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2022 Galaxy Community Conference (GCC2022), July 17-23, Minneapolis, Minnesota, USA
by Pratik Jagtap 28 Feb '22

28 Feb '22

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_…> May 12: Early registration <https://learning.umn.edu/portal/events/reg/participantTypeSelection.do?meth…> ends June 3: Demo and poster abstracts due <https://docs.google.com/forms/d/1z29z8Nd8Gho0trS7DySvWAii6hisbZr67cuI--lcZ_…> 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_…> 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_…> 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! *Organizers of the Galaxy Community Conference (GCC2022)* https://galaxyproject.org/events/gcc2022/

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10 years of the Galactic News: we need your help
by Beatriz Serrano-Solano 10 Jan '22

10 Jan '22

Dear all, Happy new year! For 10 years, we have been sharing news through the monthly Galactic News. This is a milestone and we are so proud of the community that we built together. A lot can change over 10 years and we want to know which parts of the Galaxy newsletter are the most useful and which parts may need to be modified to suit your needs. Please take *2 minutes to fill out **this survey <https://docs.google.com/forms/d/e/1FAIpQLSdws7R3y_4qB4LNNbqx4qYRNlkmuwmnqQ5…>* so that we can create a newsletter that will better serve our growing community. Thank you for reading and here's to the next 10 years, Assunta and Bea

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Release of Galaxy 21.09
by Marius van den Beek 02 Nov '21

02 Nov '21

Dear Community, The Galaxy Committers team is pleased to announce the release of Galaxy 21.09. - Developer and admin release announcement <https://docs.galaxyproject.org/en/latest/releases/21.09_announce.html> - User release announcement <https://docs.galaxyproject.org/en/latest/releases/21.09_announce_user.html> . A few release highlights are: Tool Panel Views We now have "Tool Panel Views"! These are different views into the same toolbox and might help make it easier to find the tools you want. In the future, there are plans to create user-customisable toolboxes, but until then go explore the new EDAM Ontology-based toolboxes which organise tools around scientific areas or processes. For example, a category like "Filtering" might have tools like "select lines" or "filter bam by quality", both doing the same process of filtering, despite their different file types and formats. Unfortunately, not all tools are fully annotated yet, and while we also pull terms from bio.tools, this still doesn't get us full coverage and many tools will still appear under a large section "Uncategorized". Hopefully, this will improve as users and tool developers annotate these tools with the appropriate terms that help everyone find them. Collections (Beta History Updates) Did you ever create *a collection with the wrong dbkey or datatype*? Well, in the Beta History you can now change collections' datatypes and dbkeys! This should save a lot of time for everyone working with large datasets (Pull Request 11799 <https://github.com/galaxyproject/galaxy/pull/11799/>). Additionally, did a *collection ever fail* for you? And you wondered why? Now you can find out with the view details button for collections (Pull Request 12261 <https://github.com/galaxyproject/galaxy/pull/12261>)! Importing Data Selecting datasets from the Remote Files view has gotten easier! Now, you can select folders and files and import at once all of the datasets recursively in those folders. Previously, you could only select files within a folder, so this is a huge improvement in the usability of such a key new feature of Galaxy (Pull Request 12310 <https://github.com/galaxyproject/galaxy/pull/12310>). But with great power comes great responsibility, be careful not to import the entirety of NCBI! Reports Report components used to automatically arrange themselves in a smart way, but due to some issues with the floating of components, these will now be full width until we can figure out a good way to provide a similar feature (Pull Request 12085 <https://github.com/galaxyproject/galaxy/pull/12085>). Enhancements for Working with Remote Data and Distributed Computing Resources Many fixes and enhancements were made to improve how Galaxy can import and write to remote data using the configured file source plugins. In addition to the History Export functionality, which can write to remote locations, we have added an Export datasets Tool for exporting individual Datasets and Dataset collections to configured remote locations. The Tool will automatically maintain the name and structure of Datasets and Dataset Collections. We have added the possibility to import entire folders of remote data and made the data selection dialog more intuitive. We also added numerous improvements and fixes to the extended metadata collection strategy and Pulsar <https://github.com/galaxyproject/pulsar>, so that many more tools are able to run in Pulsar <https://github.com/galaxyproject/pulsar> and write data back to storage without passing through Galaxy first. Migration to FastAPI and Extended Documentation of API Routes We have modernized and migrated many more API routes to FastAPI and have extended the documentation and validation of these routes. Migration to SQLAlchemy 1.4 and Declarative Mapping Galaxy is now using SQLAlchemy <https://www.sqlalchemy.org/> version 1.4, which is a prerequisite for asynchronously interacting with the database. We also modernized the way our database models are defined to the more commonly used Declarative Mapping approach, which is more concise and better documented. Modernization of Tool Form Interface The tool form interface has been almost completely migrated from Backbone <https://backbonejs.org/> to Vue <https://vuejs.org/>. This improves the reactivity of parameter validation and enables the migration of tool parameters to Vue, which will also allow us to add many more types of tool parameters. We further migrated the tool form variant for the Workflow Editor, the Workflow run form and the Show Dataset Parameter page to Vue. New User Welcome Page We have added a page that new users will be directed to after creating a new Galaxy account. Release Notes Please see the full release notes <https://docs.galaxyproject.org/en/latest/releases/21.09_announce.html> for a lot more details and instructions for upgrading your Galaxy installation. Thanks for using Galaxy!

