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December 2020 Galaxy Newsletter: And what a month it is
by Dave Clements 08 Dec '20

08 Dec '20

Hello all, The December 2020 newsletter is out https://galaxyproject.org/news/2020-12-galaxy-update/ And there is a lot to it: ---------------- Event news: Webinars: Use Galaxy anywhere, right now, December 9 Chloroplast Genome Assembly, December 10 First Metabolomics Community Call, December 10 Galaxy Developer Round Table: Working Groups, December 10 Papercuts CollaborationFest: December 17 Galaxy Admin Training: Apply by December 18 Tripal CodeFest 2021: January 11-15 GTN Smörgåsbord: A Global Galaxy Course. Register by February 1 Galaxy platform news: CLIP-Explorer, a new server for CLIP-Seq data GenAP expansion funded by CANARIE (Canada!) UseGalaxy.eu gets more storage and GPUs through deNBI-Cloud Plus more UseGalaxy.* news Blog posts: Outcome of the BioHackathon Europe Accessible single-cell RNA-sequencing bioinformatics training using Galaxy TIaaS and training feedback Training material and doc updates: Chloroplast genome assembly Compute and analyze Essential Biodiversity Variables with PAMPA toolsuite 16S Microbial analysis with Nanopore data Publications Metaproteomics, CLIP-Explorer, GIANT, and package management is your friend Q: Who's hiring? Europe: Max Planck IIE, University of Oslo, Hannover Medical School, EMBL Rome, Norwegian University of Life Science, Sorbonne-Université North America: Roche, Johns Hopkins (AnVIL, 2 positions; Galaxy, 2 Positions), Cleveland Clinic A: Everyone, it seems. New releases: Galaxy 20.09 ENA submission OMERO accessible from Galaxy CloudLaunch Other news too -------------------- Happy Holidays! Dave C and Beatriz, on behalf of, well, everyone -- https://galaxyproject.org/

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Release of Galaxy 20.09
by Marius van den Beek 17 Nov '20

17 Nov '20

Dear Community, The Galaxy Committers team is pleased to announce the release of Galaxy 20.09. The release announcement for developers and admins can be found at https://docs.galaxyproject.org/en/master/releases/20.09_announce.html and user facing release notes are at https://docs.galaxyproject.org/en/master/releases/20.09_announce_user.html. A few release highlights are: GTN In Galaxy -------------------- The Galaxy Training Network tutorials can now be accessed from within Galaxy using the graduation cap icon. For updated tutorials, tools will be highlighted as blue buttons. When clicked, these buttons will hide the GTN and take you directly to the correct version of the correct tool within the Galaxy interface. Plugin framework for uploading datasets ------------------------------------------------------ Galaxy administrators can now configure different sources from which users may upload files. These include global or user-specifc webdav servers, dropbox accounts as well as FTP and regular filesystem locations. Developers can add new types of sources by adding PyFileSystem2 <https://docs.pyfilesystem.org/en/latest/introduction.html> compatible plugins. Upload directly from the Tool Form ---------------------------------------------- Datasets can now be uploaded directly from the Tool Form. Workflow import from GA4GH TRS servers --------------------------------------------------------- Galaxy can now search and import workflows from GA4GH TRS servers, such as Dockstore <https://dockstore.org/> and WorkflowHub <https://workflowhub.eu/>. We hope that sharing workflows on these platforms will facilitate re-use and collaboration. Simplified workflow submission form ------------------------------------------------ Galaxy now presents a simpler and cleaner interface for submitting workflows that focuses on the parameters to set and datasets to choose. Accelerated batch job creation and workflow step scheduling --------------------------------------------------------------------------------- Galaxy now batches database interactions for the creation of batch jobs. For large batches of jobs this can speed up job creation by 100-fold or more. Check out the release notes for a lot more details - there are many more enhancements, new visualizations and bug fixes as well as instructions for upgrading your Galaxy installation. Thanks for using Galaxy!

