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From: Scott C. <sc...@sc...> - 2024-07-23 18:15:44
|
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 16:41:35
|
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/) |
From: Scott C. <sc...@sc...> - 2022-03-23 04:24:32
|
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/) |
From: Enis A. <af...@gm...> - 2022-02-28 17:04:49
|
2022 Galaxy Community Conference (GCC2022) July 17-23, Minneapolis, Minnesota, USA https://galaxyproject.org/events/gcc2022/ Deadlines: April 12: Oral presentation and lightning talk abstracts due <https://docs.google.com/forms/d/1z29z8Nd8Gho0trS7DySvWAii6hisbZr67cuI--lcZ_4/viewform?edit_requested=true> May 12: Early registration <https://learning.umn.edu/portal/events/reg/participantTypeSelection.do?method=load&entityId=32741188> ends June 3: Demo and poster abstracts due <https://docs.google.com/forms/d/1z29z8Nd8Gho0trS7DySvWAii6hisbZr67cuI--lcZ_4/viewform?edit_requested=true> The 2022 Galaxy Community Conference (GCC2022) <https://galaxyproject.org/events/gcc2022/> will be held July 17-23 in Minneapolis, Minnesota. GCC brings together hundreds of faculty, clinicians, researchers, and students, all working in and supporting data intensive science that is accessible, shareable, and reproducible. GCC2022 features oral presentations, lightning talks, posters, demos, birds-of-a-feather gatherings (BoFs), training, a CollaborationFest, and plenty of opportunities for networking. Presentations will cover the full spectrum of Galaxy applications, enhancements, and deployments. If you are working in data intensive science then GCC2022 is an ideal conference for sharing your work, learning from others, and finding new collaborators. Present your work! Abstract submission <https://docs.google.com/forms/d/1z29z8Nd8Gho0trS7DySvWAii6hisbZr67cuI--lcZ_4/viewform?edit_requested=true> for talks, lightning talks, demos, and posters is now open. If you work in data-intensive science then please consider presenting your work at GCC2022. This is a chance to present to 200+ researchers, all addressing challenges in data intensive science. Abstract submissions for oral presentations are due on April 12. Submit an abstract (or two) now! <https://docs.google.com/forms/d/1z29z8Nd8Gho0trS7DySvWAii6hisbZr67cuI--lcZ_4/viewform?edit_requested=true> Topics of Interest If you’re currently working on any of these topics, this conference is for you: - Omics data analysis: genomic sequencing, microbiome, proteomics, imaging, you name it! - Tools and visualizations for working with omics data - Compute infrastructure for enabling data intensive science - Galaxy applications in any domain or topic: ML, climate, NPL, … - Outreach and training related to data analysis Registration Registration information is available on the conference website <https://galaxyproject.org/events/gcc2022/register#in-person>. Early registration ends May 12. So, register <https://galaxyproject.org/events/gcc2022/register> early! About Galaxy Galaxy <https://galaxyproject.org/> is a platform for data integration and analysis in the life sciences. It enables researchers to build, run, share, and repeat their own complex computational analyses using only a web browser and without having to first learn system administration and command line interfaces. The Galaxy Project is driven by a vibrant community who publish workflows and analyses, wrap new tools, maintain and enhance the source code, provide support, and write documentation and training materials. Galaxy is open-source and freely available, and is deployed in hundreds of organizations, running on everything from laptops to supercomputers to public and private clouds. Over 150 of these platforms are publicly available and can be used with little or no setup. Thousands of tools have been ported to Galaxy and are deployable from the Galaxy Tool Shed. Galaxy was developed to support life science research, but the platform is domain agnostic and is now used in domains as diverse as natural language processing, computational solid geometry, and social science. Hope to see you in Minneapolis! GCC2022 Organizers <https://galaxyproject.org/events/gcc2022/organizers/> |
From: Scott C. <sc...@sc...> - 2021-07-21 18:27:42
|
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 |
From: Dave C. <cle...@ga...> - 2021-06-07 04:29:06
|
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/ |
From: Scott C. <sc...@sc...> - 2021-05-04 21:15:49
|
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 |
