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From: Peter C. <p.j...@go...> - 2024-07-24 15:43:09
|
Well done Scott - I was following some of this effort on Mastodon, having made similar efforts although not on quite the same scale with various OBF MediaWiki sites. And best wishes for your new role; you can be very proud of what you have helped GMOD to achieve! Peter On Tue, Jul 23, 2024 at 9:42 PM Fields, Christopher J <cjf...@il...> wrote: > Hi Scott, I just wanted to say a tremendous ‘thank you’ for essentially > leading GMOD efforts over the last 20+ years. Wow, has it been that > long!?! (I’m getting old). You should be incredibly proud of the work you > and all GMOD projects and developers have accomplished; it’s a tremendous > accomplishment. > > > > Hope to see you still out there somewhere in the open-bio world, and best > of luck on your next steps in your career! > > > > Best, > > > > Chris > > > > > > *From: *Scott Cain <sc...@sc...> > *Date: *Tuesday, July 23, 2024 at 1:19 PM > *To: *gmod-announce <gmo...@li...>, gmod-devel < > gmo...@li...>, gmod-ajax < > gmo...@li...>, GMOD Tripal < > gmo...@li...>, Gbrowse (E-mail) < > gmo...@li...>, GMOD Schema/Chado List < > gmo...@li...> > *Subject: *[Gmod-gbrowse] Server change for gmod.org and an announcement > > Hello all, > > > > For several years, I've wanted to port the gmod.org > <https://urldefense.com/v3/__http:/gmod.org__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLtXG8hWZg$> > MediaWiki instance to something else but was daunted by the task. Events > have finally conspired to force me to do it, so I've spent the last month > porting the content at gmod.org > <https://urldefense.com/v3/__http:/gmod.org__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLtXG8hWZg$> > to a github.io > <https://urldefense.com/v3/__http:/github.io__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLtQUw79P0$> > hosted page. It was a real slog, but thank goodness for recursive wget, > Pandoc and command line Perl to allow me to change thousands of markdown > files at a time. > > > > Since gmod.org > <https://urldefense.com/v3/__http:/gmod.org__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLtXG8hWZg$> > is now hosted at github.io > <https://urldefense.com/v3/__http:/github.io__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLtQUw79P0$>, > changes to this page can now be made with commits to the > https://github.com/GMOD/gmod.github.io > <https://urldefense.com/v3/__https:/github.com/GMOD/gmod.github.io__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLtU5TvTYs$> > repo. That means that fixes and additions can be made by creating and > editing markdown files in the gmod.github.io > <https://urldefense.com/v3/__http:/gmod.github.io__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLtViLqSVk$> > repo and merging the changes into the main branch. > > > > AND NOW THE ANNOUNCEMENT > > > > At the end of July, I will be stepping away from my role as GMOD project > coordinator, which on one hand, makes me very sad, but on the other, fills > me with immense pride in what we as the GMOD community have achieved over > the last 22 years. We have truly democratized organism genomics, allowing a > small lab to distribute data on whatever organisms are of interest to them > with (relatively) little effort. We can compare that to the MODs that > existed in the early aughts, that had staffs of many software developers to > make the same thing happen. We all did that, and I think the world is a > better place for it. > > > > I can't say yet where I'm going, as I have a few opportunities on the > table that haven't been finalized, but I hope to be fulfilling a similar > role in another community. If you're really interested, you can follow me > on Mastodon at @sco...@ge...cial. > > > > Thank you to all of you--I have really enjoyed working with and growing > this community, > > Scott > > > > > -- > > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott > at scottcain dot net > > GMOD Project Manager (http://gmod.org/ > <https://urldefense.com/v3/__http:/gmod.org/__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLt_a75Ac4$>) > 216-392-3087 > > WormBase Developer (http://wormbase.org/ > <https://urldefense.com/v3/__http:/wormbase.org/__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLtqyOTGjk$> > ) > > Alliance of Genome Resources Group Leader (http://alliancegenome.org/ > <https://urldefense.com/v3/__http:/alliancegenome.org/__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLtfgzLlII$> > ) > > VirusSeq Project Manager (https://virusseq-dataportal.ca/ > <https://urldefense.com/v3/__https:/virusseq-dataportal.ca/__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLt7Qo4Y2Y$> > ) > > Human Cancer Models Initiative Project Manager ( > https://hcmi-searchable-catalog.nci.nih.gov/ > <https://urldefense.com/v3/__https:/hcmi-searchable-catalog.nci.nih.gov/__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLtmGSQ6iE$> > ) > _______________________________________________ > Gmod-gbrowse mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > |
|
From: Fields, C. J <cjf...@il...> - 2024-07-23 20:42:03
|
Hi Scott, I just wanted to say a tremendous ‘thank you’ for essentially leading GMOD efforts over the last 20+ years. Wow, has it been that long!?! (I’m getting old). You should be incredibly proud of the work you and all GMOD projects and developers have accomplished; it’s a tremendous accomplishment. Hope to see you still out there somewhere in the open-bio world, and best of luck on your next steps in your career! Best, Chris From: Scott Cain <sc...@sc...> Date: Tuesday, July 23, 2024 at 1:19 PM To: gmod-announce <gmo...@li...>, gmod-devel <gmo...@li...>, gmod-ajax <gmo...@li...>, GMOD Tripal <gmo...@li...>, Gbrowse (E-mail) <gmo...@li...>, GMOD Schema/Chado List <gmo...@li...> Subject: [Gmod-gbrowse] Server change for gmod.org and an announcement Hello all, For several years, I've wanted to port the gmod.org<https://urldefense.com/v3/__http:/gmod.org__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLtXG8hWZg$> MediaWiki instance to something else but was daunted by the task. Events have finally conspired to force me to do it, so I've spent the last month porting the content at gmod.org<https://urldefense.com/v3/__http:/gmod.org__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLtXG8hWZg$> to a github.io<https://urldefense.com/v3/__http:/github.io__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLtQUw79P0$> hosted page. It was a real slog, but thank goodness for recursive wget, Pandoc and command line Perl to allow me to change thousands of markdown files at a time. Since gmod.org<https://urldefense.com/v3/__http:/gmod.org__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLtXG8hWZg$> is now hosted at github.io<https://urldefense.com/v3/__http:/github.io__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLtQUw79P0$>, changes to this page can now be made with commits to the https://github.com/GMOD/gmod.github.io<https://urldefense.com/v3/__https:/github.com/GMOD/gmod.github.io__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLtU5TvTYs$> repo. That means that fixes and additions can be made by creating and editing markdown files in the gmod.github.io<https://urldefense.com/v3/__http:/gmod.github.io__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLtViLqSVk$> repo and merging the changes into the main branch. AND NOW THE ANNOUNCEMENT At the end of July, I will be stepping away from my role as GMOD project coordinator, which on one hand, makes me very sad, but on the other, fills me with immense pride in what we as the GMOD community have achieved over the last 22 years. We have truly democratized organism genomics, allowing a small lab to distribute data on whatever organisms are of interest to them with (relatively) little effort. We can compare that to the MODs that existed in the early aughts, that had staffs of many software developers to make the same thing happen. We all did that, and I think the world is a better place for it. I can't say yet where I'm going, as I have a few opportunities on the table that haven't been finalized, but I hope to be fulfilling a similar role in another community. If you're really interested, you can follow me on Mastodon at @sco...@ge...cial. Thank you to all of you--I have really enjoyed working with and growing this community, Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Project Manager (http://gmod.org/<https://urldefense.com/v3/__http:/gmod.org/__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLt_a75Ac4$>) 216-392-3087 WormBase Developer (http://wormbase.org/<https://urldefense.com/v3/__http:/wormbase.org/__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLtqyOTGjk$>) Alliance of Genome Resources Group Leader (http://alliancegenome.org/<https://urldefense.com/v3/__http:/alliancegenome.org/__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLtfgzLlII$>) VirusSeq Project Manager (https://virusseq-dataportal.ca/<https://urldefense.com/v3/__https:/virusseq-dataportal.ca/__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLt7Qo4Y2Y$>) Human Cancer Models Initiative Project Manager (https://hcmi-searchable-catalog.nci.nih.gov/<https://urldefense.com/v3/__https:/hcmi-searchable-catalog.nci.nih.gov/__;!!DZ3fjg!52Q62W3iW7xVMDtjuX8aI0ERASShyuFSzx1QhGHzTs0rUDwEQEseN2Y1pAcT-BvCXZ256zzVDXLtmGSQ6iE$>) |
