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May 2021 Galaxy Newsletter: GCC2021 Deadlines Extended
by Dave Clements 04 May '21

04 May '21

Hello all, *The May 2021 edition of Galaxy News <https://galaxyproject.org/news/2021-05-galaxy-update/> is out! * The big news is that *several deadlines for the 2021 Galaxy Community Conference <https://galaxyproject.org/news/2021-05-galaxy-update/#community-news> have been extended, and the deadline for submitting James Taylor videos <https://galaxyproject.org/news/2021-05-galaxy-update/#featured-news> has been extended to this Friday.* And there are other upcoming deadlines too: - *ISMB/ECCB and BOSC 2021 abstracts <https://galaxyproject.org/news/2021-05-galaxy-update/#event-news> are due this Thursday.* - *Apply for the Galaxy Australia Variant Calling Workshops <https://galaxyproject.org/news/2021-05-galaxy-update/#event-news> by May 12.* We also have - *open positions <https://galaxyproject.org/news/2021-05-galaxy-update/#community-news>* - *webinars, CoFests, workshops, community meetups, and other events <https://galaxyproject.org/news/2021-05-galaxy-update/#event-news>*, - news about *public Galaxy platforms <https://galaxyproject.org/news/2021-05-galaxy-update/#galaxy-platforms-news>* , - recent *blog posts <https://galaxyproject.org/news/2021-05-galaxy-update/#galactic-blog-activity>* , - *training and doc updates <https://galaxyproject.org/news/2021-05-galaxy-update/#doc-hub-and-training-…>* , - recent *open-access Galaxy-related publications <https://galaxyproject.org/news/2021-05-galaxy-update/#publications>*, and - *new releases <https://galaxyproject.org/news/2021-05-galaxy-update/#releases>.* As always, thanks for using Galaxy, Dave Clements and Beatriz Serrano-Solano, Editors -- https://galaxyproject.org/

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April 2021 Galaxy newsletter
by Beatriz Serrano-Solano 13 Apr '21

13 Apr '21

Hello all, This newsletter coincides with the anniversary of James Taylor's death <https://galaxyproject.org/news/2021-04-galaxy-update/#featured-news> on April 2, 2020. James was a Galaxy Project founder and PI, and losing him at the same time as the global COVID-19 shutdown made for a tough month, and then a tough year for the Galaxy Community. To mark this, there are two items about James below. First, *a call to share your favorite story about James* via a 30 second video (by April 30). Second, there is a link to *a note to James* written by project leadership (mainly Anton). The other big news is that registration, abstract submission, and fellowship applications for the 2021 Galaxy Community Conference are now open <https://galaxyproject.org/news/2021-04-galaxy-update/#community-news>. Abstracts and fellowship applications are due by May 7. And as always there are sections on - *upcoming events <https://galaxyproject.org/news/2021-04-galaxy-update/#event-news>*, - news about *public Galaxy platforms <https://galaxyproject.org/news/2021-04-galaxy-update/#galaxy-platforms-news>* , - recent *blog posts <https://galaxyproject.org/news/2021-04-galaxy-update/#galactic-blog-activity>* , - *training and doc updates <https://galaxyproject.org/news/2021-04-galaxy-update/#doc-hub-and-training-…>* , - recent *open-access Galaxy-related publications <https://galaxyproject.org/news/2021-04-galaxy-update/#publications>*, and - *new releases <https://galaxyproject.org/news/2021-04-galaxy-update/#releases>.* It's been a memorable twelve months. It would have been easy to curl up and hide, but we kept going, addressed gaps, and helped address the global pandemic as well. Thanks for supporting each other, Dave Clements and Beatriz Serrano-Solano, Editors

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March 2021 Galaxy Newsletter
by Dave Clements 17 Mar '21