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/ |
From: Dave C. <cle...@ga...> - 2020-12-03 21:04:04
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Hello all, This webinar is coming up next week. Please let me know if you have any questions. Thanks, Dave C *Use Galaxy on the web, the cloud, and your laptop too: **Options for using Galaxy: everywhere and right now* This Galaxy webinar on December 9 <https://galaxyproject.org/events/2020-12-webinar-where/> will introduce the many options for using Galaxy right now, anywhere in the world. We'll cover - Publicly accessible Galaxy servers on the web (there are over 100 of them) - Research and commercial cloud platforms, from Australia (Nectar) to the US (Jetstream, AnVIL), and everywhere in between (CloudLaunch) - On your laptop, using pre-packaged containers and virtual machines. *The webinar will be at 11am Eastern US time (see your time <https://www.timeanddate.com/worldclock/fixedtime.html?msg=Webinar%3A+Use+Galaxy+everywhere&iso=20201209T11&p1=419&am=55>).* Enis Afgan, Anton Nekrutenko, and Mike Schatz will present. Interested? Please sign up now <https://docs.google.com/forms/d/e/1FAIpQLSckxsyURPvbZATc-ZbK3Zwd05zb6IPVTg__7aO6cPzR-m8VEQ/viewform> . <https://galaxyproject.org/news/2020-12-webinar/#about-galaxy> About Galaxy Galaxy <https://galaxyproject.org/> is a web-based data integration and analysis platform for the life sciences (and more). It is open source and freely available and installed at organizations around the world. It is a GMOD component and has been integrated with Tripal, JBrowse, Apollo, and Maker. -- https://galaxyproject.org/ |
From: Garrett S. <ste...@gm...> - 2020-11-09 22:59:14
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We are pleased to announce the first public release of JBrowse 2! JBrowse 2 is the successor to JBrowse, but is a completely new application written with modern web standards and frameworks. Some of the features new to JBrowse 2 include: - New types of views, including circular, synteny, and dotplot views - Graphical configuration editing - Connections to resources such as UCSC Track Hubs You can see some demos of JBrowse 2 in action here <https://jbrowse.org/jb2/demos>. To get started using JBrowse 2, visit our quickstart guide here <https://jbrowse.org/jb2/docs/quickstart_web>. We'd love to hear what you think! You can find information about how to contact us here <https://jbrowse.org/jb2/contact/>. [image: jbrowse_logo.png] <https://jbrowse.org/jb2/> The JBrowse Team |
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/ |
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/ |
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 |
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/ |
From: Robin H. <Rob...@oi...> - 2020-01-28 21:34:13
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Dear All, Sorry for the multiple postings! 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. |
From: Dave C. <cle...@gm...> - 2019-12-19 20:07:16
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Hello all, There are three things going on that are of general interest to the Galaxy and GMOD communities, and that have some urgency to them (and thus this mid-month email). BCC2020 Schedule Structure ----------------------- The Bioinformatics Community Conference (BCC2020, https://bcc2020.github.io/) will be held in July, in Toronto, right after ISMB in Montréal. This event brings together the BOSC and Galaxy communities into one gathering. If you are considering attending BCC2020, then the organizers would like your input on several scheduling choices, BY JANUARY 7: https://bcc2020.github.io/blog/poll BCC2020 Training Topic Nominations ------------------------ The training offered at BCC2020 is determined by the community. We are now accepting nominations for training sessions. Nominated topics will be voted on by the community. Please submit your ideas by JANUARY 17. https://bcc2020.github.io/blog/training-nom 2020 Galaxy Admin Training ----------------------- A week long workshop on setting up your own production-grade Galaxy instance will be held in Barcelona the first week of March. Registration is now open, and is, well, pretty darn cheap too. https://galaxyproject.org/events/2020-03-admin/ And, of course, there is a lot of other stuff going on too: https://galaxyproject.org/events/ Happy Holidays, and hope to see you in the new year! Dave C, on behalf of the BCC2020 and Galaxy Admin Training organizers -- https://galaxyproject.org/ |
From: Scott C. <sc...@sc...> - 2019-11-19 03:59:56
