From 60420f6418dce76302d5e5adca80e434d3b65faa Mon Sep 17 00:00:00 2001 From: "Peter J. A. Cock" Date: Thu, 4 Dec 2025 12:25:56 +0000 Subject: [PATCH 1/4] Ignore *.bak files in git --- .gitignore | 1 + 1 file changed, 1 insertion(+) diff --git a/.gitignore b/.gitignore index 8dd6d56b8..1034e558b 100644 --- a/.gitignore +++ b/.gitignore @@ -1,2 +1,3 @@ public/ .hugo_build.lock +*.bak From bbcdefdadda054d88ffe711a8fa92aca9c53d97e Mon Sep 17 00:00:00 2001 From: "Peter J. A. Cock" Date: Thu, 4 Dec 2025 12:30:21 +0000 Subject: [PATCH 2/4] Remove trailing whitespace --- README.md | 13 +++++-------- hugo.yaml | 4 ++-- layouts/partials/footer.html | 18 ++++++++---------- layouts/partials/head.html | 4 ++-- layouts/rss.xml | 1 - layouts/shortcodes/figure.html | 4 ++-- nginx.conf | 2 +- static/css/custom.css | 1 - static/site.webmanifest | 2 +- 9 files changed, 21 insertions(+), 28 deletions(-) diff --git a/README.md b/README.md index b695a6fc8..c73c7f62a 100644 --- a/README.md +++ b/README.md @@ -67,10 +67,10 @@ 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/ @@ -86,7 +86,7 @@ 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: `![an image](/img/2025/test-image.jpg)` @@ -127,7 +127,7 @@ 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 +140,7 @@ 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 +150,3 @@ 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/hugo.yaml b/hugo.yaml index 4b1e375bd..b662efa28 100644 --- a/hugo.yaml +++ b/hugo.yaml @@ -78,7 +78,7 @@ menu: url: 'get-involved' weight: 5 - name: 'Diversity, Equity & Inclusion' - parent: 'about' + parent: 'about' url: '/obf-dei/' weight: 6 - name: 'Donate' @@ -97,7 +97,7 @@ menu: url: 'events/bosc-2025/bosc-2025-schedule/' weight: 2 - name: 'Panel (2025)' - weight: 4 + weight: 4 parent: 'bosc' url: 'events/bosc-2025/panel/' - name: "CollaborationFest (2025)" 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/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 -}} - + {{ with .Get Date: Thu, 4 Dec 2025 12:31:03 +0000 Subject: [PATCH 3/4] Remove trailing whitespace in content itself --- content/_index.md | 2 +- content/page/about-bosc.md | 4 +- content/page/adding-projects.md | 4 +- content/page/board.md | 14 +- ...sc-2019-collaborationfest-for-reference.md | 4 +- content/page/bosc-2019.md | 8 +- content/page/bosc-2020-online.md | 4 +- content/page/bosc-2021-keynotes.md | 8 +- content/page/bosc-2021.md | 2 +- content/page/bosc-2022-1.md | 2 +- content/page/bosc-2022-keynotes.md | 2 +- content/page/bosc-2022-panel-1.md | 2 +- content/page/bosc-2022-panel.md | 2 +- content/page/bosc-2022.md | 2 +- content/page/bosc-2023-1.md | 2 +- content/page/bosc-2023-keynotes.md | 4 +- content/page/bosc-2023.md | 2 +- content/page/bosc-2024-sponsors.md | 8 +- content/page/bosc-2025.md | 6 +- content/page/bosc-2026.md | 6 +- content/page/donate.md | 2 +- content/page/events.md | 1 - content/page/get-involved.md | 8 +- ...s-diversity-inclusion-and-accessibility.md | 8 +- content/page/news.md | 1 - .../page/obf-bosc-collaborationfest-2023.md | 10 +- .../page/obf-bosc-collaborationfest-2025.md | 8 +- content/page/panel.md | 2 +- content/page/project-ideas.md | 4 +- content/page/projects.md | 2 +- content/page/schedule-2025.md | 2 +- content/page/sponsors-1.md | 8 +- content/page/sponsors-2.md | 10 +- content/page/sponsors-2023.md | 10 +- content/page/sponsors-new-draft-2023.md | 6 +- content/page/sponsors.md | 4 +- content/page/sponsors2022.md | 10 +- content/page/sponsors2025.md | 2 +- content/page/submit-to-bosc-2023.md | 4 +- content/page/submit-to-bosc-2025.md | 2 +- content/page/submit-to-bosc-2026.md | 2 +- content/posts/2025-03-04-Event-Awards.md | 12 +- content/posts/2025-03-04-new-website.md | 4 +- content/posts/2025-03-09-BOSC-BOKR.md | 2 +- ...2025-03-20-award-opportunities-BOSC2025.md | 4 +- .../posts/2025-04-02-archiving-obf-posts.md | 4 +- ...rnational-Statistical-Genetics-Workshop.md | 10 +- content/posts/2025-07-15-Event-Awards.md | 6 +- .../posts/2025-08-25-Tayyaba-Alvi-ISMB2025.md | 8 +- ...