17 Mar '21

Hello all, It is a very busy time in the Galaxy. 2021 is young, but we have already had two large training events, including the largest Galaxy event ever - the GTN Smörgåsbord (with an amazing 1100+ people registered). We are ramping up for GCC2021, which will be online, global, and affordable, and will be more accessible (and likely much larger) than an in-person Galaxy Community Conference. Galaxy is also shifting with the times, and to reflect how our community has grown. This newsletter includes a new *Featured News <https://galaxyproject.org/news/2021-03-galaxy-update/#featured-news>* section highlighting 1) the *recent explosion of videos* related to Galaxy, 2) a draft *global governance model for Galaxy*, and 3) the new *Galaxy Career Center.* That's followed by another new section highlighting *community news <https://galaxyproject.org/news/2021-03-galaxy-update/#community-news>.* Arguably, *everything* here is community news, but items listed here particularly emphasize the community aspects of Galaxy. The newsletter still includes sections on - *upcoming events <https://galaxyproject.org/news/2021-03-galaxy-update/#event-news>*, - news about *public Galaxy platforms <https://galaxyproject.org/news/2021-03-galaxy-update/#galaxy-platforms-news>* , - recent *blog posts <https://galaxyproject.org/news/2021-03-galaxy-update/#galactic-blog-activity>* , - *training and doc updates <https://galaxyproject.org/news/2021-03-galaxy-update/#doc-hub-and-training-…>* , - recent *open-access Galaxy-related publications <https://galaxyproject.org/news/2021-03-galaxy-update/#publications>*, and - *new releases <https://galaxyproject.org/news/2021-03-galaxy-update/#releases>.* It's a lot to take in, but it all highlights the breadth and depth of the Galaxy Community. Enjoy, Dave Clements and Beatriz Serrano-Solano, Editors [image: 2021-03-16_14-51-56-wordcloud.png] -- https://galaxyproject.org/

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Release of Galaxy 21.01
by Marius van den Beek 16 Mar '21

16 Mar '21

Dear Community, The Galaxy Committers team is pleased to announce the release of Galaxy 21.01. The release announcement for developers and admins can be found at https://docs.galaxyproject.org/en/master/releases/21.01_announce.html and user facing release notes are at https://docs.galaxyproject.org/en/master/releases/21.01_announce_user.html. A few release highlights are: Workflows: Best Practices, Reports, Invocations ---------------------------------------------------------------- Workflows have seen huge improvements in this release! The workflow report editor is easier than ever to use, providing you with a list of common report components, interactive interfaces for embedding them in your reports, and a new workflow invocation tracker. You can now embed visualizations directly in your workflow reports making summarizing your analyses easier than ever. And, once your reports are produced, you can export them directly to pages to share your reports with colleagues.If you’re building advanced workflows utilizing Galaxy’s powerful sub-workflows for reusable workflow components, then you’ll be pleased to know you can now automatically update those to the latest version Remote Files ------------------ The Remote Files interface is an absolutely fantastic new way to browse your data. Inside Galaxy there is a new, abstract way to reference files locally and on other servers. This lets us provide a uniform interface to FTP servers, your Dropbox, public S3 buckets, and more! You'll find this under Choose Remote Files in the upload interface. This interface is also used for importing and exporting histories. Beta History Panel ------------------------- The History Panel is getting a refresh and a huge performance boost in the latest code. Does this sound exciting to you? Try it out now with the history menu option "Use Beta History Panel". This is not its final state but we'd love feedback from you, the users, on how you find it. It features both performance and usability improvements. E.g. now you can rename files without going into a separate menu, just double click the dataset title! Performance Improvements ------------------------------------- This release includes many performance improvements for browsing and searching Data libraries, improved job creation performance for certain classes of tools and copying Histories, Datasets and Dataset Collections Offload Zip Archive Creation to NGINX --------------------------------------------------- Galaxy can now utilize the NGINX module mod_zip to assemble and compress dataset collection and library dataset archives on the fly. This method is more efficient and can create large archives without affecting the Galaxy server process. The required setup is described in the admin documentation for proxying Galaxy with NGINX. Check out the full release notes <https://docs.galaxyproject.org/en/master/releases/21.01_announce.html> 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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February 2021 Galaxy Newsletter
by Beatriz Serrano-Solano 08 Feb '21