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Hello, As announced last month, there will be a GMOD codefest held before the Plant and Animal Genome meeting in San Diego, January 9-10, 2020. The meeting will be held at the Handlery hotel (down the street from the Town and Country Hotel). Logistical and other information can be found at the GMOD wiki as the details become more solid: http://gmod.org/wiki/Codefest_2020 Several potential projects are described in this document: https://docs.google.com/document/d/1_CnUW_W4tNyl7lSlihCwZDKT45VQQxcI3I-VgjnC2Dc/edit We know for sure that there will be developers from the Tripal, Apollo, JBrowse, and Chado projects. Of course, other projects like Galaxy, InterMine, and MAKER are welcome too! See you in San Diego! Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
From: Nathan D. <nat...@lb...> - 2019-10-10 23:01:15
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I plan on being there to work on user’s Apollo-based problems (or JBrowse ones if that is more pertinent). I’ve copied on the Apollo list. Looking forward to seeing you there, Nathan > On Oct 10, 2019, at 2:40 PM, Scott Cain <sc...@sc...> wrote: > > I am pleased to announce there will be a GMOD codefest occurring before the Plant and Animal Genomes meeting in San Diego. The codefest will be at the Town and Country hotel on January 9 and 10. If you would like to suggest a problem or project to address, add it to this Google Doc <https://docs.google.com/document/d/1_CnUW_W4tNyl7lSlihCwZDKT45VQQxcI3I-VgjnC2Dc/edit?usp=sharing>. The codefest is open to anyone who'd like to work on any GMOD project (or, better yet, any combination of GMOD projects), including but not limited to Tripal <http://gmod.org/wiki/Tripal>, Chado <http://gmod.org/wiki/Chado>, JBrowse <http://gmod.org/wiki/JBrowse> (1 and 2), Galaxy <http://gmod.org/wiki/Galaxy> and InterMine <http://gmod.org/wiki/InterMine>. We already know that there will be Tripal, Chado and JBrowse developers present. Registration information will be coming soon. > > You can follow the changes to this page: > > http://gmod.org/wiki/Codefest_2020 <http://gmod.org/wiki/Codefest_2020> > > to keep up to date, or follow The Tweet of GMOD (@gmodproject) on Twitter. > > See you in San Diego, > Scott > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at scottcain dot net > GMOD Coordinator (http://gmod.org/ <http://gmod.org/>) 216-392-3087 > Ontario Institute for Cancer Research > _______________________________________________ > Gmod-devel mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-devel |
From: Scott C. <sc...@sc...> - 2019-10-10 21:40:51
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I am pleased to announce there will be a GMOD codefest occurring before the Plant and Animal Genomes meeting in San Diego. The codefest will be at the Town and Country hotel on January 9 and 10. If you would like to suggest a problem or project to address, add it to this Google Doc <https://docs.google.com/document/d/1_CnUW_W4tNyl7lSlihCwZDKT45VQQxcI3I-VgjnC2Dc/edit?usp=sharing>. The codefest is open to anyone who'd like to work on any GMOD project (or, better yet, any combination of GMOD projects), including but not limited to Tripal <http://gmod.org/wiki/Tripal>, Chado <http://gmod.org/wiki/Chado>, JBrowse <http://gmod.org/wiki/JBrowse> (1 and 2), Galaxy <http://gmod.org/wiki/Galaxy> and InterMine <http://gmod.org/wiki/InterMine>. We already know that there will be Tripal, Chado and JBrowse developers present. Registration information will be coming soon. You can follow the changes to this page: http://gmod.org/wiki/Codefest_2020 to keep up to date, or follow The Tweet of GMOD (@gmodproject) on Twitter. See you in San Diego, Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
From: Dave C. <cle...@ga...> - 2019-05-15 18:12:40
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Hell0 All, An update on the 2019 Galaxy Community Conference: 1. A (final) reminder that *early registration* <https://galaxyproject.org/events/gcc2019/registration/> for the 2019 Galaxy Community Conference *ends this Friday night*, 17 May, at midnight Freiburg time (CEST / GMT +2). After that registration goes up by ~ 60%. So, register this week! 2. All accepted speakers have been notified and talks are being added to the schedule <https://gcc2019.sched.com/> as presenters confirm. There were far more talk submissions this year than in any previous year and that is reflected in the breadth and quality of the accepted talks. 3. *Poster and demo submission <https://galaxyproject.org/events/gcc2019/abstracts/> is still open!