees.
-The next deadline for travel awards is April 15, 2019. You can apply to travel to participate at any event that develops or promotes open source development and open science in the biological research community. The program is aimed at increasing diverse participation at such events. See the [OBF travel award](https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md) page for details and how to apply.
+The next deadline for travel awards is April 15, 2019. You can apply to travel to participate at any event that develops or promotes open source development and open science in the biological research community. The program is aimed at increasing diverse participation at such events. See the [OBF travel award](https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md) page for details and how to apply.
diff --git a/content/posts/urszula-w-odkowska-building-brains-in-canada.md b/content/posts/urszula-w-odkowska-building-brains-in-canada.md
index c941a87a0..fadbde010 100644
--- a/content/posts/urszula-w-odkowska-building-brains-in-canada.md
+++ b/content/posts/urszula-w-odkowska-building-brains-in-canada.md
@@ -17,24 +17,24 @@ url: /2024/07/18/urszula-building-brains/
In June of 2024, I had a great opportunity to attend the University of Waterloo’s Nengo Summer School (also known as Brain Camp). This was only possible thanks to the fellowship I received from the Open Bioinformatics Foundation.
-
+
_Urszula_ _Presenting her project to the group_.
This summer school was an important event for many reasons. First, I was excited to learn about the Nengo simulation package (https://www.nengo.ai/), which is a powerful platform for designing cognitive and neural systems. Nengo has recently become open source, and for me, using open tools means having not only a better understanding of how they work but also being able to contribute to and influence their growth. This creates a community of users that give back and support each other. The fact that Nengo is newly open source also provided a unique opportunity to talk to the creators about the challenges of transitioning into that mode.
-The Nengo Summer School also provided an introduction to the Neural Engineering Framework. The NEF has been developed by the Computational Neuroscience Research Group led by Chris Eliasmith at the Waterloo Centre for Theoretical Neuroscience as a tool for understanding neurobiological principles through constructing simulations of neural systems. Learning about it provided a satisfyingly complete view of the subject - connecting tools with theory and reasoning behind how the tools have been constructed.
+The Nengo Summer School also provided an introduction to the Neural Engineering Framework. The NEF has been developed by the Computational Neuroscience Research Group led by Chris Eliasmith at the Waterloo Centre for Theoretical Neuroscience as a tool for understanding neurobiological principles through constructing simulations of neural systems. Learning about it provided a satisfyingly complete view of the subject - connecting tools with theory and reasoning behind how the tools have been constructed.
-The two weeks I spent in Waterloo were intense. The first week focused on the introduction to the framework and practical tutorials translating theory into code. On top of that, with other participants and TAs we discussed projects that everyone brought with them to work on during the school, looking for common interests and ways to collaborate. During the second week, we worked on our projects and attended tutorials on advanced applications of Nengo. The school ended with project presentations - first, for other participants, and then in an open event at the University of Waterloo.
+The two weeks I spent in Waterloo were intense. The first week focused on the introduction to the framework and practical tutorials translating theory into code. On top of that, with other participants and TAs we discussed projects that everyone brought with them to work on during the school, looking for common interests and ways to collaborate. During the second week, we worked on our projects and attended tutorials on advanced applications of Nengo. The school ended with project presentations - first, for other participants, and then in an open event at the University of Waterloo.
-
+
_Tutorial at the Waterloo Centre for Theoretical Neuroscience_
My project focused on simulating how a mouse learns to optimally explore the environment while gradually learning the rules governing the behavioral setup. I learned a lot, especially thanks to the help of one of the TAs - Nicole Dumont. I intend to continue working on this project, so the summer school leaves a lasting impression on my research.
But my personal gain was not the only reason I wanted to attend this school. As a part of the Nencki Open Lab initiative (https://nenckiopenlab.org/) that connects young neuroscience researchers from underprivileged regions, I always see the events I attend as an opportunity to share the knowledge and connections I’ve made with others. The Nencki Open Lab events touch on two aspects - teaching people how to use open tools and how to approach research as a part of a bigger picture, connecting theory and practice. The Nengo Summer School helped me grow in both of these areas and I hope to bring the concepts and the people I’ve met there to our own summer schools.