-muhamad-haries-ramdhani-ismb-eccb-2025.md | 2 +- .../2025-09-24-BOSC2025-report-and-video.md | 2 +- content/posts/2025-09-30-gigascience.md | 4 +- content/posts/2025-10-07-Events-Awards.md | 7 +- .../posts/2025-11-03-Krasnow-ESIIL-Summit.md | 8 +- ...effects-at-informal-discussion-sessions.md | 10 +- content/posts/ISMB-CollaborationFest-2025.md | 6 +- ...YY-MM-DD-event-fellowship-blog-template.md | 12 +- content/posts/biojava-3-0-4-released.md | 8 +- .../bioperl-list-summary-january-2003.md | 44 ++-- content/posts/biopython-1-78-released.md | 2 +- content/posts/biopython-1-79-released.md | 14 +- content/posts/bioruby-1-4-3-released.md | 8 +- .../posts/bosc-2014-keynote-competition.md | 4 +- ...inishes-and-i-weep-as-i-miss-it-already.md | 10 +- ...ellowship-is-open-until-1-december-2019.md | 2 +- content/posts/cordon-bleu-bioinformatics.md | 22 +- ...s-and-don-ts-for-computational-training.md | 14 +- ...ble-gsoc-students-for-the-obf-this-year.md | 20 +- ...ourney-to-the-ismb-bosc-2022-conference.md | 6 +- ...m-bosc-s-obf-birds-of-a-feather-meeting.md | 8 +- .../global-community-biosummit-2019-mit.md | 4 +- .../goodbye-mediawiki-hello-new-website.md | 8 +- ...of-code-2021-we-need-your-project-ideas.md | 8 +- ...mer-of-code-2022-time-for-project-ideas.md | 2 +- .../iscbacademy-webinar-feb-22-yo-yehudi.md | 12 +- ...academy-webinar-on-patient-led-research.md | 6 +- ...rcing-ourselves-together-mad-price-ball.md | 2 +- ...fellowship-review-chair-farah-zaib-khan.md | 2 +- content/posts/minutes-2005-bosc-meeting.md | 6 +- content/posts/minutes-2007-bosc-meeting.md | 4 +- content/posts/minutes-2011-confcall.md | 14 +- content/posts/minutes-2013-apr-confcall.md | 4 +- content/posts/minutes-2013-dec-confcall.md | 4 +- content/posts/minutes-2014-nov-confcall.md | 2 +- content/posts/minutes-2015-may-confcall.md | 2 +- content/posts/minutes-2016-oct-confcall.md | 2 +- content/posts/minutes-2018-mar-confcall.md | 2 +- content/posts/minutes-2019-bosc.md | 4 +- content/posts/minutes-of-2002-bosc-meeting.md | 218 +++++++++--------- .../posts/o-b-f-in-google-summer-of-code.md | 2 +- ...ublic-board-meeting-2023-12-19-11am-est.md | 2 - ...te-in-light-of-the-coronavirus-covid-19.md | 8 +- ...minds-a-memorable-experience-tbnss-2024.md | 4 +- ...23-conference-hosted-in-the-mother-city.md | 14 +- ...nation-open-for-obf-board-election-2021.md | 32 +-- content/posts/students-selected-for-gsoc.md | 22 +- ...e-into-australia-and-this-is-what-i-saw.md | 8 +- .../travel-award-recipients-for-april-2019.md | 2 +- ...avel-award-recipients-for-december-2018.md | 12 +- ...la-w-odkowska-building-brains-in-canada.md | 10 +- ...ormatics-foundation-wellcomeml-part-one.md | 4 +- 101 files changed, 437 insertions(+), 446 deletions(-) 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 ![Poster session at GCCBOSC2018](/wp-content/uploads/2019/03/people-at-poster-session-GCC2018-1.jpg) - + ![OBF Treasurer Heather Wiencko introducing OBF at BOSC 2024](/wp-content/uploads/2024/08/Heather-presenting-1.jpeg) {{< endcolumns >}} diff --git a/content/page/about-bosc.md b/content/page/about-bosc.md index 0326734b1..042528376 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 @@ -7,7 +7,7 @@ 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? 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 4feb9f800..