* However, space *will* fill up and when it's gone, it's gone. Got something to present? Submit it *soon*. We hope to see you in Freiburg! Dave C on behalf of the GCC2019 Organizers ------------------ 2019 Galaxy Community Conference (GCC2019) 1-8 July, Freiburg, Germany https://galaxyproject.org/gcc2019 ------------------ The 2019 Galaxy Community Conference (GCC2019) will be held 1-8 July in Freiburg, Germany. GCC brings together hundreds of faculty, clinicians, researchers, and students, all working in and supporting data intensive science that is accessible, sharable and reproducible. GCC2019 features oral presentations, lightning talks, posters, demos, birds-of-a-feather gatherings (BoFs), training, a CollaborationFest, and plenty of opportunities for networking. Presentations will cover the full spectrum of Galaxy applications, enhancements and deployments. If you are working in data intensive science then GCC2019 is an ideal conference for sharing your work, learning from others, and finding new collaborators. Registration Early registration starts at €49/day for students and postdocs, and €79 / day for other academics and non-profit researchers. Childcare is available and travel fellowships are available as well. Early registration ends 17 May, when rates go up by 60%. So, register early. About Galaxy Galaxy (https://galaxyproject.org/) is a platform for data integration and analysis in the life sciences. It enables researchers to build, run, share, and repeat their own complex computational analyses using only a web browser and without having to first learn system administration and command line interfaces. The Galaxy Project is driven by a vibrant community who publish workflows and analyses, wrap new tools, maintain and enhance the source code, provide support, and write documentation and training materials. Galaxy is open-source and freely available, and is deployed in hundreds of organizations, running on everything from laptops through supercomputers to public and private clouds. Over 150 of these platforms are publicly available and can be used with little or no setup. Thousands of tools have been ported to Galaxy ("wrapped") and are deployable from the Galaxy Tool Shed. Galaxy was developed to support life science research, but the software is domain agnostic and is now used in domains as diverse as natural language processing, constructive solid geometry, and social science. -- https://galaxyproject.org/gcc2019/ https://galaxyproject.org/ https://usegalaxy.org/ |
From: Dave C. <cle...@ga...> - 2019-04-15 05:13:46
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2019 Galaxy Community Conference (GCC2019) 1-8 July, Freiburg, Germany https://galaxyproject.org/gcc2019 Deadlines 22 April: Oral Presentation and Lightning Talk abstracts due <https://galaxyproject.org/events/gcc2019/abstracts/> 17 May: Early registration ends <https://galaxyproject.org/events/gcc2019/registration/> The 2019 Galaxy Community Conference (GCC2019) <https://galaxyproject.org/gcc2019> will be held 1-8 July in Freiburg, Germany. GCC brings together hundreds of faculty, clinicians, researchers, and students, all working in and supporting data intensive science that is accessible, sharable and reproducible. GCC2019 features oral presentations, lightning talks, posters, demos, birds-of-a-feather gatherings (BoFs), training, a CollaborationFest, and plenty of opportunities for networking. Presentations will cover the full spectrum of Galaxy applications, enhancements and deployments. If you are working in data intensive science then GCC2019 is an ideal conference for sharing your work, learning from others, and finding new collaborators. Present your work! Abstract submission <https://galaxyproject.org/events/gcc2019/abstracts/> for talks, lightning talks, demos and posters is now open. If you work in data-intensive science then please consider presenting your work at GCC2019. This is a chance to present to 200+ researchers, all addressing challenges in data intensive science. Review of oral presentations starts on 22 April. Submit an abstract (or two) now <https://galaxyproject.org/events/gcc2019/abstracts/>! Registration Early registration <https://galaxyproject.org/events/gcc2019/registration/> starts at €49/day for students and postdocs, and €79 / day for other academics and non-profit researchers. Childcare is available <https://galaxyproject.org/events/gcc2019/childcare/> and travel fellowships are available <https://galaxyproject.org/news/2019-04-gcc-fellowships/> as