-
+
_Group photo of this year’s attendees and teachers_
diff --git a/content/posts/working-on-a-data-science-project-with-the-open-bioinformatics-foundation-wellcomeml-part-one.md b/content/posts/working-on-a-data-science-project-with-the-open-bioinformatics-foundation-wellcomeml-part-one.md
index 73bd3e294..2fb5d426f 100644
--- a/content/posts/working-on-a-data-science-project-with-the-open-bioinformatics-foundation-wellcomeml-part-one.md
+++ b/content/posts/working-on-a-data-science-project-with-the-open-bioinformatics-foundation-wellcomeml-part-one.md
@@ -38,7 +38,7 @@ The objective for my [GSoC 2021](https://summerofcode.withgoogle.com/projects/#4
During the community bonding period in which I met the mentors, got introduced to the staff of OBF and the staff of WellcomeML I virtually met also the other students working on differents OBF projects. Me and my mentor Antonio brainstormed some ideas for the TODO list of the project by creating a [Kanban board](https://github.com/wellcometrust/WellcomeML/projects/2).
-Since WellcomeML is mostly developed on UNIX/UNIX-based systems, installing and running on Windows is not as straightforward as we would expect. During the talk-with-mentors period before the proposal submission I already encountered an issue when running the WellcomeML library on my Windows laptop, that has been fixed [in this issue](https://github.com/wellcometrust/WellcomeML/issues/257) with the help of the mentors.
+Since WellcomeML is mostly developed on UNIX/UNIX-based systems, installing and running on Windows is not as straightforward as we would expect. During the talk-with-mentors period before the proposal submission I already encountered an issue when running the WellcomeML library on my Windows laptop, that has been fixed [in this issue](https://github.com/wellcometrust/WellcomeML/issues/257) with the help of the mentors.
The correct way to install WellcomeML on Windows is:
```
@@ -78,6 +78,6 @@ Now that I have a tested and running library in my laptop I can’t wait to star
## Notes:
-1. Statistics from GSoC’21: 1292 students were selected from a total of 4795.
+1. Statistics from GSoC’21: 1292 students were selected from a total of 4795.
[https://opensource.googleblog.com/2021/05/google-summer-of-code-2021-students-are.html](https://opensource.googleblog.com/2021/05/google-summer-of-code-2021-students-are.html)
1. Instruction for Windows thanks to [https://github.com/wellcometrust/WellcomeML/pull/302/files](https://github.com/wellcometrust/WellcomeML/pull/302/files)
diff --git a/hugo.yaml b/hugo.yaml
index db905bdaf..6f562e6f1 100644
--- a/hugo.yaml
+++ b/hugo.yaml
@@ -78,51 +78,57 @@ menu:
url: 'get-involved'
weight: 5
- name: 'Diversity, Equity & Inclusion'
- parent: 'about'
+ parent: 'about'
url: '/obf-dei/'
weight: 6
- name: 'Donate'
parent: 'about'
url: 'donate'
weight: 7
+ - name: 'News'
+ url: 'blog'
+ weight: 8
+
- name: 'BOSC'
identifier: 'bosc'
- weight: 2
- - name: 'BOSC 2025'
- parent: 'bosc'
- url: 'events/bosc-2025/'
weight: 1
- - name: 'Schedule'
+ - name: 'BOSC 2026'
parent: 'bosc'
- url: 'events/bosc-2025/bosc-2025-schedule/'
+ url: 'events/bosc-2026/'
weight: 2
+ - name: 'Submit an abstract'