|
From: Scott C. <sc...@sc...> - 2024-07-23 18:26:39
|
Hello all, For several years, I've wanted to port the gmod.org MediaWiki instance to something else but was daunted by the task. Events have finally conspired to force me to do it, so I've spent the last month porting the content at gmod.org to a github.io hosted page. It was a real slog, but thank goodness for recursive wget, Pandoc and command line Perl to allow me to change thousands of markdown files at a time. Since gmod.org is now hosted at github.io, changes to this page can now be made with commits to the https://github.com/GMOD/gmod.github.io repo. That means that fixes and additions can be made by creating and editing markdown files in the gmod.github.io repo and merging the changes into the main branch. AND NOW THE ANNOUNCEMENT At the end of July, I will be stepping away from my role as GMOD project coordinator, which on one hand, makes me very sad, but on the other, fills me with immense pride in what we as the GMOD community have achieved over the last 22 years. We have truly democratized organism genomics, allowing a small lab to distribute data on whatever organisms are of interest to them with (relatively) little effort. We can compare that to the MODs that existed in the early aughts, that had staffs of many software developers to make the same thing happen. We all did that, and I think the world is a better place for it. I can't say yet where I'm going, as I have a few opportunities on the table that haven't been finalized, but I hope to be fulfilling a similar role in another community. If you're really interested, you can follow me on Mastodon at @sco...@ge...cial. Thank you to all of you--I have really enjoyed working with and growing this community, Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Project Manager (http://gmod.org/) 216-392-3087 WormBase Developer (http://wormbase.org/) Alliance of Genome Resources Group Leader (http://alliancegenome.org/) VirusSeq Project Manager (https://virusseq-dataportal.ca/) Human Cancer Models Initiative Project Manager ( https://hcmi-searchable-catalog.nci.nih.gov/) |
|
From: Scott C. <sc...@sc...> - 2023-04-14 16:41:39
|
Highlights - Submit <https://www.open-bio.org/events/bosc-2023/submit/> your 1-2 page abstract by April 20 (by the end of the day anywhere in the world). (Sorry, no extensions.) - You can request registration fee assistance right on the submission form! - We have two exciting Keynote Speakers <https://www.open-bio.org/events/bosc-2023/bosc-2023-keynotes/> lined up! - We are planning a Panel Discussion about Open and Ethical Data Sharing! - BOSC and Bio-Ontologies <https://www.bio-ontologies.org.uk/ismb-annual-meeting/2023-meeting> will join forces for a joint session on July 24 or 25. - We welcome our first sponsors <https://www.open-bio.org/events/sponsors/> (more coming soon): GigaScience <https://academic.oup.com/gigascience>, GeneVia <https://geneviatechnologies.com/>, and Software Sustainability Institute <https://www.software.ac.uk/>! Keynote speakers [image: Sara El-Gebali] Sara El-Gebali <https://www.open-bio.org/events/bosc-2023/bosc-2023-keynotes/> (SciLifeLab-DataCentre-Sweden): “A New Odyssey: Pioneering the Future of Scientific Progress Through Open Collaboration.” Joseph M. Yracheta <https://www.open-bio.org/events/bosc-2023/bosc-2023-keynotes/> (Native BioData Consortium): “The Dissonance between Scientific Altruism & Capitalist Extraction: The Zero Trust and Federated Data Sovereignty Solution Abstract submission We encourage you to submit abstracts <https://www.open-bio.org/events/bosc-2023/submit/> (due April 20 – sorry, no extensions) on any topic relevant to open source bioinformatics or open science (see topic list below). After review, some abstracts will be selected for lightning talks, longer talks, or posters. A second “late poster” round of submissions will end May 18. Abstract submission is via ISMB’s EasyChair (linked from our submission page <https://www.open-bio.org/events/bosc-2023/submit/>). Note that ISMB requires a short (200-word) text-only abstract for all submissions (talk or poster), plus a “long abstract” (PDF, 2 pages max) if you want to be considered for a talk. About BOSC Since 2000, the Bioinformatics Open Source Conference <https://www.open-bio.org/events/bosc-2021/about/> has provided a forum for developers and users to interact and share research results and ideas in open source bioinformatics and open science. As usual, BOSC 2023 <https://www.open-bio.org/events/bosc-2023/> will include keynote talks, longer and shorter (lightning) talks from submitted abstracts, posters, Birds of a Feather, and more! Like last year, BOSC and Bio-Ontologies <https://www.bio-ontologies.org.uk/ismb-annual-meeting/2023-meeting> will join forces for a joint session. BOSC topics include (but are not limited to): - Open Science and Reproducible Research - Open Biomedical Data - Citizen/Participatory Science - Standards and Interoperability - Data Science - Workflows - Open Approaches to Translational Bioinformatics - Open Science for Global Health - Developer Tools and Libraries - Inclusion, Outreach and Training - Bioinformatics Open Source Project Reports (about new or existing projects) - Open and interoperable ontologies (joint session with Bio-Ontologies) Registration fee assistance We realize that the cost of ISMB may be prohibitive for some. If you are submitting an abstract to BOSC and would have difficulty covering the cost of registration, you can request to be considered for a registration fee waiver right on the abstract submission form (your request will not be seen by reviewers). Fee waivers are made possible by our sponsors <https://www.open-bio.org/events/sponsors/>. Sponsors We welcome the first Silver sponsors <https://www.open-bio.org/events/sponsors/> of BOSC 2023! If you’re interested in becoming a sponsor, let us know! [image: Gigascience] <https://academic.oup.com/gigascience> <https://geneviatechnologies.com/> <https://www.software.ac.uk/> ------------------------------ Key Dates - April 20, 2023: Deadline for submitting talk/poster abstracts <https://www.open-bio.org/events/bosc-2023/submit/> - May 11: Talk/poster acceptance notifications - May 18: Late poster submission deadline - May 25: Late poster acceptance notifications - July 24-25: BOSC 2023 <https://www.open-bio.org/events/bosc-2023/> (part of ISMB/ECCB 2023 in Lyon, France, and online) - CollaborationFest <https://www.open-bio.org/events/bosc-2023/obf-bosc-collaborationfest-2023/> (CoFest) – July 22-23 (Lyon, France, and online) Join our community! - BOSC announcements mailing list: <http://lists.open-bio.org/mailman/listinfo/bosc-announce> https://groups.google.com/forum/#!forum/bosc-announce - Slack: https://join.slack.com/t/obf-bosc/shared_invite/zt-n5ur1gsj-z2C~69_4lYTFPg5tbWA8Ew - Twitter: @OBF_BOSC <https://twitter.com/OBF_BOSC>, #BOSC2023 - Mastodon: https://genomic.social/@BOSC - Website: <https://www.open-bio.org/wiki/BOSC_2019> https://www.open-bio.org/events/bosc/ ------------------------------ We look forward to reading your abstract and seeing you (in person or virtually) at BOSC 2023! Sincerely, BOSC 2023 Organizing Committee (Nomi Harris, Karsten Hokamp, Hervé Ménager, Monica Munoz-Torres, Deepak Unni, Jason Williams, Chris Fields, Jessica Maia, Radhika Khetani) -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Project Manager (http://gmod.org/) 216-392-3087 WormBase Developer (http://wormbase.org/) Alliance of Genome Resources Group Leader (http://alliancegenome.org/) VirusSeq Project Manager (https://virusseq-dataportal.ca/) Human Cancer Models Initiative Project Manager ( https://hcmi-searchable-catalog.nci.nih.gov/) |