well. Early registration ends 17 May, when rates go up by 60%. So, register early <https://galaxyproject.org/events/gcc2019/registration/>. About Galaxy Galaxy <https://galaxyproject.org/> is a platform for data integration and analysis in the life sciences. It enables researchers to build, run, share, and repeat their own complex computational analyses using only a web browser and without having to first learn system administration and command line interfaces. The Galaxy Project is driven by a vibrant community who publish workflows and analyses, wrap new tools, maintain and enhance the source code, provide support, and write documentation and training materials. Galaxy is open-source and freely available, and is deployed in hundreds of organizations, running on everything from laptops through supercomputers to public and private clouds. Over 150 of these platforms are publicly available and can be used with little or no setup. Thousands of tools have been ported to Galaxy ("wrapped") and are deployable from the Galaxy Tool Shed. Galaxy was developed to support life science research, but the software is domain agnostic and is now used in domains as diverse as natural language processing, constructive solid geometry, and social science. Galaxy has been a GMOD component for over a decade and interoperates with many other components, including Tripal, Apollo, JBrowse, and InterMine. We hope to see you in Freiburg! GCC2019 Organizers <https://galaxyproject.org/events/gcc2019/organizers/> -- https://galaxyproject.org/gcc2019/ https://galaxyproject.org/ https://usegalaxy.org/ |
From: Scott C. <sc...@sc...> - 2019-04-09 19:17:52
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Reminder: the abstract deadline for BOSC is April 11! On Thu, Mar 28, 2019 at 8:18 PM Scott Cain <sc...@sc...> wrote: > Hi All, > > I meant to send this out last week--sorry for letting it slip my mind. > Note that the abstract deadline is April 11! > > Scott > > > ---------- Forwarded message --------- > From: Fields, Christopher J <cjf...@il...> > Date: Tue, Mar 19, 2019 at 2:12 PM > Subject: Call for abstracts: BOSC 2019 Bioinformatics Open Source > Conference > To: Scott Cain <sc...@sc...> > > > Scott, can you suggest any email lists where this could be sent? > > Thanks, > > chris > > On March 19, 2019 at 4:01:52 PM, cjf...@il... ( > cjf...@il...) wrote: > > [image: BOSC_2019_Banner] > BOSC 2019: Bioinformatics Open Source Conference An ISMB/ECCB Community > of Special Interest (COSI) > > *BOSC 2019 Dates*: July 24-25, 2019 > > *Location*: Basel, Switzerland > > *Website*: https://www.open-bio.org/wiki/BOSC_2019 (new, improved > website coming soon!) > > *Email BOSC organizers*: bo...@op... > > *BOSC announcements mailing list*: > http://lists.open-bio.org/mailman/listinfo/bosc-announce > > *Twitter*: @OBF_BOSC <https://twitter.com/OBF_BOSC>, #BOSC2019 > <https://twitter.com/search?f=tweets&vertical=default&q=%23BOSC2019&src=typd> > *Key Dates*: > > *April 11, 2019:* Deadline for submitting talk/poster abstracts > <https://www.open-bio.org/wiki/BOSC_Abstract_Submission> > > *April 15:* OBF travel fellowship > <https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md> application > deadline > > *May 9:* First-round authors notified about talk/poster acceptance > > *May 15:* Late poster / late-breaking lightning talk abstract deadline > > *May 23:* Late poster / late-breaking lightning talk authors notified > > *July 21-25, 2019:* ISMB/ECCB 2019 <https://www.iscb.org/ismbeccb2019>, > Basel, Switzerland > > *July 24-25 (last two days of ISMB):* BOSC 2019, Basel, Switzerland > > *July 26-28:* CollaborationFest (CoFest) 2019 > <https://www.open-bio.org/wiki/CoFest_2019>, Basel > About BOSC > > Since 2000, the yearly Bioinformatics Open Source Conference (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. > > In 2018, BOSC was held jointly with GCC > <https://f1000research.com/collections/BOSC?&selectedDomain=articles> as > a combined GCCBOSC <https://gccbosc2018.sched.com/> conference. In 2019, > BOSC will be part of ISMB/ECCB <https://www.iscb.org/ismbeccb2019> in > Basel. We hope to partner with GCC again in 2020 or 2021. Read more here > about why we decided to hold BOSC with GCC in 2018 and ISMB in 2019. > <https://news.open-bio.org/2018/08/02/taking-turns/> > > ISMB now consists of multiple parallel tracks called COSIs (formerly > SIGs). The BOSC COSI will take place the last two full days of ISMB (July > 24-25). You can register for the full ISMB/ECCB meeting (July 21-25) or for > just two days (there is no single-day registration option). > > A limited number of partial travel fellowships will be granted to some > accepted speakers who would not otherwise be able to attend BOSC--please > see https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md for > more information. The travel fellowship application deadline is *April > 15.