+ parent: 'bosc'
+ url: 'events/bosc-2026/submit/'
+ weight: 3
- name: 'Keynotes'
- weight: 3
parent: 'bosc'
- url: 'events/bosc-2025/bosc-2025-keynotes/'
- - name: 'Panel'
- weight: 4
+ url: 'events/bosc-2026/bosc-2026-keynotes/'
+ weight: 4
+ - name: 'Schedule (NEW)'
parent: 'bosc'
- url: 'events/bosc-2025/panel/'
- - name: "CollaborationFest"
+ url: 'events/bosc-2026/bosc-2026-schedule/'
weight: 5
- parent: 'bosc'
- url: 'events/bosc-2025/ismb-collaborationfest-2025/'
- - name: 'BOSC News'
+ - name: 'Panels'
weight: 6
parent: 'bosc'
- url: 'category/bosc/'
- - name: 'About BOSC'
- parent: 'bosc'
+ url: 'events/bosc-2026/panels/'
+ - name: 'CollaborationFest'
weight: 7
- url: 'events/bosc/about/'
+ parent: 'bosc'
+ url: '/events/bosc/collaborationfest/'
- name: 'Sponsors'
weight: 8
parent: 'bosc'
url: 'events/bosc/sponsors/'
- - name: 'News'
- url: 'blog'
- weight: 4
+ - name: 'BOSC News'
+ weight: 9
+ parent: 'bosc'
+ url: 'category/bosc/'
+ - name: 'About BOSC'
+ parent: 'bosc'
+ weight: 10
+ url: 'events/bosc/about/'
+
permalinks:
section:
diff --git a/layouts/partials/footer.html b/layouts/partials/footer.html
index 95009cd67..7ed4c4c1b 100644
--- a/layouts/partials/footer.html
+++ b/layouts/partials/footer.html
@@ -16,7 +16,7 @@
- {{ if isset .Params "bosc" }}
+ {{ if isset .Params "bosc" }}
{{- partial "footer_custom.html" . }}
Follow OBF
@@ -116,7 +116,7 @@
Follow OBF
{{- else -}}
-
{{- end -}}
@@ -168,22 +168,20 @@
Follow OBF
$(function(){
$('#show-comments').on('click', function(){
var disqus_shortname = '{{ .Site.Config.Services.Disqus.Shortname }}';
-
+
(function() {
- var disqus = document.createElement('script');
- disqus.type = 'text/javascript';
+ var disqus = document.createElement('script');
+ disqus.type = 'text/javascript';
disqus.async = true;
disqus.src = '//' + disqus_shortname + '.disqus.com/embed.js';
(document.getElementsByTagName('head')[0] || document.getElementsByTagName('body')[0]).appendChild(disqus);
})();
-
- $(this).hide();
+
+ $(this).hide();
});
});
-
+
{{ end }}
-
-
diff --git a/layouts/partials/head.html b/layouts/partials/head.html
index 306a5bf20..75cb6bba1 100644
--- a/layouts/partials/head.html
+++ b/layouts/partials/head.html
@@ -45,7 +45,7 @@
{{- with .Site.Params.author.name }}
{{- end }}
-{{- partial "seo/main.html" . }}
+{{- partial "seo/main.html" . }}
{{- with .Site.Params.favicon }}
{{- end -}}
@@ -81,7 +81,7 @@
{{- end -}}
-
+
{{- if .Site.Params.staticman.recaptcha -}}
{{- end -}}
diff --git a/layouts/partials/seo/opengraph.html b/layouts/partials/seo/opengraph.html
new file mode 100644
index 000000000..aa32a432e
--- /dev/null
+++ b/layouts/partials/seo/opengraph.html
@@ -0,0 +1,19 @@
+{{- with .Title | default .Site.Title }}
+
+{{- end }}
+{{- with .Description | default .Params.subtitle | default .Summary }}
+
+{{- end }}
+{{ if isset .Params "bosc" }}
+
+{{ else }}
+{{- with .Params.share_img | default .Params.image | default .Site.Params.logo }}
+
+{{- end }}
+{{ end }}
+{{- with .Site.Params.fb_app_id }}
+
+{{- end }}
+
+
+
diff --git a/layouts/rss.xml b/layouts/rss.xml
index 63952db72..6de6dd0dc 100644
--- a/layouts/rss.xml
+++ b/layouts/rss.xml
@@ -57,4 +57,3 @@
{{- end }}