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From: Robin H. <Rob...@oi...> - 2023-02-24 19:52:58
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Good news, the Open Genome Informatics group was accepted to participate in Google Summer of Code 2023. If anyone in your lab/team has project ideas and is interested in mentoring, please ask them to reach out or they can also submit your ideas here<https://can01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fgmod.org%2Fwiki%2FGSOC_Project_Ideas_2023&data=05%7C01%7CRobin.Haw%40oicr.on.ca%7C9cb8522af5ce45af0a1408db03446d82%7C9df949f8a6eb419d9caa1f8c83db674f%7C0%7C0%7C638107364656556895%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=wNofkMqnucDhtBbykI3lX%2FLv3fYMUdlOwZjieZ2FrzE%3D&reserved=0>. Thanks, Robin From: Robin Haw <Rob...@oi...> Date: Monday, January 30, 2023 at 11:34 PM To: Michelle Brazas <Mic...@oi...>, Lincoln Stein <lin...@gm...>, Philip Awadalla <Phi...@oi...>, Sagi Abelson <Sag...@oi...>, Juri Reimand <Jur...@oi...>, Shraddha Pai <Shr...@oi...>, Jared Simpson <Jar...@oi...>, Ian Holmes <ihh...@gm...>, Robert Buels <rb...@gm...>, Melanie Courtot <Mel...@oi...>, Morgan Taschuk <Mor...@oi...>, Denis Yuen <Den...@oi...>, David Sutton <DS...@oi...>, Gino Yearwood <Gin...@oi...>, bio...@li... <bio...@li...>, soft-eng <sof...@oi...>, rea...@re... Developers <rea...@re...>, Galaxy Dev List <gal...@li...>, jbr...@li... <jbr...@li...>, gmo...@li... <gmo...@li...>, gmo...@li... <gmo...@li...> Cc: Scott Cain <sc...@sc...>, Marc Gillespie <gil...@gm...>, Robin Haw <Rob...@oi...> Subject: [GSoC 2023] Announcing Google Summer of Code 2023 - Open Genome Informatics organization application due 7th February Dear All, Last week, Google announced this years’ Google Summer of Code (GSoC). GSoC is a global, online program focused on bringing new contributors into open source software development. GSoC contributors work with an open source organization on a 12+ week programming project under the guidance of mentors. The Open Genome Informatics team, which I administer with the help of Scott Cain and Marc Gillespie, serves as an “umbrella" organization to support the efforts of many open-access open-source bioinformatics projects for Google Summer of Code (GSoC<https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsummerofcode.withgoogle.com%2F&data=05%7C01%7CRobin.Haw%40oicr.on.ca%7C9cb8522af5ce45af0a1408db03446d82%7C9df949f8a6eb419d9caa1f8c83db674f%7C0%7C0%7C638107364656556895%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=18JNgvFrXaKl9%2FctWMXSc78v26b8XSv1ZExxiI5Ho0Y%3D&reserved=0>). The list of previously involved projects includes JBrowse, Reactome, Galaxy, WormBase, and others. Over the last 12 years, we have been submitting applications to particiapte in GSoC. We are seeking project ideas to post and attract talented contributors to this years’ Summer of Code competition. If you have a project idea for which you would like to mentor a student, please contact me, Marc or Scott. You can also submit your ideas here<https://can01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fgmod.org%2Fwiki%2FGSOC_Project_Ideas_2023&data=05%7C01%7CRobin.Haw%40oicr.on.ca%7C9cb8522af5ce45af0a1408db03446d82%7C9df949f8a6eb419d9caa1f8c83db674f%7C0%7C0%7C638107364656556895%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=wNofkMqnucDhtBbykI3lX%2FLv3fYMUdlOwZjieZ2FrzE%3D&reserved=0>. For more information, please refer to the Open Genome Informatics page on the GMOD.org website<https://can01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fgmod.org%2Fwiki%2FGSoC&data=05%7C01%7CRobin.Haw%40oicr.on.ca%7C9cb8522af5ce45af0a1408db03446d82%7C9df949f8a6eb419d9caa1f8c83db674f%7C0%7C0%7C638107364656556895%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=ttJnCiYqnFkkJ%2BDR66%2Bk9gPybSuv750clP5uXGVmf6o%3D&reserved=0>. The program is open to students and to beginners in open source software development. The length of the projects is 175 and 350-hours, and there is an option to extend the program from the standard 12 weeks up to 22 weeks. Applications for organizations will close on February 7, 2023 at 18:00 UTC. So, if you are interested in taking part with the team, please let us know as soon as possible. Please forward this to others who might be interested in taking part. If you have any questions, please let us know. Thanks, Robin, Scott, and Marc Robin Haw, PhD Program Manager – Genome Informatics and Computational Biology Tel: 647-260-7985 rob...@oi...<mailto:rob...@oi...> Adaptive Oncology Ontario Institute for Cancer Research MaRS Centre, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3 @OICR_news | oicr.on.ca<https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Foicr.on.ca%2F&data=05%7C01%7CRobin.Haw%40oicr.on.ca%7C9cb8522af5ce45af0a1408db03446d82%7C9df949f8a6eb419d9caa1f8c83db674f%7C0%7C0%7C638107364656556895%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=YJtyurNort6ADlFrUiWArCX7kTbFXnT274ksFnddslI%3D&reserved=0> | genome informatics<https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Foicr.on.ca%2Fprograms%2Fgenome-informatics%2F&data=05%7C01%7CRobin.Haw%40oicr.on.ca%7C9cb8522af5ce45af0a1408db03446d82%7C9df949f8a6eb419d9caa1f8c83db674f%7C0%7C0%7C638107364656556895%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=hMIZJ2tHiRyFXIMI3%2F0Q2Qql%2FDC12nyhL1r9IyYIPZk%3D&reserved=0> | computational biology<https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Foicr.on.ca%2Fprograms%2Fcomputational-biology%2F&data=05%7C01%7CRobin.Haw%40oicr.on.ca%7C9cb8522af5ce45af0a1408db03446d82%7C9df949f8a6eb419d9caa1f8c83db674f%7C0%7C0%7C638107364656556895%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Kba4MKXEzvpO1aAtJsMxqZy5j6%2BkXesSdUR%2B0iF0hbY%3D&reserved=0> Collaborate. Translate. Change lives. This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization. |
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From: Robin H. <Rob...@oi...> - 2023-01-31 07:07:52
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Dear All, Last week, Google announced this years’ Google Summer of Code (GSoC). GSoC is a global, online program focused on bringing new contributors into open source software development. GSoC contributors work with an open source organization on a 12+ week programming project under the guidance of mentors. The Open Genome Informatics team, which I administer with the help of Scott Cain and Marc Gillespie, serves as an “umbrella" organization to support the efforts of many open-access open-source bioinformatics projects for Google Summer of Code (GSoC<https://summerofcode.withgoogle.com/>). The list of previously involved projects includes JBrowse, Reactome, Galaxy, WormBase, and others. Over the last 12 years, we have been submitting applications to particiapte in GSoC. We are seeking project ideas to post and attract talented contributors to this years’ Summer of Code competition. If you have a project idea for which you would like to mentor a student, please contact me, Marc or Scott. You can also submit your ideas here<http://gmod.org/wiki/GSOC_Project_Ideas_2023>. For more information, please refer to the Open Genome Informatics page on the GMOD.org website<http://gmod.org/wiki/GSoC>. The program is open to students and to beginners in open source software development. The length of the projects is 175 and 350-hours, and there is an option to extend the program from the standard 12 weeks up to 22 weeks. Applications for organizations will close on February 7, 2023 at 18:00 UTC. So, if you are interested in taking part with the team, please let us know as soon as possible. Please forward this to others who might be interested in taking part. If you have any questions, please let us know. Thanks, Robin, Scott, and Marc Robin Haw, PhD Program Manager – Genome Informatics and Computational Biology Tel: 647-260-7985 rob...@oi...<mailto:rob...@oi...> Adaptive Oncology Ontario Institute for Cancer Research MaRS Centre, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3 @OICR_news | oicr.on.ca<https://oicr.on.ca/> | genome informatics<https://oicr.on.ca/programs/genome-informatics/> | computational biology<https://oicr.on.ca/programs/computational-biology/> Collaborate. Translate. Change lives. This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization. |