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). ` >}} @@ -50,7 +50,7 @@ Bioinformatician at the [International Center of Insect Physiology and Ecology, link= "https://lappland.io" title= "[Hilmar Lapp](https://orcid.org/0000-0001-9107-0714)" caption=` -_At-large Member_ +_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/), Open Research Faculty at [Neuro 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 ![Dr. Lara Mangravite](/wp-content/uploads/2021/04/Lara-Mangravite.jpeg) -### 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​ ​CodeFest​s (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​ ​CodeFest​s (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 -[![](/wp-content/uploads/2021/04/image.png)](https://elifesciences.org/) -[![Genevia](/wp-content/uploads/2021/06/genevia_logo_cmyk.png)](https://geneviatechnologies.com/) +[![](/wp-content/uploads/2021/04/image.png)](https://elifesciences.org/) +[![Genevia](/wp-content/uploads/2021/06/genevia_logo_cmyk.png)](https://geneviatechnologies.com/) [![Oxford University Press](/wp-content/uploads/2021/06/OUP_logo_navy.png)](https://oup.com/)[![](/wp-content/uploads/2021/07/logo_bioteam_transp_bg.png)](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 f141c6091..df327439d 100644 --- a/content/page/bosc-2025.md +++ b/content/page/bosc-2025.md @@ -26,7 +26,7 @@ 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)! -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). @@ -144,7 +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 @@ -178,7 +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 6b3a62b24..201513c44 100644 --- a/content/page/bosc-2026.md +++ b/content/page/bosc-2026.md @@ -21,7 +21,7 @@ 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 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)! + [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/). @@ -73,7 +73,7 @@ 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). @@ -150,7 +150,7 @@ Interested in sponsoring BOSC 2026? Please see our [sponsors page](/events/bosc/ {{< 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/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..e70ad1f44 100644 --- a/content/page/get-involved.md +++ b/content/page/get-involved.md @@ -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. ![](/wp-content/uploads/2019/02/obf_membership.jpg) ## 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/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-2025.md b/content/page/obf-bosc-collaborationfest-2025.md index 3747aac3f..62d168deb 100644 --- a/content/page/obf-bosc-collaborationfest-2025.md +++ b/content/page/obf-bosc-collaborationfest-2025.md @@ -31,7 +31,7 @@ Limited remote participation will be possible, but engagement opportunities will {{< column >}} -![Lunch at CoFest 2023](/wp-content/uploads/2023/08/CoFest2023-lunch-1-736x1024.png) +![Lunch at CoFest 2023](/wp-content/uploads/2023/08/CoFest2023-lunch-1-736x1024.png) {{< 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/panel.md b/content/page/panel.md index 4c221584a..918fa2e09 100644 --- a/content/page/panel.md +++ b/content/page/panel.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/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
- + ## [Panel: Data Sustainability](/events/bosc-2025/panel/) Panelists 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​ ​CodeFest​s (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​ ​CodeFest​s (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 -[![](/wp-content/uploads/2021/04/image.png)](https://elifesciences.org/) -[![Genevia](/wp-content/uploads/2021/06/genevia_logo_cmyk.png)](https://geneviatechnologies.com/) +[![](/wp-content/uploads/2021/04/image.png)](https://elifesciences.org/) +[![Genevia](/wp-content/uploads/2021/06/genevia_logo_cmyk.png)](https://geneviatechnologies.com/) [![Oxford University Press](/wp-content/uploads/2021/06/OUP_logo_navy.png)](https://oup.com/)[![](/wp-content/uploads/2021/07/logo_bioteam_transp_bg.png)](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​ ​CodeFest​s (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​ ​CodeFest​s (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 -[![](/wp-content/uploads/2021/04/image.png)](https://elifesciences.org/) -[![Genevia](/wp-content/uploads/2021/06/genevia_logo_cmyk.png)](https://geneviatechnologies.com/) -[![Oxford University Press](/wp-content/uploads/2021/06/OUP_logo_navy.png)](https://oup.com/)[![](/wp-content/uploads/2021/07/logo_bioteam_transp_bg.png)](https://bioteam.net) +[![](/wp-content/uploads/2021/04/image.png)](https://elifesciences.org/) +[![Genevia](/wp-content/uploads/2021/06/genevia_logo_cmyk.png)](https://geneviatechnologies.com/) +[![Oxford University Press](/wp-content/uploads/2021/06/OUP_logo_navy.png)](https://oup.com/)[![](/wp-content/uploads/2021/07/logo_bioteam_transp_bg.png)](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​ ​CodeFest​s (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​ ​CodeFest​s (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 -[![](/wp-content/uploads/2021/04/image.png)](https://elifesciences.org/) -[![Genevia](/wp-content/uploads/2021/06/genevia_logo_cmyk.png)](https://geneviatechnologies.com/) -[![Oxford University Press](/wp-content/uploads/2021/06/OUP_logo_navy.png)](https://oup.com/)[![](/wp-content/uploads/2021/07/logo_bioteam_transp_bg.png)](https://bioteam.net) +[![](/wp-content/uploads/2021/04/image.png)](https://elifesciences.org/) +[![Genevia](/wp-content/uploads/2021/06/genevia_logo_cmyk.png)](https://geneviatechnologies.com/) +[![Oxford University Press](/wp-content/uploads/2021/06/OUP_logo_navy.png)](https://oup.com/)[![](/wp-content/uploads/2021/07/logo_bioteam_transp_bg.png)](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​ ​CodeFest​s (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​ ​CodeFest​s (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 e4c2983c7..1cbbd6097 100644 --- a/content/page/sponsors.md +++ b/content/page/sponsors.md @@ -7,7 +7,7 @@ bosc: yes ---
- + ### Sponsoring BOSC {{< columns >}} @@ -99,7 +99,7 @@ was part of the main ISMB/ECCB conference. ## 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/sponsors2022.md b/content/page/sponsors2022.md index b4cb5f4bf..9226f0e67 100644 --- a/content/page/sponsors2022.md +++ b/content/page/sponsors2022.md @@ -56,7 +56,7 @@ 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 @@ -65,7 +65,7 @@ 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​ ​CodeFest​s (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​ ​CodeFest​s (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. @@ -113,8 +113,8 @@ We acknowledge our sponsors before, during and after the event in multiple ways: ## BOSC 2021 Silver Sponsors -[![](/wp-content/uploads/2021/04/image.png)](https://elifesciences.org/) -[![Genevia](/wp-content/uploads/2021/06/genevia_logo_cmyk.png)](https://geneviatechnologies.com/) -[![Oxford University Press](/wp-content/uploads/2021/06/OUP_logo_navy.png)](https://oup.com/)[![](/wp-content/uploads/2021/07/logo_bioteam_transp_bg.png)](https://bioteam.net) +[![](/wp-content/uploads/2021/04/image.png)](https://elifesciences.org/) +[![Genevia](/wp-content/uploads/2021/06/genevia_logo_cmyk.png)](https://geneviatechnologies.com/) +[![Oxford University Press](/wp-content/uploads/2021/06/OUP_logo_navy.png)](https://oup.com/)[![](/wp-content/uploads/2021/07/logo_bioteam_transp_bg.png)](https://bioteam.net) If you are interested in becoming a sponsor, please contact us at bosc@open-bio.org! diff --git a/content/page/sponsors2025.md b/content/page/sponsors2025.md index 036ca5f9f..0b33bbfe7 100644 --- a/content/page/sponsors2025.md +++ b/content/page/sponsors2025.md @@ -98,7 +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 ![](/wp-content/uploads/2022/01/Screen-Shot-2022-01-19-at-3.59.31-PM.png) -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 