-
diff --git a/layouts/shortcodes/figure.html b/layouts/shortcodes/figure.html
index dd3735346..e9948b909 100644
--- a/layouts/shortcodes/figure.html
+++ b/layouts/shortcodes/figure.html
@@ -3,7 +3,7 @@
{{- if .Get "link" -}}
{{- end -}}
-
+
{{- $u := urls.Parse (.Get "src") -}}
{{- $src := $u.String -}}
{{- if not $u.IsAbs -}}
@@ -11,7 +11,7 @@
{{- $src = .RelPermalink -}}
{{- end -}}
{{- end -}}
-
+
+
+[Panel 1: Policies and Strategies for Resilient Open Science](/events/bosc-2026/panels/)
+
+{{< column >}}
+
+
+
+
+
+[KEYNOTE: Eric Green](/events/bosc-2026/bosc-2026-keynotes)
+
+
+[KEYNOTE: Maryam Zaringhalam](/events/bosc-2026/bosc-2026-keynotes)
+
+### 2026 Gold Sponsors
{{< columns >}}
-
-
+
+
+
+
+
+
+{{< column >}}
+
+Ann Novakowski, MPH, is Associate Technical Director of Product Strategy at Sage Bionetworks, where she helps translate policy, governance, and community needs into products that support open and responsible biomedical research. Her work spans federated data ecosystems, data access and reuse, digital use conditions, and emerging approaches to AI-enabled research. Drawing on more than 20 years of experience in public health, global health, and research infrastructure, she is particularly interested in how technical systems, governance models, and community practices can work together to make open science more sustainable, trustworthy, and resilient. She holds an MPH from Yale University and a BS in Molecular and Cellular Biology from the University of Arizona.
+
+{{< endcolumns >}}
+
+### Mallory Freeberg
+**EMBL-EBI**
+
+{{< columns >}}
+
+Mallory Freeberg, PhD, is the Human Genomics Team Leader at EMBL’s European Bioinformatics Institute (EMBL-EBI). She directs major genomic variation resources, including the Ensembl Variant Effect Predictor (VEP) tool, human variation interpretation platforms (such as DECIPHER and Gene2Phenotype), and the European Genome-phenome Archive (EGA). Mallory’s career is dedicated to promoting the responsible and standardized sharing of FAIR human clinical and omics data. She actively guides international data harmonization frameworks and serves as Co-Lead of the Global Alliance for Genomics and Health (GA4GH) Implementation Forum, facilitating interoperability between clinical and research domains. She earned her PhD in Bioinformatics from the University of Michigan.
+
+{{< column >}}
+
+
+
+{{< endcolumns >}}
+
+### Guy Cochrane
+**Global BioData Coalition (GBC)**
+
+{{< columns >}}
+
+
+
+{{< column >}}
+
+Guy Cochrane, PhD, is the Scientific Head of the Global BioData Coalition (GBC) and a faculty member at EMBL-EBI. He works internationally to unite life science and biomedical funding organizations around long-term sustainability models for core data infrastructure. Guy previously served as the Head of the European Nucleotide Archive (ENA) and led critical pandemic-response infrastructure as a leader of the European COVID-19 Data Platform. His long-standing advocacy for open data encompasses policy development for access and benefit sharing, international metadata standards development, and leadership within the International Nucleotide Sequence Database Collaboration (INSDC).