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From: Scott C. <sc...@sc...> - 2022-03-23 04:26:46
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BOSC 2022 dates: July 13-14, as part of ISMB 2022 Location: Madison, WI, USA, and virtual Website: <https://www.open-bio.org/wiki/BOSC_2019> https://www.open-bio.org/events/bosc/ BOSC announcements mailing list: <http://lists.open-bio.org/mailman/listinfo/bosc-announce> https://groups.google.com/forum/#!forum/bosc-announce Slack channel: https://join.slack.com/t/obf-bosc/shared_invite/zt-n5ur1gsj-z2C~69_4lYTFPg5tbWA8Ew Twitter: @OBF_BOSC <https://twitter.com/OBF_BOSC>, #BOSC2022 Key Dates - April 21, 2022: Deadline for submitting talk/poster abstracts <https://www.open-bio.org/events/bosc-2022/submit/> - May 12: Talk/poster acceptance notifications - May 19: Late poster (and Late-Breaking Lightning Talk) submission deadline - May 26: Late poster / LBLT acceptance notifications - July 13-14: BOSC 2022 <https://www.open-bio.org/events/bosc-2022/> - July 15-16: CollaborationFest (CoFest) About BOSC The Bioinformatics Open Source Conference promotes and facilitates the open source development of bioinformatics tools and open science. Since 2000, BOSC has provided a forum for developers and users to interact and share research results and ideas in open source bioinformatics and open science. BOSC’s broad spectrum of topics includes practical techniques for solving bioinformatics problems; software development practices; standards and ontologies; approaches that promote open science and sharing of data, results and software; and ways to grow open source communities while promoting diversity within them. As usual, BOSC will include keynote talks, longer and shorter (lightning) talks from submitted abstracts, posters, Birds of a Feather, and more! New this year: Joint session with Bio-Ontologies <https://www.open-bio.org/2022/03/03/bosc-and-bio-ontologies-joint-session/> ! We are excited to announce that BOSC and Bio-Ontologies <https://www.bio-ontologies.org.uk/ismb-annual-meeting> will join forces for part of a day at ISMB 2022. The joint session will feature keynote speaker Melissa Haendel as well as talks chosen from abstracts submitted to BOSC or Bio-Ontologies. Keynote Speakers <https://open-bio.org/events/bosc-2022/bosc-2022-keynotes> Melissa Haendel is the Chief Research Informatics Officer at University of Colorado Anschutz Medical Campus, and Director of the Center for Data to Health (CD2H). With expertise in molecular genetics and developmental biology as well as translational informatics, Dr. Haendel focuses on open science and data integration to improve rare-disease diagnosis and mechanism discovery. She is a leader in ontologies and standards for data sharing. Lior Pachter is the Bren professor of computational biology at Caltech. He is a Fellow of the International Society of Computational Biology <https://www.iscb.org/iscb-fellows> and has been awarded a National Science Foundation CAREER award, a Sloan Research Fellowship His research interests span the mathematical and biological sciences, including algorithms, combinatorics, comparative genomics, algebraic statistics, molecular biology and evolution. Dr. Pachter is known as a vociferous advocate of open and accountable science. A third keynote speaker will be announced soon! Abstract submission We encourage you to submit abstracts <https://www.open-bio.org/events/bosc-2022/submit/> (due April 21 – sorry, no extensions) on any topic relevant to open source bioinformatics or open science. After review, some abstracts will be selected for lightning talks, longer talks, or posters. Abstracts that are not chosen for talks will automatically be considered for posters. Abstract submission will be via ISMB’s EasyChair. Note that ISMB/ECCB requires a short (200-word) text-only abstract for all submissions (talk or poster), plus a “long abstract” (PDF, 2 pages max) if you want to be considered for a talk. A second, later round of submissions will end May 19. Abstracts submitted in the late round will be considered only for posters and a limited number of “late-breaking lightning talk” slots; they are not eligible for longer talks. Registration fee assistance We realize that the cost of ISMB may be prohibitive for some. If you are submitting an abstract to BOSC and would have difficulty covering the cost of registration, you can request a registration fee waiver right on the abstract submission form (which will not be seen by reviewers). Those who are not submitting abstracts can apply for an OBF Event Fellowship <https://www.open-bio.org/event-awards/> (deadline April 1, 2022). BOSC topics include (but are not limited to): - Ontologies: Open Source Tools and Approaches (new this year – joint session with Bio-Ontologies COSI <http://www.bio-ontologies.org.uk/>) - Open Science and Reproducible Research - Open Biomedical Data - Citizen/Participatory Science - Standards and Interoperability - Data Science - Workflows - Open Approaches to Translational Bioinformatics - Open Science for Global Health - Developer Tools and Libraries - Inclusion, Outreach and Training - Bioinformatics Open Source Project Reports (about new or existing projects) - Open and interoperable ontologies (joint session with Bio-Ontologies <https://www.open-bio.org/2022/03/03/bosc-and-bio-ontologies-joint-session/> ) We look forward to reading your abstract and seeing you (in person or virtually) at BOSC 2022! Sincerely, BOSC 2022 Organizing Committee: Nomi Harris, Karsten Hokamp, Hervé Ménager, Monica Munoz-Torres, Deepak Unni, Nicole Vasilevsky, Jason Williams -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Project Manager (http://gmod.org/) 216-392-3087 WormBase Developer (http://wormbase.org/) Alliance of Genome Resources Group Leader (http://alliancegenome.org/) VirusSeq Project Manager (https://virusseq-dataportal.ca/) |
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From: Scott C. <sc...@sc...> - 2022-01-05 18:33:15
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Oh, I haven't touched this code in a very long time. Did you try what it suggested (ie, changing the 'defined(@array)' to just '@array')? If that doesn't work, I'll have to set up a fresh dev environment to work on this, which may take a little time. Are you by any chance using Tripal too? That might be a "faster" path to getting your data into the database. Scott On Wed, Jan 5, 2022 at 10:04 AM leben <821...@ca...> wrote: > When I use this script gmod_load_bulk_gff3.pl , I get an error,like this, > > Can't use 'defined(@array)' (Maybe you should just omit the defined()?) at > /usr/local/share/perl/5.26.1/Bio/GMOD/DB/Adapter.pm line 498. > Compilation failed in require at /usr/local/bin/gmod_bulk_load_gff3.pl > line 13. > BEGIN failed--compilation aborted at /usr/local/bin/gmod_bulk_load_gff3.pl > line 13. > > This is a perl compilation kernel error that disables defined(@array) > > I tried to change Perl to an older version, but it still didn't work. Is > there a solution? > > _______________________________________________ > Gmod-devel mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-devel > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Project Manager (http://gmod.org/) 216-392-3087 WormBase Developer (http://wormbase.org/) Alliance of Genome Resources Group Leader (http://alliancegenome.org/) VirusSeq Project Manager (https://virusseq-dataportal.ca/) |
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From: leben <821...@ca...> - 2022-01-05 09:43:36
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When I use this script gmod_load_bulk_gff3.pl , I get an error,like this, Can't use 'defined(@array)' (Maybe you should just omit the defined()?) at /usr/local/share/perl/5.26.1/Bio/GMOD/DB/Adapter.pm line 498. Compilation failed in require at /usr/local/bin/gmod_bulk_load_gff3.pl line 13. BEGIN failed--compilation aborted at /usr/local/bin/gmod_bulk_load_gff3.pl line 13. This is a perl compilation kernel error that disables defined(@array) I tried to change Perl to an older version, but it still didn't work. Is there a solution? |