index 3fde99023..0e2eb6f2c 100644 --- a/content/page/submit-to-bosc-2026.md +++ b/content/page/submit-to-bosc-2026.md @@ -99,7 +99,7 @@ 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/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 ![Images of the workshop welcome sign and the room in which the workshop took place](/img/2025/2025-04-30-Kyra-Feuer-01.jpg) *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. ![Images of myself and others at the poster session](/img/2025/2025-04-30-Kyra-Feuer-02.jpg) *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 ![Images of cusisine from Rosetta Hall](/img/2025/2025-04-30-Kyra-Feuer-03.jpg) *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. ![Images of the view of the Flatirons from the hotel and the Open Space park](/img/2025/2025-04-30-Kyra-Feuer-04.jpg) *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. ![Images of the view from the Lost Gulch Overlook](/img/2025/2025-04-30-Kyra-Feuer-05.jpg) *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 8e410db96..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 @@ -12,7 +12,7 @@ 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)_**. @@ -35,7 +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 @@ -46,7 +46,7 @@ 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. ![John Lennon Peace Monument on the left, and the Wheel of Liverpool on the right](/img/2025/2025-08-25-TA5.png) 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 9b97dee91..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. 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/2025-11-03-Krasnow-ESIIL-Summit.md b/content/posts/2025-11-03-Krasnow-ESIIL-Summit.md index a1fec3f6f..15a9886b0 100644 --- a/content/posts/2025-11-03-Krasnow-ESIIL-Summit.md +++ b/content/posts/2025-11-03-Krasnow-ESIIL-Summit.md @@ -1,7 +1,7 @@ --- author: rmk118 date: 2025-11-03 -category: +category: - community - event-fellowship - travel-fellowship @@ -10,9 +10,9 @@ tag: - 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: +url: /2025/11/03/2025-11-03-Krasnow-ESIIL-Summit/ +editor_options: + markdown: wrap: sentence --- 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! -[![CoFest gallery](/wp-content/uploads/2025/01/CoFest-gallery.png)](/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. +[![CoFest gallery](/wp-content/uploads/2025/01/CoFest-gallery.png)](/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 aac199651..65eda79b6 100644 --- a/content/posts/YYYY-MM-DD-event-fellowship-blog-template.md +++ b/content/posts/YYYY-MM-DD-event-fellowship-blog-template.md @@ -2,7 +2,7 @@ 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. @@ -79,7 +79,7 @@ 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"** @@ -171,5 +171,5 @@ Thank your funders, mentors, collaborators, or community members. --- -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/) -[![C. Titus Brown](https://pbs.twimg.com/profile_images/2341608206/1v12iz3xg0w80911u76a_normal.png)](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/) +[![C. Titus Brown](https://pbs.twimg.com/profile_images/2341608206/1v12iz3xg0w80911u76a_normal.png)](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. ![](https://lh3.googleusercontent.com/2hnxxOt_KWFjNV-q51dGeodBwJQ_LjK9bom4AP2irMkBE1I6d5YE0eCZ_NrQqqT9_MCJAUAUnfV3cXMzj6CkySLpqdm6u8Pef25o76H9K4BPhMup6DwhNFN1Zf8mKd_fl63fKpCb)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. ![](https://lh4.googleusercontent.com/npS5DuQPIX_4hhHWCzDthPHDjRCykY8e4dAZeCkWxcP9G6i3C2nLMyELMo4QkXdGxgVwmyB7PzgfQNfq1gVXBRfYa0Tz2Ssjz3MzE04hIqrqxskrjGOKRZM1exhsmpvOndIq9BWt)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! ![](https://lh3.googleusercontent.com/lLZ26IxGrCPVJRK-Khv_Ljy7hPpP_w6MiSOCl6qoJOqRUYbCHsOJfYuefKPsc0tgSPQizZAYnZtChcT4b3hzxqO1_6XX98jVFrntGnChIjNrkFhkQ-pCy9Yyj-Mgv0zNyqhxVA38)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. ![](https://lh3.googleusercontent.com/2fp5QayJNDfcjc7XBlMiOTpYKkYmYY_tq_QI4gWo9BCdgo0lTzieGmH3Qa3MPUCkKf5CSKtAw_ZCZdwkXinl2bSuek7tFzGL5AKPDDvKpaIbaVfgWOa0Y5kmRzUdyo4RKDyNOEG0)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. -![](https://i.imgur.com/5ppP8SE.jpg)Diversity