+
+{{< endcolumns >}}
+
+### Sam Halabi
+**Georgetown University**
+
+{{< columns >}}
+
+Sam Halabi, JD, MPhil, is the Bette Jacobs Endowed Professor in Georgetown University's Department of Health Management and Policy and directs the Center for Transformational Health Law at the O'Neill Institute for National and Global Health Law. His research focuses on the law and ethics of pandemic preparedness, global vaccine deployment, and the complexities of international biomedical data sharing. He has authored over 100 manuscripts and five books covering data sharing, global health security, and liability in emergency public health responses. He regularly advises or has advised the World Health Organization (WHO), the World Bank, and the COVAX Facility, and is a member of the WHO’s Working Group on Regulatory Approaches to AI and Health. He holds a JD from Harvard University and an MPhil from the University of Oxford.
+
+{{< column >}}
+
+
+
+{{< endcolumns >}}
+
+### MODERATOR: Mónica Muñoz Torres
+
+{{< columns >}}
+
+
+
+{{< column >}}
+
+Dr. Muñoz Torres is an Associate Professor at the University of Colorado Anschutz. Her work focuses on the critical challenge of developing the socio-technical foundations needed to realize the promise of artificial intelligence in biomedical sciences. Her expertise includes genomics, biocuration, knowledge representation, and data harmonization. She leads the NIH-funded Bridge to Artificial Intelligence (Bridge2AI)’s team focused on Standards, Practices, and Quality Assessment. She is also Co-Lead of the Clinical & Phenotypic Data Capture Work Stream of the Global Alliance for Genomics and Health (GA4GH).
+
+{{< endcolumns >}}
+
+
+
+{{< column >}}
+
+Aida Miro-Herrans is the Bioinformatics Librarian at the University of Florida Libraries, where she focuses on supporting open science, open education, and instruction in bioinformatics methods. Her current work investigates the intersection of artificial intelligence and life science education, specifically exploring how generative AI tools can optimize student learning. Her upcoming presentation at BOSC 2026 highlights a specialized workshop design that empowers life science instructors to leverage AI chatbots to craft active learning activities built entirely on open-source software and open-access datasets.
+
+{{< endcolumns >}}
+
+### Nahid Zeinali
+**California Medical Innovations Institute**
+
+{{< columns >}}
+
+Nahid Zeinali, PhD, is an AI Research Scientist at the California Medical Innovations Institute (CalMI2) and a core team member at the FAIR Data Innovations Hub (FAIRHub). She specializes in natural language processing, deep learning, and artificial intelligence architectures tailored for healthcare and biomedical data. She completed her PhD in Informatics at the University of Iowa in 2025, where her research focused on turning complex multi-modal data into deployable, trustworthy digital biomarkers and healthcare solutions. At CalMI2, her work bridges advanced machine learning methods with open data frameworks to build interoperable, AI-driven medical products.
+
+{{< column >}}
+
+
+
+{{< endcolumns >}}
+
+### Alex Bateman
+**EMBL-EBI**
+
+{{< columns >}}
+
+
+
+{{< column >}}
+
+Alex Bateman, PhD, is a Senior Team Leader for Protein Sequence Resources at EMBL-EBI. He serves as a Principal Investigator for the UniProt consortium and has broad oversight over protein and non-coding RNA databases, including RNAcentral. Before joining EMBL-EBI in 2012, Alex managed several of the community's most widely utilized biological resources at the Wellcome Sanger Institute, including Pfam and Rfam. He has driven open-source data standards as a former Chairman of the International Society for Biocuration (ISB) Executive Committee, and has served as the Executive Editor for *Bioinformatics* and the Editor of *Nucleic Acids Research* Database Issue.
+
+{{< endcolumns >}}
+
+### Eric Green
+**Illumina**
+
+{{< columns >}}
+
+Eric Green, MD, PhD, is the Chief Medical Officer at Illumina and a legendary figure in the history of genomics. He spent over two decades directing a premier research program at the National Human Genome Research Institute (NHGRI) at the U.S. National Institutes of Health, where he played a start-to-finish role in the historic Human Genome Project and founded the NIH Intramural Sequencing Center. He subsequently served as the Director of NHGRI for over 15 years, acting as a primary driver of the integration of genomics into clinical care and public health globally. An elected member of the National Academy of Medicine, he currently focuses on guiding global efforts to broaden access to precision medicine, ensure diversity in genomic data, and navigate the clinical applications of genomics in an era increasingly defined by advanced computational and AI tools.