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November 2021 Galaxy Newsletter
by Dave Clements 01 Nov '21

01 Nov '21

Happy November from Galaxy! The November newsletter is thin, *but powerful*: - Galaxy India Launches this Month <https://galaxyproject.org/news/2021-11-galaxy-update/#community-news> - 7 new openings (13 total) <https://galaxyproject.org/news/2021-11-galaxy-update/#community-news> - 9 upcoming Events <https://galaxyproject.org/news/2021-11-galaxy-update/#event-news> - Blog posts on SARS-CoV-2 training in Africa; Sunsetting CloudLaundh; and TIaaS <https://galaxyproject.org/news/2021-11-galaxy-update/#galactic-blog-posts> - UseGalaxy.* Updates <https://galaxyproject.org/news/2021-11-galaxy-update/#galaxy-platforms-news> - Other News too: BY-COVID Launches <https://galaxyproject.org/news/2021-11-galaxy-update/#other-news> Have something for the next newsletter? Please let us know and we will spread the word. Beatriz Serrano-Solano and Dave Clements, Editors -- https://galaxyproject.org/

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October Galaxy News
by Dave Clements 11 Oct '21

11 Oct '21

Hello all, The October Newsletter is out <https://galaxyproject.org/news/2021-10-galaxy-update/>. and it covers Galaxy involvement in Hacktoberfest, and Outreachy, plus a nice batch of trainings, talks and a Galaxy Papercuts CoFest day too. It also brings news of new job openings on two continents, two new platforms, blog posts (where My Little Pony makes an appearance, really), GTN updates (few in number but big in their coolness), publications, and releases. In other words, another active month in the Galaxy. Beatriz Serrano-Solano and Dave Clements, Editors -- https://galaxyproject.org/

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September 2021 News: Papercuts resumes; Misconceptions; Hub updated; microGalaxy Community, ...
by Dave Clements 15 Sep '21

15 Sep '21

Hi all, The September newsletter <https://galaxyproject.org/news/2021-09-galaxy-update/> brings lots of news, including - 12 recent use cases for UseGalaxy.eu, covering a broad spectrum of research. - Want to help address misconceptions about Galaxy? - The Galaxy Community Hub is now using Gridsome. - ELIXIR community updates - JXTX Foundation 2021 Awards - 7 open positions in Belgium, Italy, and the US - The Galaxy YouTube channel is growing up - Upcoming events - Galaxy Platforms News - Recent Blog Posts - Doc, Hub, and Training Updates - Recent Publications - and other news too. Sit back, get comfortable, and explore the Galaxy... Beatriz Serrano-Solano and Dave Clements, Editors -- https://galaxyproject.org/

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Galaxy Newsletter: August 2021
by Beatriz Serrano-Solano 05 Aug '21

05 Aug '21

Hello all, The August newsletter brings news of GCC2021 (just finished) and GCC2022 (in Minneapolis); the launch of the Galaxy India community, and open positions in 7 countries <https://galaxyproject.org/news/2021-08-galaxy-update/#community-news>; event news <https://galaxyproject.org/news/2021-08-galaxy-update/#event-news>; Galaxy platform news <https://galaxyproject.org/news/2021-08-galaxy-update/#galaxy-platforms-news>; Galactic blog posts <https://galaxyproject.org/news/2021-08-galaxy-update/#galactic-blog-activity>; training and doc updates <https://galaxyproject.org/news/2021-08-galaxy-update/#doc-hub-and-training-…>; recent open-access Galaxy-related publications <https://galaxyproject.org/news/2021-08-galaxy-update/#publications>; and other news too <https://galaxyproject.org/news/2021-08-galaxy-update/#other-news>.** Dave Clements and Beatriz Serrano-Solano, Editors PS: Subscribe to the Galaxy Announce mailing list <https://lists.galaxyproject.org/?count=100&all-lists=> and receive an email whenever this newsletter is published. -- Dr Beatriz Serrano-Solano (she/her) <https://www.hrc.org/resources/talking-about-pronouns-in-the-workplace> Bioinformatics Group Dept. Computer Science Albert-Ludwigs-Universität Freiburg Georges-Köhler-Allee, 106 79110 Freiburg Germany

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Galaxy Newsletter: July 2021
by Dave Clements 01 Jul '21

