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自动回复: galaxy-announce Digest, Vol 105, Issue 1
by 2496867710 22 Mar '22

22 Mar '22

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Announcing BOSC 2022, the 23rd Bioinformatics Open Source Conference
by Bérénice Batut 22 Mar '22

22 Mar '22

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_4lYTFPg5… 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

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Release of Galaxy 22.01
by Marius van den Beek 15 Mar '22

15 Mar '22

Dear Community, The Galaxy Committers team is pleased to announce the release of Galaxy 22.01. - Developer and admin release announcement <https://docs.galaxyproject.org/en/master/releases/22.01_announce.html>. - User release announcement <https://docs.galaxyproject.org/en/master/releases/22.01_announce_user.html> . A few release highlights are: New Colour Selector Do you use tools which require colour inputs, like Circos? Previously, we had a very restricted colour input which gave you a very limited palette. Now, you have complete freedom of choice with the modern colour selector. Improved File Export If you've been exporting files from Galaxy lately, you've probably seen the amazing new remote file source export, which allows you to export files to FTP, Dropbox, and other locations. Improved File Uploads Previously, Galaxy servers used a variety of methods to let you upload large files easily, including some servers which required FTP for large files. We have replaced this with a new upload method, which will be enabled on all usegalaxy servers soon. This will make file uploads significantly smoother, and will be more tolerant of network failures and interruptions! You do not need to make any changes. Beta History: Collection Improvements If you've been trying out the beta history (which will be the default history in the next release!), it has been updated to indicate whether collections are homogeneous or heterogeneous. This will help you see more easily if you've accidentally included an incorrect dataset. Galaxy starts as a FastAPI application by default Starting Galaxy via run.sh will use the new gravity process manager <https://github.com/galaxyproject/gravity>. The new configuration uses Gunicorn <https://gunicorn.org/> and FastAPI <https://fastapi.tiangolo.com/> to drive Galaxy's web process, and starts job handler and Celery <https://docs.celeryproject.org/> processes automatically. For more details and instructions, please consult the Migrating to Gunicorn documentation <https://docs.galaxyproject.org/en/latest/admin/migrating_to_gunicorn>. User Preferences can be encrypted in Galaxy Vault Galaxy can now be configured to store secrets in an external vault, which is useful for secure handling and centralization of secrets management. In particular, information fields in the "Manage information" section of the user profile, such as dropbox keys, can be configured to be encrypted at rest in a vault (Hashicorp, Custos or database) instead of being stored as plain text in the user preferences table. For detailed information on configuration, refer to the vault section <https://docs.galaxyproject.org/en/release_22.01/admin/special_topics/vault.…> of the admin documentation. Release Notes Please see the full release notes <https://docs.galaxyproject.org/en/latest/releases/22.01_announce.html> for a lot more details and instructions for upgrading your Galaxy installation. Thanks for using Galaxy!

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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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