+
+{{< column >}}
+
+
+
+{{< column >}}
+
+Jason Williams, is the Assistant Director of Cold Spring Harbor's Dolan DNA Learning Center.
+He was elected an AAAS Fellow in 2026. In 2025, he won the Elizabeth W. Jones Award for Excellence in Education.
+Mr. Williams has been instrumental in bringing the latest technologies and teaching approaches for working with DNA into classrooms around the world through dedicated hands-on programs for students and teachers.
+He develops national and international biology education and professional development programs. In addition to his work at the DNALC, Williams is the founder of LifeSciTrainers.org, a global initiative promoting a community of practice among professionals who develop short-format training for life scientists.
+He is also the Lead Investigator of the [NSF Arecibo Center for STEM Education, Computing, and Community Engagement](https://areciboc3.org/).
+
+{{< endcolumns >}}
diff --git a/content/page/project-ideas.md b/content/page/project-ideas.md
index 16d4a1e59..4a673df3c 100644
--- a/content/page/project-ideas.md
+++ b/content/page/project-ideas.md
@@ -101,7 +101,7 @@ The overall goal of this project is to improve the configurability of the featur
**Project description**
-OpenMS is a framework for computational mass spectrometry. Modern mass spectrometers produce large files (e.g., 100 GB) that can’t be easily stored or accessed in the established XML file format mzML. Recently, an update to mzML has been developed that uses HDF5 to store Blosc compressed spectra in binary format: called mzMLb.
+OpenMS is a framework for computational mass spectrometry. Modern mass spectrometers produce large files (e.g., 100 GB) that can’t be easily stored or accessed in the established XML file format mzML. Recently, an update to mzML has been developed that uses HDF5 to store Blosc compressed spectra in binary format: called mzMLb.
In this project, the student will add a reader and writer for the mzMLb file format to OpenMS. To some extent, code from the OpenMS reader and writer for the mzML file format can be reused, as well as inspiration can be taken from reference implementations by other parties.
**Project size**
@@ -144,7 +144,7 @@ In this project, the student will add a reader and writer for the mzMLb file for
**Project description**
-OpenMS is a framework for computational mass spectrometry. It features a wide range of algorithms and data structures to process and analyze mass spectra. For some very computationally demanding parts, we performed manual code conversion to make the layout of our data better fit the data access patterns of our algorithms. We observed the biggest speedup switching the data layout from an Array of Structs (AoS) to a Structure of Arrays (SoA).
+OpenMS is a framework for computational mass spectrometry. It features a wide range of algorithms and data structures to process and analyze mass spectra. For some very computationally demanding parts, we performed manual code conversion to make the layout of our data better fit the data access patterns of our algorithms. We observed the biggest speedup switching the data layout from an Array of Structs (AoS) to a Structure of Arrays (SoA).
In this project, the GSoC contributor will adapt our core data structure for mass spectra to AoS. Ideally, the contributor should be using a modern C++ zero-cost abstraction (e.g., building on https://github.com/crosetto/SoAvsAoS) that makes the old code work without (or minimal) manual changes.
**Project size**
diff --git a/content/page/projects.md b/content/page/projects.md
index 0b0cfe90f..e263a08a2 100644
--- a/content/page/projects.md
+++ b/content/page/projects.md
@@ -48,4 +48,4 @@ The OBF has [a process for projects in the open bioinformatics realm to become m
* [BlipKit](https://github.com/cmungall/blipkit): Chris Mungall’s Prolog toolkit for Bioinformatics and BioMedical Informatics.
* [Biolib](https://github.com/biolib/obf-biolib): Cross-project/language C bindings for a shared codebase across the different Bio* projects (Pjotr Prins).