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November 2020 Galaxy News
by Dave Clements 03 Nov '20

03 Nov '20

Hello all, The November newsletter is out: https://galaxyproject.org/news/2020-11-galaxy-update/ Topics: * JXTX: The James P. Taylor Foundation for Open Science New name, and meet our first awardees * Event news Lots of them, with one starting today (if you are in Australia / East Asia) Galaxy Admin Training will be in late January * Galaxy platform news GalaxyTrakr, Galaxy Africa, Australia, Europe, and UseGalaxy.* * Blog post Advanced Microbiology with Galaxy and TIaaS at Strathclyde * Training material and doc updates Metaproteomics, calling variants, and auto-generated video (!) * Publications Pub curation is on hiatus, but some pubs just can't be ignored :-) * Open positions At 8 organizations. (Yes eight!) * New releases The new Galaxy Language Server Thanks for using Galaxy, Dave C and Beatriz -- https://galaxyproject.org/

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October Galaxy Newsletter
by Dave Clements 07 Oct '20

07 Oct '20

Hello all, The October Galaxy Newsletter is out. https://galaxyproject.org/news/2020-10-galaxy-update/ News on * Event news & JTech Scholarships * Galaxy platform news: BRIDGE, BioCompute Object, French Galaxies, PhagePromoter, and UseGalaxy.* * Blog posts: Remote training, EOSC-Life calls * Training material and doc updates: refgenie magic * Publications * Q: Who's hiring? A: Ten different groups * New releases * Other news too If you have anything to include to next month's newsletter, then please send it to outreach(a)galaxyproject.org. Thanks, Dave C and Bea ________________________________ -- https://galaxyproject.org/

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September 2020 Galaxy Newsletter
by Dave Clements 01 Sep '20

01 Sep '20

Hello all, After a one month hiatus, the monthly Galaxy newsletter (https://galaxyproject.org/news/2020-09-galaxy-update/) is back (and there is a lot going on): * BCC2020 wrap up, and GCC2021 is on the way * More event news (some this week) * Galaxy platform news on * UseGalaxy.fr (!), ML Workbench, deepTS, BioCompute Object, and PiRATE * Blog posts * GVL Bets, SARS-CoV-2 (x2), climate science, get your tool in Galaxy, and Galaxy hits 10K pubs * Training material and doc updates (13 new and updated) * Publications (19 highlighted, 671 total) * Who's hiring * Institut Pasteur, UConn, Johns Hopkins, BSC, VIB & NCBI * New releases of Nebulizer and BioBlend * And other news too If you have anything to include in next month's newsletter, then please send it to outreach(a)galaxyproject.org. Cheers, Dave C -- https://bcc2020.github.io/ https://galaxyproject.org/

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July Galaxy News: BCC2020 Deadlines, Schedule, Fellowships; Galaxy Dev Roundtable, ...
by Dave Clements 01 Jul '20

01 Jul '20

The July 2020 Galaxy News is here: https://galaxyproject.org/news/2020-07-galaxy-update/ In the July 2020 Issue * BCC2020 starts July 17 * Early registration ends July 10 * BoF proposals due July 10 * Fellowships due July 5 * New Silver Sponsor: GalaxyWorks * Full training, talk, and poster/demo schedules are online * Galaxy and the NCBI Sequence Read Archive (SRA) * Upcoming events * Including the new Galaxy Developer Roundtable * Galaxy Platform News * Training material and doc updates * Who's Hiring * New blog posts * New Releases See you online in just over 2 weeks, Dave C -- https://galaxyproject.org/

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Release of Galaxy 20.05
by Marius van den Beek 30 Jun '20

30 Jun '20

Dear Community, The Galaxy Committers team is pleased to announce the release of Galaxy 20.05. The release announcement for developers and admins can be found at https://docs.galaxyproject.org/en/master/releases/20.05_announce.html and user facing release notes are at https://docs.galaxyproject.org/en/master/releases/20.05_announce_user.html. A few release highlights are: Many new Interactive Tools ------------------------------------ Galaxy interactive tools allow a greater depth of analysis via access to GUI-based tools inside an instance. 10 new interactive tools (some previously available only on the UseGalaxy.eu server) join the standard base toolset. Improvements to the Higlass interactive tool now also allow for a more in-depth visualization of multiple datasets in various formats simultaneously. Data Tables can now be backed by refgenie ---------------------------------------------------------- Refgenie manages storage, access, and transfer of reference genome resources. Galaxy can now fill data tables that were received from a refgenie installation. Tool Shed is now Python3 ready ------------------------------------------ As the last component in the Galaxy Codebase the Tool Shed has been ported to Python 3. This concludes a 4 year effort to port the Galaxy codebase to Python 3. Workflow Editor and Workflow Run Form in Vue.js ------------------------------------------------------------------ The Workflow Editor and Workflow Run Form have been re-written in Vue.js. While the functionality has been preserved this lays the groundwork for creating beautiful and reactive custom variants of these components in the future Accelerated Galaxy Startup ------------------------------------- Galaxy now caches expanded tool documents, delays creating the tool search index until after startup and creates search indexes incrementally Check out the release notes for a lot more details - there are many more enhancements such as social login, tool recommendations, visualizations, datatypes and bug fixes. Thanks for using Galaxy!