* > Abstract submission > > We encourage you to submit abstracts > <https://www.open-bio.org/wiki/BOSC_Abstract_Submission> (*due April 11*) > on any topic relevant to open source bioinformatics or open science. After > review, some abstracts will be selected for lightning talks, longer talks > and/or posters. (Only first-round abstracts are eligible for longer talks.) > > Abstract submission instructions and a link to the EasyChair submission > portal can be found on > https://www.open-bio.org/wiki/BOSC_Abstract_Submission. > > BOSC session 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 > - Developer Tools and Libraries > - Inclusion, Outreach and Training > - Bioinformatics Open Source Project Reports (about new or existing > projects) > > We look forward to receiving your abstract and meeting you at BOSC 2019! > > Sincerely, > > *BOSC 2019 Organizing Committee:* Nomi Harris (chair), Heather Wiencko > (co-chair), Peter Cock, Chris Fields, Bastian Greshake Tzovaras, Michael > Heuer, Karsten Hokamp, Monica Munoz-Torres, Bastian Rieck, Yo Yehudi. > > *P.S. Don't forget to submit your BOSC abstract by April 11 at* > https://www.open-bio.org/wiki/BOSC_Abstract_Submission ! > > Please share this announcement with your colleagues! > > > > — chris > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at scottcain > dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
From: Scott C. <sc...@sc...> - 2019-03-29 03:19:06
|
Hi All, I meant to send this out last week--sorry for letting it slip my mind. Note that the abstract deadline is April 11! Scott ---------- Forwarded message --------- From: Fields, Christopher J <cjf...@il...> Date: Tue, Mar 19, 2019 at 2:12 PM Subject: Call for abstracts: BOSC 2019 Bioinformatics Open Source Conference To: Scott Cain <sc...@sc...> Scott, can you suggest any email lists where this could be sent? Thanks, chris On March 19, 2019 at 4:01:52 PM, cjf...@il... ( cjf...@il...) wrote: [image: BOSC_2019_Banner] BOSC 2019: Bioinformatics Open Source Conference An ISMB/ECCB Community of Special Interest (COSI) *BOSC 2019 Dates*: July 24-25, 2019 *Location*: Basel, Switzerland *Website*: https://www.open-bio.org/wiki/BOSC_2019 (new, improved website coming soon!) *Email BOSC organizers*: bo...@op... *BOSC announcements mailing list*: http://lists.open-bio.org/mailman/listinfo/bosc-announce *Twitter*: @OBF_BOSC <https://twitter.com/OBF_BOSC>, #BOSC2019 <https://twitter.com/search?f=tweets&vertical=default&q=%23BOSC2019&src=typd> *Key Dates*: *April 11, 2019:* Deadline for submitting talk/poster abstracts <https://www.open-bio.org/wiki/BOSC_Abstract_Submission> *April 15:* OBF travel fellowship <https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md> application deadline *May 9:* First-round authors notified about talk/poster acceptance *May 15:* Late poster / late-breaking lightning talk abstract deadline *May 23:* Late poster / late-breaking lightning talk authors notified *July 21-25, 2019:* ISMB/ECCB 2019 <https://www.iscb.org/ismbeccb2019>, Basel, Switzerland *July 24-25 (last two days of ISMB):* BOSC 2019, Basel, Switzerland *July 26-28:* CollaborationFest (CoFest) 2019 <https://www.open-bio.org/wiki/CoFest_2019>, Basel About BOSC Since 2000, the yearly Bioinformatics Open Source Conference (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. In 2018, BOSC was held jointly with GCC <https://f1000research.com/collections/BOSC?&selectedDomain=articles> as a combined GCCBOSC <https://gccbosc2018.sched.com/> conference. In 2019, BOSC will be part of ISMB/ECCB <https://www.iscb.org/ismbeccb2019> in Basel. We hope to partner with GCC again in 2020 or 2021. Read more here about why we decided to hold BOSC with GCC in 2018 and ISMB in 2019. <https://news.open-bio.org/2018/08/02/taking-turns/> ISMB now consists of multiple parallel tracks called COSIs (formerly SIGs). The BOSC COSI will take place the last two full days of ISMB (July 24-25). You can register for the full ISMB/ECCB meeting (July 21-25) or for just two days (there is no single-day registration option). A limited number of partial travel fellowships will be granted to some accepted speakers who would not otherwise be able to attend BOSC--please see https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md for more information. The travel fellowship application deadline is *April 15.