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From: Meg S. <me...@gm...> - 2021-08-20 00:40:22
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Dear Researchers, Breeders, Database Providers, Funders, Editors, Students, Software Engineers, and other Scientists, *Do you want easy access to better quality data?* We are THRILLED to announce that AgBioData (https://www.agbiodata.org/) has received a three-year NSF RCN award to expand our community committed to improving quality and access to agricultural data. New activities will include organizing workshops, establishing new working groups, and developing FAIR curriculum for scientists. We are expanding the consortium and welcome new members, especially students, post-docs, big-data scientists, funding agency scientists and members of the scientific publishing community interested in solving common FAIR data issues. *We invite all of you to an important kickoff All-Hands Meeting on Sept 1st* at 10 am PDT (find your local time - https://bit.ly/389VeJA). At this meeting you will hear about our RCN objectives, the benefits of joining AgBioData, and how YOU can make a difference in the biological data environment for years to come. *Please pre-register* for this meeting at https://iastate.zoom.us/meeting/register/tJcld-iqqD4vE9awJKcFGnmHwxtCNc_a7UJM *We are also hiring a scientist to coordinate AgBioData activities*, outreach and curriculum development. Please help us publicize this opportunity! Applications should be submitted by August 31 to https://phoenix-bioinformatics.hirehive.com/job/83452/scientific-program-coordinator-newark?source=TAIR . Thank you! The AgBioData Steering Committee: Monica Poelchau, Sook Jung, Ethy Cannon, Jacqueline Campbell, Lisa Harper, Leonore Reiser, Marcela Tello-Ruiz, Laurel Cooper, Eva Hula, Meg Staton, and Darwin Campbell *About AgBioData:* https://www.agbiodata.org *AgBioData RCN*: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2126334 -- Margaret Staton Associate Professor Department of Entomology and Plant Pathology Office: 154 PBB Mail: 370 PBB, 2505 EJ Chapman Drive Knoxville, TN 37996-4560 she/her/hers 864-506-4515 Mobile mst...@ut... *Advanced Out of Office Notice* *October 11-15, 2021* |
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From: Scott C. <sc...@sc...> - 2021-07-27 20:36:25
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Hi, Here's a reminder that "today" (that is, tomorrow morning for me) there is a Birds of a Feather meeting to discuss GMOD topics at ISMB/BOSC, including JBrowse but other GMOD topics as well. The BoF starts at 15:20 UTC (7:20 PDT, 10:20 EDT) on July 28. If you are attending ISMB, please feel free to drop in and chat about good stuff you're doing or want to do: https://ismbeccb2021.showcare.io/sessions/28-3-bof/ Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
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From: Scott C. <sc...@sc...> - 2021-07-21 17:53:57
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Hello, If you are attending BOSC or any other ISCM meeting next week, please feel free to come to the GMOD/JBrowse Birds of a Feather on Wednesday, July 28 from 15:20 to 16:20 UTC (yes, that is 7:20 AM west coast US time). Several GMOD folks will be there; you can talk about new developments with JBrowse 2 or discuss any of several other GMOD components. https://www.iscb.org/ismbeccb2021-program/bof#bof4 The meeting will take place in the Research Exchange Forum, which hopefully will make sense when attending the meeting! :-) See you all next week! Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
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From: Dave C. <cle...@ga...> - 2021-06-07 04:29:06
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Hi all, Some updates: - 8 June: Early reg ends (save 50%) - 14 June: Poster/Demo abstract deadline - 25 June: All registration closes - 28 June GCC training week starts. - The full talk schedule is now online <https://gcc2021.sched.com/>. Please redistribute to any communities that might be interested, and hope to see you there, Dave C *2021 Galaxy Community Conference (GCC2021)* <https://www.vibconferences.be/events/gcc2021-virtual-edition> 28 June through 10 July <https://gcc2021.sched.com/> Virtual, in both European Central Time, and US Eastern Time Deadlines 8 June: Early Registration closes <https://galaxyproject.org/news/2021-05-gcc-reg/> 14 June: Poster/Demo submission deadline <https://galaxyproject.org/news/2021-05-gcc-posterdemo/> 17 June: GCC2021 CoFest Prep Day <https://galaxyproject.org/events/2021-06-papercuts/> 25 June: All registration closes *About GCC2021* The 2021 Galaxy Community Conference <https://www.vibconferences.be/events/gcc2021-virtual-edition> will take place in a virtual format from 28 June to 10 July and bring together clinicians, researchers and students working in data science. The event features - 5 days of online training (28 June - 2 July) - a 3 day meeting (6-8 July) - a 2 day CollaborationFest (9-10 July) * The combination of very low registration, plus content in multiple time zones (see below for details on both) make this event the most affordable and accessible GCC ever. * If you are working in data intensive science (life sciences and beyond), GCC2021 is an ideal conference to share your work, learn from others, and find new collaborators. We look forward to meeting you there! *About Galaxy* Galaxy <https://galaxyproject.org/> is an open data integration and analysis platform used and supported by a global community of researchers, bioinformaticians, developers, infrastructure providers, and trainers, all doing and supporting data intensive research Galaxy was originally developed to support life science research, but is now used in multiple fields including computational chemistry and molecular modelling, climate modeling, social science, and natural language processing. *Training Week* Training <https://galaxyproject.org/events/gcc2021/training/> will run for 5 days, from 28 June through 2 July. This will be an online event, spanning all time zones. All training sessions are pre-recorded, so you can work through them at your own pace, and manage your own time. A large community of GTN trainers will be available 24/7 online support to answer all your questions on Slack. Training Week features 3 tracks: 1. Galaxy for Scientists <https://galaxyproject.org/events/gcc2021/training/#science-track> 2. Galaxy for Developers <https://galaxyproject.org/events/gcc2021/training/#developer-track> 3. Galaxy for Administrators <https://galaxyproject.org/events/gcc2021/training/#admin-track> (enrollment is limited) *GCC2021 Meeting* The conference includes a 3 day meeting, 8-10 July, and features accepted talks, Q&A, poster/demos, sponsors, birds-of-a-feather sessions, and lots of social interaction and networking. Talks will be pre-recorded, but EVERYTHING else, including Q&A will be live. *All material will be presented twice each day, once in the original Central European time zone, and then again 9 hours later in the Americas. * * Poster/Demo Abstract Submission* We welcome poster/demo submissions <https://galaxyproject.org/news/2021-05-gcc-posterdemo/> that use, implement or extend the Galaxy platform and ecosystem, including integrating and analyzing datasets in any research area, enhancing reproducibility in computational analyses, and fostering collaboration in scientific workflow development Poster/Demos will be presented live at Remo.co tables and will not be limited to a single large PDF. They are an opportunity to fully communicate your work. Submit your abstract by 14 June <https://www.vibconferences.be/events/gcc2021-virtual-edition#abstracts> * Registration* Registration rates are very affordable <https://galaxyproject.org/news/2021-04-gcc-reg/>, with deep discounts for researchers and students, and especially for researchers and students in developing economies. Early registration rates for students in developing economies start at €3.25 for Training Week, and €6.00 for the meeting (plus VAT). *Early registration ends 1 June.* -- https://galaxyproject.org/ |