01 Jul '21

Hello all, The big news for July is that the 2021 Galaxy Community Conference <https://gcc2021.sched.com/> is under way. With GCC going on, this is one of our thinner newsletters <https://galaxyproject.org/news/2021-07-galaxy-update/>, but there are still *open positions <https://galaxyproject.org/news/2021-07-galaxy-update/#community-news>*, *event news <https://galaxyproject.org/news/2021-07-galaxy-update/#event-news>*, *Galaxy platform news <https://galaxyproject.org/news/2021-07-galaxy-update/#galaxy-platforms-news>*, *Galactic blog posts <https://galaxyproject.org/news/2021-07-galaxy-update/#galactic-blog-activity>*, *training and doc updates <https://galaxyproject.org/news/2021-07-galaxy-update/#doc-hub-and-training-…>*, recent *open-access Galaxy-related publications <https://galaxyproject.org/news/2021-07-galaxy-update/#publications>*, *new releases <https://galaxyproject.org/news/2021-07-galaxy-update/#releases>, and other news too <https://galaxyproject.org/news/2021-07-galaxy-update/#other-news>.* We hope to see you at GCC events this week and next. Dave Clements and Beatriz Serrano-Solano, Editors PS: It is too late to register for the 3 day conference next week. It is also officially too late to sign up for the CoFest on 9-10 July, but if you follow this link <https://docs.google.com/forms/d/e/1FAIpQLScdJHTzw7LWVxFaqGI30COZlcxGPksjGL_…>, you just mind find yourself invited anyway. -- https://gaaxyproject.org/ <https://galaxyproject.org/>

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Release of Galaxy 21.05
by Marius van den Beek 10 Jun '21

10 Jun '21

Dear Community, The Galaxy Committers team is pleased to announce the release of Galaxy 21.05. The release announcement for developers and admins can be found at https://docs.galaxyproject.org/en/master/releases/21.05_announce.html and user facing release notes are at https://docs.galaxyproject.org/en/master/releases/21.05_announce_user.html. A few release highlights are: ¡Galaxy, ahora en español! ------------------------------------ Thanks to Wendi Bacon, the Spanish language translation of Galaxy has been finalised and merged, so if you prefer to use Galaxy in Spanish, now you can! This update will be part of an ongoing project from Spanish speakers within the Galaxy community to keep the Galaxy interface localisation up to date, and to produce some Spanish language training materials in the GTN. Bugfixes and Stability ----------------------------- This release of Galaxy features fewer user-facing changes, as a huge amount of developer time went into making this a maintenance release with better testing, better stability, and more bugfixes. But watch out, this is all in preparation for the next release of Galaxy, 21.09, which will have some of the biggest changes in years! New development stack -------------------------------- Galaxy release 21.09 will ship with a new web framework (fastAPI <https://fastapi.tiangolo.com/>), Celery <https://docs.celeryproject.org/en/stable/index.html> task queue and process management using Circus <https://circus.readthedocs.io/en/latest/>. You can preview this new stack now by running *APP_WEBSERVER=dev ./run.sh*. Celery for background tasks -------------------------------------- Galaxy can now run certain tasks in the background. The Celery workers are currently not required, but if activated can perform certain long-running tasks, such as creating history export archives. Celery tasks will bridge the gap between rapid requests that can be handled during a web request and jobs that require extensive and relatively slow setup. More robust selection of job handlers ------------------------------------------------- Job throughput can be increased by starting Galaxy with multiple external job handler processes. Jobs were traditionally assigned to a job handler process by the web handler or workflow handler process that created the job. Since Release 19.01 Galaxy has supported additional mechanisms that use database serialization techniques to let job handlers assign processes to themselves. This mechanism is more robust and doesn't require that all job handler processes be alive and known by the web handler process. Galaxy now determines the best method for assigning jobs based on the database in use, if the assignment method is not set explicitly. Older job assignment methods will be removed in Galaxy release 21.09. For more details see the Job Handler Assignment Methods section <https://docs.galaxyproject.org/en/release_21.05/admin/scaling.html#job-hand…> of the Galaxy documentation. Check out the full release notes <https://docs.galaxyproject.org/en/master/releases/21.05_announce.html> for a lot more details, there are many more enhancements, new visualizations and bugfixes as well as instructions for upgrading your Galaxy installation. Thanks for using Galaxy!

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GCC2021 Deadlines Approaching
by Dave Clements 04 Jun '21

04 Jun '21

Hello all, The early registration deadline for the 2021 Galaxy Community Conference has been moved back to June 8. This gives you more time to take advantage of the 50% discount off full registration prices, so make sure you sign up now so you don't miss out! Register here <https://www.vibconferences.be/events/gcc2021-virtual-edition#attendees>. The draft program <https://gcc2021.sched.com/> and the speakers are now also available online. Please bear in mind that the times are set for the Europe/Middle East/Africa - Asia/Pacific window, and that the same schedule will run 9 hours later for the Americas. The availability of the speakers for the Q&A session will depend on the time zone in which they are located. Posters and demo sessions can still be submitted <https://www.vibconferences.be/events/gcc2021-virtual-edition#abstracts> until the 14th of June. Feel free to distribute this message further in your network. We hope to meet you online! Dave Clements on behalf of the GCC2021 Organizing Committee -- https://galaxyproject.org/

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