* Abstract submission We encourage you to submit abstracts <https://www.open-bio.org/wiki/BOSC_Abstract_Submission> (*due April 11*) on any topic relevant to open source bioinformatics or open science. After review, some abstracts will be selected for lightning talks, longer talks and/or posters. (Only first-round abstracts are eligible for longer talks.) Abstract submission instructions and a link to the EasyChair submission portal can be found on https://www.open-bio.org/wiki/BOSC_Abstract_Submission. BOSC session 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 - Developer Tools and Libraries - Inclusion, Outreach and Training - Bioinformatics Open Source Project Reports (about new or existing projects) We look forward to receiving your abstract and meeting you at BOSC 2019! Sincerely, *BOSC 2019 Organizing Committee:* Nomi Harris (chair), Heather Wiencko (co-chair), Peter Cock, Chris Fields, Bastian Greshake Tzovaras, Michael Heuer, Karsten Hokamp, Monica Munoz-Torres, Bastian Rieck, Yo Yehudi. *P.S. Don't forget to submit your BOSC abstract by April 11 at* https://www.open-bio.org/wiki/BOSC_Abstract_Submission ! Please share this announcement with your colleagues! — chris -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
From: Scott C. <sc...@sc...> - 2019-03-14 19:21:28
|
Hello, I wanted to forward this to a few mailing lists where I think it might be of interest. Adhemar is proposing a new project that is a web front end to Chado based on Django be a GMOD project. Please feel free to reply to this email with comments and questions. Thanks, Scott ---------- Forwarded message --------- From: Adhemar <az...@gm...> Date: Thu, Mar 14, 2019 at 10:09 AM Subject: Nominate software: machado To: <he...@gm...> Nominate software: machado https://github.com/lmb-embrapa/machado machado is a Django2-based application that contains tools to interact with Chado databases. It provides users with a framework to store, search and visualize biological data. - Data loaders for the major bioinformatics formats: fasta, gff, obo, bibtex, blast, interproscan, orthomcl - The machado API delivers data directly to the JBrowse genome browser - The Haystack framework provides a very fast query interface using the Elasticsearch engine *Requirements for the nomination process* The development of machado was triggered by an undergoing research project at EMBRAPA, the largest public research institute on agriculture in Brazil. In this project we'll analyze over 50 genomes of plants by integrating diverse data, such as, RNA-Seq, orthology and functional annotation (blast, diamond, interproscan). As an initial approach, the project leaders chose to store data in an well-established ontology-based database (chado) using Python3 and started to develop machado with some objectives in mind: i) to have it integrated to JBrowse via API, and ii) to implement generic data loading tools to store data from some of the main bioinformatics data formats (fasta, gff, obo, bibtex, blast, interproscan, orthomcl). Future demands include the implementation of databases for mammalians species and the development of tools for additional data files such as vcf. The software is in early stage of development and there are many functionalities still remaining to be concluded, most of them related to visualization and interfaces. It is open source under the GPL license. Comprehensive documentation related to software installation/configuration and the data loading/visualization is available at http://machado.readthedocs.io We put extra efforts to make sure it's an inviting open environment in urge for new developers. It is hosted by Github and has a few quality control features, such as, continuous integration, and unit tests. The code contains type annotations and follow the coding styles specified at PEP8 (Style Guide for Python Code) and PEP20 (The Zen of Python). The Github's 'Issues' is the main communication method to inform bugs, request new functionalities and discuss code contributions. We intend to massively use it in further research projects and will be happy to support users and collaborators for the next few years. EMBRAPA is hosting a demo of machado containing only 4 genomes at http://www.machado.cnptia.embrapa.br -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
From: Scott C. <sc...@sc...> - 2019-01-28 23:58:15
|