08 Feb '21

Hi Galaxy Community! The *February 2021 Newsletter <https://galaxyproject.org/news/2021-02-galaxy-update/#event-news>* is out. This time we announce that *GCC2021 goes virtual*, unfortunately. However, this will make it more affordable, and globally accessible to everyone. Other updates include: - *Event news <https://galaxyproject.org/news/2021-02-galaxy-update/#event-news>*: training, webinars, CoFests, conferences... - *Platform news <https://galaxyproject.org/news/2021-02-galaxy-update/#galaxy-platforms-news>*: ATACgraph, corGAT on Laniakea, UseGalaxy.eu - *9 Blog posts <https://galaxyproject.org/news/2021-02-galaxy-update/#galactic-blog-activity>* - *Training material and doc updates <https://galaxyproject.org/news/2021-02-galaxy-update/#doc-hub-and-training-…>*: Admin training, scRNA-seq, videos, new tutorials... - *Publications <https://galaxyproject.org/news/2021-02-galaxy-update/#publications>*: 8 highlights - *Who’s hiring?* <https://galaxyproject.org/news/2021-02-galaxy-update/#whos-hiring> more than 12 open positions - *New releases <https://galaxyproject.org/news/2021-02-galaxy-update/#releases>* - *Other news <https://galaxyproject.org/news/2021-02-galaxy-update/#other-news>* If you have anything to include to next month’s newsletter, then please send it to outreach(a)galaxyproject.org. Thanks for reading, Dave C and Bea

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January 2021 Galaxy Newsletter
by Dave Clements 07 Jan '21

07 Jan '21

Hello all, We are pleased to announce the first newsletter of 2021. As you can see there is a lot happening this month, starting with a working groups call about one hour from now. Thank you for persevering through 2020, and we hope that 2021 will be a better year for the world, and for this community. Dave Clements and Beatriz Serrano-Solano - *Event news <https://galaxyproject.org/news/2021-01-galaxy-update/#event-news>*: - 2nd Galaxy-ELIXIR webinar series, *starts January 20* - Galaxy Developer Roundtables, *January 7 & 21* - Papercuts CollaborationFest: *January 21* - Future Galaxy Admin Trainings, *Register your interest* - Tripal CodeFest 2021: *January 11-15* - Structural Variant Detection using ONT Data, *January 26* - GTN Smörgåsbord: A Global Galaxy Course. *Register by February 1* - Single-cell RNA-seq & network analysis using Galaxy and Cytoscape, *Apply by 26 February* - *Galaxy platform news <https://galaxyproject.org/news/2021-01-galaxy-update/#galaxy-platforms-news>:* - UseGalaxy.no - VINYL on Laniakea - W4M on UseGalaxy.fr - Center for Phage Technology server upgraded and improved - Plus more UseGalaxy.* news - *Blog posts <https://galaxyproject.org/news/2021-01-galaxy-update/#galactic-blog-activity>:* - Involvement of the Galaxy community in OLS-2 and invitation to apply to the next cohort - DDA and DIA proteomic analysis in Galaxy - GTN plant-related trainings - *Training material and doc updates <https://galaxyproject.org/news/2021-01-galaxy-update/#doc-hub-and-training-…>*: - Videos: Galactic Introductions - Videos: Quick Tips - *Publications <https://galaxyproject.org/news/2021-01-galaxy-update/#publications>* - Metaproteomics, CorGAT (SARS-CoV-2), GAIT-GM (metabolites), and training - *Q: Who's hiring? <https://galaxyproject.org/news/2021-01-galaxy-update/#whos-hiring>* - Europe: - Norwegian University of Life Science, IFB, VIB - North America: - Roche, Johns Hopkins (AnVIL, 2 positions; Galaxy, 2 Positions) - *New releases <https://galaxyproject.org/news/2021-01-galaxy-update/#releases>*: - Planemo 0.74.1 -- https://galaxyproject.org/

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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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