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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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BCC2020 meeting will be held online
by Dave Clements 24 Mar '20

24 Mar '20

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 before the main meeting, and a CollaborationFest 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://galaxyproject.org/

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Release of Galaxy 20.01
by Marius van den Beek 27 Feb '20

27 Feb '20

Dear Community, The Galaxy Committers team is pleased to announce the release of Galaxy 20.01. The release announcement for developers and admins can be found at https://docs.galaxyproject.org/en/master/releases/20.01_announce.html and user facing release notes are at https://docs.galaxyproject.org/en/master/releases/20.01_announce_user.html. A few release highlights are: Workflow Executions Menu ------------------------ This menu can be reached from the User menu -> Workflow Invocations and lists your recent Workflow executions, their status and links to the Workflow Editor and the History with the results of the Workflow run. Enhanced workflow functionality ------------------------------- Workflows can now make use of optional datasets and optional parameters, optional parameter default values and dataset inputs can now be restricted to user-defined datatypes. The workflow editor and execution engine have been enhanced to allow defining options to choose from, and these options can be connected to compatible text, integer, float, color and select tool parameters for more flexible and universally reusable workflows Galay Markdown Pages and Workflow Reports as PDF ------------------------------------------------ An additional link has been added to Galaxy Markdown Pages and Workflow reports that exports your document as a standalone PDF. Screen Reader friendly Navigation -------------------------------- The top menu and the Workflow Editor have been improved for easier navigation using Screen Readers and the Keyboard. Email-notification for completed jobs ------------------------------------- You can now select to be notified by email when a tool run has finished. Check out the release notes for a lot more details - there are many more enhancements such as new interface elements, visualizations, datatypes and bug fixes as well as instructions for upgrading your Galaxy installation to Python 3. Thanks for using Galaxy!

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BCC2020 Training Topic Voting is Open
by Dave Clements 11 Feb '20

11 Feb '20

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-3GM…>. 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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January Galaxy News: BCC2020, PAG & ABRF; New pubs, platforms, tutorials...
by Dave Clements 08 Jan '20

08 Jan '20

Hello all, The January 2020 Galactic News is out! https://galaxyproject.org/news/2020-01-galaxy-update/ - 13 Upcoming Events - BCC2020 training topic nominations, Register for Galaxy Admin Training, Galaxy @ PAG & ABRF, and training @ Earlham and Rennes. - 172 new publications - Six highlighted pubs from RT-qPCR to functional genomics - Two new blog posts - PGP-UK and Crowdsourcing Science - Galaxy Platform News - Three new platforms, UseGalaxy.* news, and platforms in pubs - Training material and doc updates - R, RStudio, ATAC-Seq, Scanpy, and Single Cell RNA-Seq - And other news too If you have anything to include to next month's newsletter, then please send it to outreach(a)galaxyproject.org. And a happy new year too, :-) Dave C on behalf of the Galaxy community -- https://galaxyproject.org/

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