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June 2020 Galaxy News
by Dave Clements 11 Jun '20

11 Jun '20

Hello all, The June 2020 issue is hot off the presses: https://galaxyproject.org/news/2020-06-galaxy-update/ In this issue: - James Taylor Foundation - BCC2020 will be online, global, affordable, and accessible - Galaxy and the NCBI Sequence Read Archive (SRA) - Upcoming events - Galaxy Platform News - Training material and doc updates - Who's Hiring - New Releases - New publications - And other cool news too If you have anything to include to next month's newsletter, then please send it to outreach(a)galaxyproject.org. Thanks, Dave C -- https://galaxyproject.org/

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May News: James Taylor, BCC2020 Abstracts Close Friday, and much, much more.
by Dave Clements 04 May '20

04 May '20

Hello all, This is our first newsletter since January. It has been an eventful and sorrowful four months for the world, and for the Galaxy Community too: This newsletter starts with the tragic loss of James Taylor, one of Galaxy’s founders and leaders. We lost James at the beginning of April. This community, I suspect, will always feel that loss. The May 2020 issue https://galaxyproject.org/news/2020-05-galaxy-update/ James Peter Taylor , 1979-2020 * BCC2020 will be online, global, affordable, and accessible * All abstracts are due May 8 * Galaxy COVID-19 Response * Upcoming events * Blog posts * Galaxy Platform News * Training material and doc updates * Who’s Hiring * New Releases * New publications (671 of them) * And other cool news too If you have anything to include to next month’s newsletter, then please send it to outreach(a)galaxyproject.org. Thanks, for everything, Dave C -- https://galaxyproject.org/

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BCC2020 Abstract submission and Registration are open
by Dave Clements 27 Apr '20

27 Apr '20

2020 Bioinformatics Community Conference (BCC2020) Online, July 17-26 https://bcc2020.github.io/ The 2020 Bioinformatics Community Conference (BCC2020) will be online, global, affordable, and accessible to all. Key Dates: May 8: Deadline for submitting talk/poster abstracts (this will not be extended) June 6: Authors notified about talk/poster acceptance July 10: Early registration ends July 17-19: BCC2020 tutorials July 19-22: BCC2020 main meeting July 22-24, 24-26: CollaborationFest Core and Encore BCC2020 -> https://bcc2020.github.io/ BCC2020 is a joint event bringing together the BOSC and Galaxy Communities. If you are working in data intensive life science research then there will be no better event this year to share your work, and to learn from others. BCC2020 will be held July 17-26, and offer 2 days of training, a 3 day meeting, and a 4 day CollaborationFest. BCC2020 is Online -> https://bcc2020.github.io/blog/going-virtual All BCC2020 events will be held online. 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 -> https://bcc2020.github.io/blog/going-global BCC2020 events will be held twice: once in the originally scheduled Toronto time zone (BCC West), and then again 12 hours later in the Eastern hemisphere (BCC 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, with participants from every part of the world. BCC2020 is Affordable -> https://bcc2020.github.io/Registration/ We have slashed registration rates for BCC2020, 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 is free. BCC2020 is Accessible Going online and global, combined with the low registration rates make this the most accessible Galaxy and 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 -> https://bcc2020.github.io/submit/ BCC2020 is seeking oral presentations, lightning talks, posters, and demos, from researchers working in bioinformatics, and from all over the world. Abstracts are due May 8 (and that deadline will not be extended). Please submit your work today. Register Now -> https://bcc2020.github.io/Registration/ BCC2020 registration is now open. 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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