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From: Dave C. <cle...@ga...> - 2021-05-06 18:47:23
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Hi All, There is a webinar next Wednesday, May 12, that might be of interest to this group: Galaxy Resources for Tool Developers <https://galaxyproject.org/events/2021-05-gr4-tool-devs> Dan Blankenberg will introduce resources for defining your tools for the Galaxy ecosystem, so that anyone running a Galaxy instance can easily use your tools. Anthony Bretaudeau will highlight resources for making your tool easily accessible to researchers in Docker-based Galaxy containers, and Petr Novak will talk about making your tools available by setting up your own publicly accessible Galaxy server. The webinar is at 10am US Eastern, 4pm European Central. *See your time <https://www.timeanddate.com/worldclock/fixedtime.html?msg=Galaxy+Resources+for+Tool+Developers+Webinar&iso=20210512T10&p1=419&ah=1>.* Finally, see this preprint <https://www.biorxiv.org/content/10.1101/2020.11.16.385211v1> for why you might want to get your tools into Galaxy (and other platforms too). Please let me know if you have any questions, and hope to see you there. Cheers, Dave C -- https://galaxyproject.org/ |
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From: Scott C. <sc...@sc...> - 2021-05-04 21:15:49
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Don't forget to get your abstracts in for BOSC! ---------- Forwarded message --------- From: BOSC, the Bioinformatics Open Source Conference < bos...@gm...> Date: Tue, May 4, 2021 at 1:50 PM Subject: [bosc-announce] Reminder: BOSC abstract deadline is May 6! To: <bos...@go...> <https://www.open-bio.org/events/bosc/> The BOSC 2021 abstract submission <https://www.open-bio.org/events/bosc-2021/submit/> deadline is May 6th; see our announcement <https://www.open-bio.org/2021/03/24/join-us-at-bosc-2021/> for more info. This year’s BOSC is a track of ISMB/ECCB 2021 online <https://www.iscb.org/ismbeccb2021/>. What time on May 6th is the deadline? The official ISMB/ECCB deadline is 11:59pm EDT on May 6 (which is 03:59 UTC on May 7), but we convinced them to let us keep submissions for BOSC open until 11:59pm Hawaii time (which is six hours later, 09:59 UTC on May 7). We are unfortunately unable to grant any additional extensions. Late Poster deadline is June 3. If you can’t make the May 6th submission deadline, we encourage you to submit for a Late Poster (deadline June 3). As space permits, we will choose a few Late Poster submissions for Late-Breaking Lightning Talks. Fee assistance. Just check a box on the abstract submission form to request registration fee assistance! Join us on Slack! Our BOSC Slack workspace <https://join.slack.com/t/obf-bosc/shared_invite/zt-n5ur1gsj-z2C~69_4lYTFPg5tbWA8Ew> is open to the community! Follow us on Twitter! @OBF_BOSC <http://twitter.com/OBF_BOSC>, #BOSC2021 -- You received this message because you are subscribed to the Google Groups "bosc-announce" group. To unsubscribe from this group and stop receiving emails from it, send an email to bos...@go.... To view this discussion on the web visit https://groups.google.com/d/msgid/bosc-announce/CAK27n1fyqV9KP1pR%2BOdYh%3D5rW%2BGdah-KQPJajCUxMMKXgqADZQ%40mail.gmail.com <https://groups.google.com/d/msgid/bosc-announce/CAK27n1fyqV9KP1pR%2BOdYh%3D5rW%2BGdah-KQPJajCUxMMKXgqADZQ%40mail.gmail.com?utm_medium=email&utm_source=footer> . -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
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From: Dave C. <cle...@ga...> - 2021-05-04 02:07:25
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Hello all, Please consider participating in GCC2021, and redistributing this to any of your communities that might be interested. Thanks, Dave C PS: And BOSC (part of ISMB/ECCB 2021) abstracts are due this Thursday. Please consider presenting your work there too. *2021 Galaxy Community Conference (GCC2021)* <https://www.vibconferences.be/events/gcc2021-virtual-edition> 28 June through 10 July <https://gcc2021.sched.com/> Virtual, in both European Central Time, and US Eastern Time Deadlines 7 May: Abstracts due <https://galaxyproject.org/news/2021-04-gcc-abstracts/> 7 May: Galaxy Community Fund Fellowship applications due <https://galaxyproject.org/news/2021-04-gcc-fellowships/> 1 June: Early registration ends <https://galaxyproject.org/news/2021-04-gcc-reg/> *About GCC2021* The 2021 Galaxy Community Conference <https://www.vibconferences.be/events/gcc2021-virtual-edition> will take place in a virtual format from 28 June to 10 July and bring together clinicians, researchers and students working in data science. The event features - 5 days of online training (28 June - 2 July) - a 3 day meeting (6-8 July) - a 2 day CollaborationFest (9-10 July) * The combination of very low registration, plus content in multiple time zones (see below for details on both) make this event the most affordable and accessible GCC ever. * If you are working in data intensive science (life sciences and beyond), GCC2021 is an ideal conference to share your work, learn from others, and find new collaborators. We look forward to meeting you there! *About Galaxy* Galaxy <https://galaxyproject.org/> is an open data integration and analysis platform used and supported by a global community of researchers, bioinformaticians, developers, infrastructure providers, and trainers, all doing and supporting data intensive research Galaxy was originally developed to support life science research, but is now used in multiple fields including computational chemistry and molecular modelling, climate modeling, social science, and natural language processing. *Training Week* Training <https://galaxyproject.org/events/gcc2021/training/> will run for 5 days, from 28 June through 2 July. This will be an online event, spanning all time zones. All training sessions are pre-recorded, so you can work through them at your own pace, and manage your own time. A large community of GTN trainers will be available 24/7 online support to answer all your questions on Slack. Training Week features 3 tracks: 1. Galaxy for Scientists <https://galaxyproject.org/events/gcc2021/training/#science-track> 2. Galaxy for Developers <https://galaxyproject.org/events/gcc2021/training/#developer-track> 3. Galaxy for Administrators <https://galaxyproject.org/events/gcc2021/training/#admin-track> (enrollment is limited) *GCC2021 Meeting* The conference includes a 3 day meeting, 8-10 July, and features accepted talks, Q&A, poster/demos, sponsors, birds-of-a-feather sessions, and lots of social interaction and networking. Talks will be pre-recorded, but EVERYTHING else, including Q&A will be live. *All material will be presented twice each day, once in the original Central European time zone, and then again 9 hours later in the Americas. * * Abstract Submission*Talks and poster/demo presentations will be selected from abstract submissions. Talks can be either full (15-20 minutes) or lightning (5-7 minutes). We welcome submissions that use, implement or extend the Galaxy platform and ecosystem, including integrating and analyzing datasets in any research area, enhancing reproducibility in computational analyses, and fostering collaboration in scientific workflow development. *Abstract submissions are due 7 May* <https://galaxyproject.org/news/2021-04-gcc-abstracts/>. * Registration* Registration rates are very affordable <https://galaxyproject.org/news/2021-04-gcc-reg/>, with deep discounts for researchers and students, and especially for researchers and students in developing economies. Early registration rates for students in developing economies start at €3.25 for Training Week, and €6.00 for the meeting (plus VAT). In addition students and researchers for developing countries can also apply for GCC2021 Fellowship <https://galaxyproject.org/news/2021-04-gcc-fellowships/> from the Galaxy Community Fund (apply by 7 May). *Early registration ends 1 June.* -- https://galaxyproject.org/ |
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From: Sebastian H. <pr...@in...> - 2020-12-07 09:20:32
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Apologies for cross-posting Dear all, We are proud to announce DBpedia Archivo (https://archivo.dbpedia.org) an augmented ontology archive and interface to implement FAIRer ontologies. Each ontology is rated with 4 stars measuring basic FAIR features. We discovered 890 ontologies reaching on average 1.95 out of 4 stars. Many of them have no or unclear licenses and have issues w.r.t. retrieval and parsing. # Community action on individual ontologies We would like to call on all ontology maintainers and consumers to help us increase the average star rating of the web of ontologies by fixing and improving its ontologies. You can easily check an ontology at https://archivo.dbpedia.org/info. If you are an ontology maintainer just release a patched version - archivo will automatically pick it up 8 hours later. If you are a user of an ontology and want your consumed data to become FAIRer, please inform the ontology maintainer about the issues found with Archivo. The star rating is very basic and only requires fixing small things. However, theimpact on technical and legal usability can be immense. # Community action on all ontologies (quality, FAIRness, conformity) Archivo is extensible and allows contributions to give consumers a central place to encode their requirements. We envision fostering adherence to standards and strengthening incentives for publishers to build a better (FAIRer) web of ontologies. 1. SHACL (https://www.w3.org/TR/shacl/, co-edited by DBpedia’s CTO D. Kontokostas) enables easy testing of ontologies. Archivo offers free SHACL continuous integration testing for ontologies. Anyone can implement their SHACL tests and add them to the SHACL library on Github. We believe that there are many synergies, i.e. SHACL tests for your ontology are helpful for others as well. 2. We are looking for ontology experts to join DBpedia and discuss further validation (e.g. stars) to increase FAIRness and quality of ontologies. We are forming a steering committee and also a PC for the upcoming Vocarnival at SEMANTiCS 2021. Please message hel...@in... <mailto:hel...@in...>if you would like to join. We would like to extend the Archivo platform with relevant visualisations, tests, editing aides, mapping management tools and quality checks. # How does Archivo work? Each week Archivo runs several discovery algorithms to scan for new ontologies. Once discovered Archivo checks them every 8 hours. When changes are detected, Archivo downloads and rates and archives the latest snapshot persistently on the DBpedia Databus. # Archivo's mission Archivo's mission is to improve FAIRness (findability, accessibility, interoperability, and reusability) of all available ontologies on the Semantic Web. Archivo is not a guideline, it is fully automated, machine-readable and enforces interoperability with its star rating. - Ontology developers can implement against Archivo until they reach more stars. The stars and tests are designed to guarantee the interoperability and fitness of the ontology. - Ontology users can better find, access and re-use ontologies. Snapshots are persisted in case the original is not reachable anymore adding a layer of reliability to the decentral web of ontologies. Let’s all join together to make the web of ontologies more reliable and stable, Johannes Frey, Denis Streitmatter, Fabian Götz, Sebastian Hellmann and Natanael Arndt Paper: https://svn.aksw.org/papers/2020/semantics_archivo/public.pdf |
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From: Sebastian H. <pr...@in...> - 2020-11-24 09:08:01
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Apologies for cross-posting Over the last year, the DBpedia core team has consolidated great amount of technology around DBpedia. This tutorial targets developers (in particular of DBpedia Chapters) that wish to learn how to replicate local infrastructure such as loading and hosting an own SPARQL endpoint. A core focus will also be the new DBpedia Stack, which contains several dockerized applications that are automatically loading data from the DBpedia databus. The third tutorial will be held on December 8, 2020 at 17:30 CET and it will cover the following topics: - Using Databus collections (Download) - Creating customized Databus collections - Uploading data to the Databus - Using collections in Databus-ready Docker applications - Creating dockerized applications for the DBpedia Stack #Quick Facts - Web URL: https://wiki.dbpedia.org/tutorials/3rd-dbpedia-stack-tutorial - When: December 8, 2020 at 17:30-18:30 CET - Where: The tutorial will be organized online.Registration is required though. - Databus: https://databus.dbpedia.org/ #Registration Attending the DBpedia Stack tutorial is free. Registration is required though. After the registration for the event, you will receive an email with more instructions. Please register here to be part of the meeting: https://wiki.dbpedia.org/tutorials/3rd-dbpedia-stack-tutorial #Organisation - Milan Dojchinovski, AKSW/KILT, DBpedia Association - Jan Forberg, AKSW/KILT, DBpedia Association - Julia Holze, InfAI, DBpedia Association - Sebastian Hellmann, AKSW/KILT, DBpedia Association We are looking forward to meeting you online! With kind regards, The DBpedia Team |
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From: Dave C. <cle...@gm...> - 2020-07-10 17:18:12
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Hi all, Just a reminder that there are a couple of BCC2020 (BOSC + Galaxy) deadlines today, July 10: 1. Birds of a feather submissions: https://bit.ly/bcc-propose-a-bof If you are attending the meeting part of BCC, and you would benefit from gathering your community at a BoF then please submit a proposal. We also need these. Right now we have lots of attendees, and very few BoFs (https://bcc2020.sched.com/overview/subject/BoF). This combination may not work well in an online setting. We might also extend the deadline to Sunday night. However, we might not. So if you see this today, then please submit in the next ~12 or so hours. 2. Early registration closes: https://bcc2020.github.io/Registration/ At US Pacific time. (about 13:45 from right now). Registration rates double after that, although they still aren't expensive. However, this event might sell out before the end of the day. So, might want to register now.... Thanks everyone, Dave C -- https://galaxyproject.org/ |
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From: Sebastian H. <pr...@in...> - 2020-06-23 17:06:48
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Apologies for cross-posting
Over the last year, the DBpedia core team has consolidated great amount
of technology around DBpedia. This tutorial is targeted for developers
(in particular of DBpedia Chapters) that wish to learn how to replicate
local infrastructure such as loading and hosting an own SPARQL endpoint.
A core focus will also be the new DBpedia Stack, which contains several
dockerized applications that are automatically loading data from the
databus. The tutorial will cover the following topics:
- Using Databus collections (Download)
- Creating customized Databus collections
- Uploading data to the Databus
- Using collections in Databus-ready Docker applications
- Creating dockerized applications for the DBpedia Stack
The first tutorial will be held on July 1st, 2020 at 9:00-10:00 am
CEST.The tutorial will be repeated once more at a later time.
# Quick Facts
- Web URL:https://wiki.dbpedia.org/tutorials/1st-dbpedia-stack-tutorial
- When: July 1st, 2020 9:00-10:00 am CEST
- Where: The tutorial will be organized online. Registration is required
though.
- Databus: https://databus.dbpedia.org/
# Registration
Attending the DBpedia Stack tutorial is free. Registration is required
though. After the registration for the event, you will receive an email
with more instructions. Please register here to be part of the meeting:
https://docs.google.com/forms/d/e/1FAIpQLSfI3x5YE6bYmxTM57001MBfy5_1EjyjUV52llhhEY9ib5P8rA/viewform
# Program
- Please check the schedule for the upcoming DBpedia Stack Tutorial
here: https://wiki.dbpedia.org/tutorials/1st-dbpedia-stack-tutorial
# Organisation
- Milan Dojchinovski, AKSW/KILT, DBpedia Association
- Jan Forberg, AKSW/KILT, DBpedia Association
- Sebastian Hellmann, AKSW/KILT, DBpedia Association
We are looking forward to meeting you online!