and Inclusion CCMcr19 +![](https://i.imgur.com/5ppP8SE.jpg)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. -![](https://lh4.googleusercontent.com/LE_vl3pKIFuweLbd8pAXB7vT9XOm9VWAOAOCU9hcDPEFGsack9AzVKWpHklMxX35CiA4X7Ksa7LHPWUDeZtKX3j2DSyavX_THyI4Bz6Ptfu-G-3-di6QONsM1f8kh40qELlynJWr7X-qV9ti8hvbV6M) -Some of the cool people I meet at BOSC: _panelist Jenea Adams and keynote speaker Jason Williams_. +![](https://lh4.googleusercontent.com/LE_vl3pKIFuweLbd8pAXB7vT9XOm9VWAOAOCU9hcDPEFGsack9AzVKWpHklMxX35CiA4X7Ksa7LHPWUDeZtKX3j2DSyavX_THyI4Bz6Ptfu-G-3-di6QONsM1f8kh40qELlynJWr7X-qV9ti8hvbV6M) +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/)_ ![No photo description available.](https://scontent.fgau3-1.fna.fbcdn.net/v/t1.0-9/s960x960/67842987_2309735785809363_3830016113882693632_o.jpg?_nc_cat=101&_nc_oc=AQm74VYRk_p9ARtE5OLImFJCu8MxugqdsQ55hIVnqJnTXHznMYznmJQHelCqxSxfAes&_nc_ht=scontent.fgau3-1.fna&oh=58c849b2e805e6e004f10d37e9558771&oe=5E56663C) 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/). ![](https://lh4.googleusercontent.com/DySsict0S9ROodG_qjzQ20qLu77TEoYYPsQVL-86m0XjsUUGSp9KFcemiKK-0v7ev2iNVeWBEt5pUa-wP47lUg3BMjbRZ28ADD3E4u2ft4vZaLOz2y-Mun9uQfuRRpImJYXkEQtU) -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/ --- ![](/wp-content/uploads/2019/02/farah-presentation.jpg)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. -![](https://lh7-rt.googleusercontent.com/docsz/AD_4nXdvZDIeHR5Gegera5ClPE4hs9LLTwFoJ1jCfBYzLwCJoO-XYbGnQ_tr_gZWc1cDn6iUynXQ5N8Nxgf6p0f3GBspZ_w0886oDwp5n_ktD6dnB82mGzZg7RqIko4KtzqDDTUxSP8L1AknnDRcmeU-buo6G9bn?key=KYQfERLZnhhk-DQ5svV-Bw) +![](https://lh7-rt.googleusercontent.com/docsz/AD_4nXdvZDIeHR5Gegera5ClPE4hs9LLTwFoJ1jCfBYzLwCJoO-XYbGnQ_tr_gZWc1cDn6iUynXQ5N8Nxgf6p0f3GBspZ_w0886oDwp5n_ktD6dnB82mGzZg7RqIko4KtzqDDTUxSP8L1AknnDRcmeU-buo6G9bn?key=KYQfERLZnhhk-DQ5svV-Bw) _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. ![](https://lh5.googleusercontent.com/t0YzIrVivPm7UuWqaYPNOuCeRgyLTFpVncqziSrg8JD009-vxDXkKqsPBm4BOZQYtHgS6s82Ap9i3H2WqUWKjc7cUFasO7SjkdTgmc1u1Rn3x1GDaIOGHZkYCwUW4WlmDYsNPCNW2ZrEEYO569ZKwA) @@ -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. -![](https://lh4.googleusercontent.com/IND_tgHCmknXDXUwmVK-IxpHuGndNgWBA6asSZlt-uwMV2_LmXQDzwPIVkizK9tpanA3c_Px5ZL46se929xKEXqMWxS1hxzYH5LdYCkWhP-g_VCA4aEu63koTF3FeJAn1V_VUFHPkaffUG38FWuTuA) +![](https://lh4.googleusercontent.com/IND_tgHCmknXDXUwmVK-IxpHuGndNgWBA6asSZlt-uwMV2_LmXQDzwPIVkizK9tpanA3c_Px5ZL46se929xKEXqMWxS1hxzYH5LdYCkWhP-g_VCA4aEu63koTF3FeJAn1V_VUFHPkaffUG38FWuTuA) **_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. -![](/wp-content/uploads/2024/07/IMG_1711-scaled.jpg) +![](/wp-content/uploads/2024/07/IMG_1711-scaled.jpg) _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. -![](/wp-content/uploads/2024/07/IMG_1563-scaled.jpg) +![](/wp-content/uploads/2024/07/IMG_1563-scaled.jpg) _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. -![](/wp-content/uploads/2024/07/IMG_1518-scaled.jpg) +![](/wp-content/uploads/2024/07/IMG_1518-scaled.jpg) _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) From 1967bb2b3530783ab8e375b8152fd23c9b97ff03 Mon Sep 17 00:00:00 2001 From: "Peter J. A. Cock" Date: Thu, 4 Dec 2025 12:35:22 +0000 Subject: [PATCH 4/4] Basic pre-commit hooks inc max 500kb file size (for images esp) --- .pre-commit-config.yaml | 13 +++++++++++++ 1 file changed, 13 insertions(+) create mode 100644 .pre-commit-config.yaml 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']