galaxy-announce March 2022

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自动回复: galaxy-announce Digest, Vol 105, Issue 2
by 2496867710 29 Mar '22

29 Mar '22

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MiniGateways 2022 Conference, April 5-7 - It’s FREE
by Beatriz Serrano-Solano 29 Mar '22

29 Mar '22

*Registration for MiniGateways 2022 is FREE but required. **Register now!* <http://ec2-54-202-43-228.us-west-2.compute.amazonaws.com/x/d?c=20511062&l=4…> *MiniGateways 2022* /April 5-7, 2022/ Connections for the Future Registration <http://ec2-54-202-43-228.us-west-2.compute.amazonaws.com/x/d?c=20511062&l=4…>for MiniGateways 2022 is NOW OPEN! Save your spot and sign up for tutorials! Last December we announced MiniGateways 2022 with a “Save the Date” message. The *schedule and presenters* <http://ec2-54-202-43-228.us-west-2.compute.amazonaws.com/x/d?c=20511062&l=3…>are now finalized. The virtual conference is open for *registration: **https://sciencegateways.org/minigateways2022-registration* <https://urldefense.proofpoint.com/v2/url?u=https-3A__sciencegateways.org_mi…> Register before April 1 to receive a surprise in the mail! *MiniGateways 2022* <http://ec2-54-202-43-228.us-west-2.compute.amazonaws.com/x/d?c=20511062&l=3…>**will offer a variety of presentations, tutorials, options for interaction, and opportunities to build connections for the future with the community around science gateways. /What you’ll get from our program:/ * Join us on Tuesday and Wednesday for exciting Tutorial sessions where you can *gain in-depth expertise on specific topics* * Join us on Wednesday and Thursday for exciting *short talks on topics contributed by the community * * Join our interactive Open Forum on Thursday *for discussing emerging topics for science gateways* * Opportunities to *grow your network* by meeting people in the community who are users, developers, or providers of gateways

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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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galaxy-announce March 2022