With kind regards,
The DBpedia Team
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From: Dave C. <cle...@gm...> - 2020-04-27 18:36:58
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2020 Bioinformatics Community Conference (BCC2020) Online, July 17-26 https://bcc2020.github.io/ The 2020 Bioinformatics Community Conference (BCC2020) <https://bcc2020.github.io/> will be online, global, affordable, and accessible. Key Dates: May 8: Deadline for submitting talk/poster/demo abstracts <https://bcc2020.github.io/submit/> (this will not be extended) June 6: Authors notified about talk/poster/demo acceptance July 10: Early registration <https://bcc2020.github.io/Registration/> ends July 17-19: BCC2020 Training sessions <https://bcc2020.github.io/training/> July 19-22: BCC2020 Main meeting <https://bcc2020.github.io/schedule/> July 22-24, 24-26: CollaborationFest Core and Encore <https://bcc2020.github.io/cofest/> BCC2020 BCC2020 <https://bcc2020.github.io/> is a joint event bringing together the Bioinformatics Open Source Conference (BOSC) <https://www.open-bio.org/events/bosc/> and Galaxy <https://galaxyproject.org/> Communities. If you are working in data intensive life science research then there is no better event for sharing your work, and learning from other researchers addressing the challenges of modern data driven biology. BCC2020 will be held July 17-26 <https://bcc2020.sched.com/>, and offer 2 days of training <https://bcc2020.sched.com/overview/type/Training>, a 3 day meeting <https://bcc2020.sched.com/overview/type/Meeting>, and a 4 day CollaborationFest <https://bcc2020.sched.com/overview/type/CoFest>. BOSC is organized by the Open Bioinformatics Foundation (OBF) <https://www.open-bio.org/>, a non-profit group dedicated to promoting the practice and philosophy of open source software development and open science within the biological research community. Galaxy <https://galaxyproject.org/> is an open source data integration and analysis platform for the life sciences that is used, deployed, maintained and extended by a worldwide community of researchers, students, software engineers, and infrastructure providers. BCC2020 is Online All BCC2020 events will be held online <https://bcc2020.github.io/blog/going-virtual>. Training will be live and interactive. The meeting will feature keynotes, accepted talks, lightning talks, posters, demos, and birds-of-a-feather and other networking opportunities. Talks (with the possible exception of keynotes) will be pre-recorded. Posters, demos, and BoFs will be live and interactive. The CoFest will also be live and interactive. BCC2020 is Global BCC2020 events will be held twice <https://bcc2020.github.io/blog/going-global>: once in the originally scheduled Toronto time zone (BCC West) <https://bcc2020.sched.com/venue/West>, and then again 12 hours later in the Eastern hemisphere (BCC East) <https://bcc2020.sched.com/venue/East>. Training will differ between East and West, with enrollment open to all, regardless of where you are. The main conference content will be presented in both East and West. We are striving to have the CoFest run continuously <https://bcc2020.sched.com/overview/type/CoFest>, with participants from every part of the world. BCC2020 is Affordable We have slashed registration rates for BCC2020 <https://bcc2020.github.io/Registration/>, and are offering even larger discounts to participants based in low and lower-middle income countries. Pricing starts at US$3 per training session, and $12 for the 3 day meeting. The CoFest <https://bcc2020.github.io/cofest/> is free. BCC2020 is Accessible Going online and global, combined with the low registration rates this enables, makes this the most accessible Galaxy or BOSC conference ever. If you work in open source bioinformatics then this is 2020’s best opportunity to share your work and learn from others. Abstracts Due May 8 BCC2020 is seeking oral presentations, lightning talks, posters, and demos, from researchers working in bioinformatics, and all over the world. Abstracts are due May 8 (and that deadline will not be extended). Please submit your work <https://bcc2020.github.io/submit/> today. Register Now BCC2020 registration is now open <https://bcc2020.github.io/Registration/>. Registering early saves 50% off of the full rates. We hope to see you in July at BCC2020, BCC2020 Organizers -- https://galaxyproject.org/ |
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From: Dave C. <cle...@gm...> - 2020-03-24 16:28:14
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Hello all, *The Organizing Committee of the 2020 Bioinformatics Community Conference (BCC2020) <https://bcc2020.github.io/> has come to the difficult decision to hold the conference online.* We are making this decision after much consideration of the ongoing spread of COVID-19, striving to take the most socially responsible action while maintaining a forum in which our community can share their work and discovery. It is hard to predict what things will look like in July, but given current reports and models, it seems unlikely that the situation will be back to “business as usual”. We also considered that, even if some people were able to attend, it is possible that many people would still find it difficult to travel to Toronto. We believe that making this decision now will allow us to focus on organizing an engaging conference in this new format. We will be inviting our community to engage in new ways, and hope that BCC2020 will be an important space for discussion for the Open Source bioinformatics community. *The virtual meeting will still take place as planned, on July 18-21.* There will be opportunities for training <https://bcc2020.github.io/training> before the main meeting, and a CollaborationFest <https://bcc2020.github.io/cofest> starting on July 22. We are discussing how to arrange the schedule to allow for participation across the globe; more details will be coming soon. *Registration will open in a few weeks*, and fees will be lower than for an in-person meeting. *The abstract submission deadline has been postponed to April 30th.* Abstracts will follow the usual submission and review processes. There are many details to be worked out – for example, a meeting schedule that takes into account time zones, videoconferencing technology, ways to enrich our online interactions (while acknowledging that nothing can replace the vital social interaction that in-person meetings provide), etc. Many of these aspects are new for us too; we welcome your input, particularly if you have suggestions about how to make our first Virtual Bioinformatics Community Conference a success. We are looking forward to exploring this new meeting format, and we hope you will join us. Stay well, BCC2020 Organizers <https://bcc2020.github.io/about/#team> -- https://galaxyproject.org/ |
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From: Scott C. <sc...@sc...> - 2020-02-21 02:16:34
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Hello, I am very pleased to announce that GMOD in conjunction with Reactome, Galaxy and OICR/WormBase, together forming Open Genome Informatics, has been accepted for the Google Summer of Code. If you or someone you know might be a student interested in participating in GSoC, please take a look at http://gmod.org/wiki/GSOC_Project_Ideas_2020 where there are proposed projects that cover a fair number of technologies. Official proposals from students will be due in mid March (more on that later). But WAIT! There's more: if you might be interested in being a mentor and working with a student this summer, it's not too late! You can add new project ideas to the page above (contact me if you need an account), or you can even volunteer to add yourself to one of the existing ideas as a potential mentor. Please feel free to forward this to other mailing lists or people who might be interested. We are already an eclectic, dispersed group, so everyone is welcome. Thanks, Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
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From: Dave C. <cle...@gm...> - 2020-02-11 14:36:31
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Hello all, The The Bioinformatics Community Conference (BCC2020) <https://bcc2020.github.io/>, will bring together the Galaxy Community Conference (GCC) and the Bioinformatics Open Source Conference (BOSC) in Toronto, Canada in July 2020, following ISMB 2020 <https://www.iscb.org/ismb2020> in Montréal. BCC2020 will start with a dedicated training day, followed by 3 days of mixed meeting and training events. The community (you!) determines what training will be offered at BCC2020. *Nominations from the community <https://bcc2020.github.io/training/>* are now ready for review and voting. If you are possibly attending BCC2020 then please take a few minutes to review the nominations and then submit your ballot <https://docs.google.com/forms/d/e/1FAIpQLSfmOowsHt0cL1ukiGvOdh7WxWKoSuT-3GMnUFGQGvmarxlzQg/viewform>. Voting closes on February 21. Thanks in advance for your input, and we hope to see you in Toronto, BCC2020 Organizers -- https://galaxyproject.org/ |
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From: Robin H. <Rob...@oi...> - 2020-01-28 21:24:20
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Dear Eric, The Open Genome Informatics team serves as an “umbrella" organization to support the efforts of many open access open-source bioinformatics projects for Google Summer of Code (GSoC)<https://summerofcode.withgoogle.com/>. Among this list of projects are GMOD and its software projects -- GBrowse, JBrowse; Galaxy; Reactome; WormBase; DockStore; Bioconda; and others. Call for 2020 Project Ideas and Mentors: We are seeking project ideas to post and attract talented students to this year’s Summer of Code competition. If you have a project idea for which you would like to mentor a student, please contact Robin Haw, Marc Gillespie, Dave Clements, Dannon Baker, and Scott Cain (emails above). You can also submit your ideas here<http://gmod.org/wiki/GSOC_Project_Ideas_2020>. For more information please refer to the Open Genome Informatics page on the GMOD.org website<http://gmod.org/wiki/GSoC#Google_Summer_of_Code_2020>. The mentoring organization application deadline with GSoC is February 5th at 2 pm EST. So, if you are interested in taking part with the team please let us know as soon as possible. Please forward this to others who might be interested in taking part. If you have any questions please let us know. Thanks, Robin, Marc, Dave, Dannon, and Scott. Robin Haw, PhD Reactome | JBrowse - Senior Project Manager and Outreach Co-ordinator rob...@oi...<mailto:rob...@oi...> Ontario Institute for Cancer Research MaRS Centre, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3 @OICR_news | www.oicr.on.ca | @reactome | reactome.org | @JBrowseGossip | jbrowse.org Collaborate. Translate. Change lives. This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization. |
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