* DAS / BioDAS: The Distributed Annotation System defines a communication protocol used to exchange annotations on genomic or protein sequences.
-* [EMBOSS](https://emboss.sourceforge.net/): An analysis package developed for the needs of the molecular biology (e.g. EMBnet) user community.
+* [EMBOSS](https://emboss.sourceforge.net/): An analysis package developed for the needs of the molecular biology (e.g. EMBnet) user community.
diff --git a/content/page/schedule-2025.md b/content/page/schedule-2025.md
index 15d975d74..5aa31048b 100644
--- a/content/page/schedule-2025.md
+++ b/content/page/schedule-2025.md
@@ -32,7 +32,7 @@ Working together to develop, promote and protect our data resources: Lessons lea
diff --git a/content/page/schedule-2026.md b/content/page/schedule-2026.md
new file mode 100644
index 000000000..0ffcf1378
--- /dev/null
+++ b/content/page/schedule-2026.md
@@ -0,0 +1,64 @@
+---
+author: nlharris
+date: "2026-05-25T00:09:44+00:00"
+title: BOSC 2026 Schedule
+url: /events/bosc-2026/bosc-2026-schedule/
+bosc: yes
+
+---
+
+
+
+We invite abstracts on this topic. Some might be selected to give talks at BOSC (which will be part of ISMB 2026).
+We may also invite some of the chosen speakers to participate in a panel. The [submission deadline](/events/bosc-2026/submit/) is April 9.
+
+For example, here are some possible topics (but don't feel restricted to these):
+
+- Reuse: how can we encourage and facilitate reuse of tools and frameworks when AI makes it easy to code things up from scratch?
+- Evaluating open source projects: AI tools can generate thousands of lines of code in seconds. The most costly process is now verifying that code for scientific accuracy (https://arxiv.org/abs/2507.09089). What are some good approaches to address this?
+- Contribution guidelines: balancing scale and utility of AI-assisted development with community-building
+ - How should an open source project assess pull requests from AI agents?
+ - Are zero-tolerance bans on submissions generated using AI reasonable? (e.g., https://medium.com/@livewyer/ai-disruption-to-open-source-software-oss-377f10be2d8a)
+ - How can humans and AI agents best work together?
+- Attribution and credit:
+ - How should we recognize contributions in an age of AI-assisted commits?
+ - Transparency: Should there be mandatory requirements to disclose AI use, including models and prompts used?
+ - Human ownership: should authors always remain legally and ethically accountable for the outputs of their code?
+ - Licensing: do open source licenses still mean anything when coding agents can translate or reimplement code?
+- Sustainability: who does the long-term hard work of maintaining open source projects when AI does the "easy" work?
+- Credit for training data: part of what AI proposes is reusing existing human-coded work without crediting it. Can there be a way to fairly credit the contribution of an open source project to the (often non open-source) models?
+- When AI is the user: should open source projects be designed for machine consumers?
+- The deadly feedback loop: models are trained on what they produce. Does this really work?
+- Open data in the AI era: balancing access with protection from misuse
+
+We look forward to seeing your thoughts on these topics! Please be sure to [submit your abstract](/events/bosc-2026/submit/) by April 9 if you want to be considered for a talk.
diff --git a/content/posts/2026-05-13-CoFest-2026.md b/content/posts/2026-05-13-CoFest-2026.md
new file mode 100644
index 000000000..a36c7d66e
--- /dev/null
+++ b/content/posts/2026-05-13-CoFest-2026.md
@@ -0,0 +1,35 @@
+---
+author: nlharris
+category:
+ - bosc
+ - ismb
+ - community
+date: "2026-05-13T02:30:32+00:00"
+draft: false
+tag:
+ - bosc
+ - ismb
+ - conferences
+
+title: "CollaborationFest 2026"
+url: /posts/CollaborationFest-2026/
+---
+
+