Hello GMOD, Last week, Yannick Wurm of SequenceServer fame approached me about adding SequenceServer as a GMOD project. It seems like a great fit to me as a general and widely used tool. Please take a moment to read a little about it if you aren't already familiar and if you have any thoughts (pro or con), please let me know. I included email groups of projects that I thought might be interested in SequenceServer. If you know of somebody else involved with GMOD who isn't covered by one of these lists, please feel free to forward it to them. In case you weren't aware, GMOD has guidelines for adding new projects: http://gmod.org/wiki/GMOD_Membership Here is what Yannick wrote in support of his nomination: ----------------------------------------------------------- Dear all, I would like to nominate SequenceServer as a GMOD tool. Background: A major hurdle I stumbled upon a few years ago as collaborators and I began to obtain transcriptome and genome assemblies from new species, was the lack of a simple manner of BLASTing unpublished data. Using a perl/cgi blast script was horrible - and it had a counterintuitive user interface. Same with the tool for custom databases that NCBI supplied at the time. To overcome this, Anurag Priyam (an undergraduate at the time) and I began developing SequenceServer. Its had 3 main aims: - provide an intuitive user interface and elegant user experience that increases researchers productivity - make it easy for individual users to run it autonomously on unpublished or custom data - make it easy to share a BLAST interface with others - in a lab or on a community database (including the - now deprecated antgenomes.org which I ran) It was open source from the start, and has decent success: - 60,000 downloads - >50 citations. - >70 github forks and 130 stars - >190 members on mailing list It is used on dozens of GMOD-esque community sites - often in combination with jBrowse, including: reefgenomics.org http://www.daphnia-stressordb.uni-hamburg.de, hymenopterabase, http://spottedwingflybase.org , bovine genome database, Lepbase, http://www.wheat-tilling.com, PHIbase, GenomeHubs, http://pristionchus.org/about.html, http://planmine.mpi-cbg.de/planmine/begin.do, and many more. Allow me to provide specific comments regarding the GMOD membership criteria below. Please do not hesitate if you have any questions. Kind regards, Yannick ----- Meets a Common Need Growing citations & userbase demonstrate this. Useful Over Time Usage has steadily increased since 2012. The tool wraps BLAST (we are seeking funding to hopefully also wrap DIAMOND). We are implementing novel visualisations to increase analysis power/researchers productivity (including thanks to a recent GSoC). Configurable and Extensible All source code is open. Key configurable things are separated out. - e.g. can use built-tin "sinatra" web server - or go via apache or nginx (as we do on antgenomes.org) - the most common customization is to add links from BLAST hits to specific databases (e.g. genome browser or other cross-ref) - this is done in a modular manner, using custom "links.rb" plugins that remain stable even when the rest of sequenceserver is upgraded. E.g. see http://gmod.org/wiki/JBrowse_FAQ#How_can_I_link_BLAST_results_to_JBrowse Open Source License for All Users GNU AGPL v3 Interoperable With Other GMOD Components All it needs is a directory of one or more FASTA files. There is no internal database (the directory is scanned on launch) - thus we don't connect to Chado. We do nothing with annotations and thus don't support GFF. (the jbrowse page actually has a decent section on linking things up - http://gmod.org/wiki/JBrowse_FAQ#How_can_I_link_BLAST_results_to_JBrowse ) Commitment of Support We've been supporting this without specfic funds since 2012 and hope to be able to continue doing so. Being part of GMOD will hopefully also help attract funding. Mailing list is here: https://groups.google.com/forum/?fromgroups#!forum/sequenceserver The code is well documented, the site and doc page are decent - http://www.sequenceserver.com and http://www.sequenceserver.com/doc/ Issue tracker is here: https://github.com/wurmlab/sequenceserver/issues We are happy to commit to continuing these efforts. We have encouraged (and attracted) code contributions in the past and will continue to do so. Users and Support Mailing List(s) https://groups.google.com/forum/?fromgroups#!forum/sequenceserver Issue tracker is here: https://github.com/wurmlab/sequenceserver/issues Public repository https://github.com/wurmlab/sequenceserver -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |