- galaxy-announce - lists.galaxyproject.org

🗓️Reminder: 5 days left to submit GCC2024 abstracts
by Natalie Whitaker-Allen 10 Apr '24

10 Apr '24

[logo]<https://galaxyproject.us22.list-manage.com/track/click?u=099b2f5f23bf0134dc…> GCC2024 Announcements Abstracts for Talks Only 5 days left to submit! This is a friendly reminder that there are only 5 days left to submit abstracts for talks at GCC2024. The deadline for abstract submission is April 15th, 2024. We welcome abstract submissions for oral presentations on a wide range of topics related to Galaxy, including methods and pipelines, new Galaxy features, and data science education with Galaxy. Don't miss this chance to be a part of GCC2024 and contribute to the vibrant Galaxy community; submit your abstract today! Submit your Abstract<https://galaxyproject.us22.list-manage.com/track/click?u=099b2f5f23bf0134dc…> Thank you for being a part of Galaxy! Get more timely information by following us on Mastodon<https://galaxyproject.us22.list-manage.com/track/click?u=099b2f5f23bf0134dc…>, Bluesky<https://galaxyproject.us22.list-manage.com/track/click?u=099b2f5f23bf0134dc…>, and LinkedIn<https://galaxyproject.us22.list-manage.com/track/click?u=099b2f5f23bf0134dc…>! View email in browser<https://mailchi.mp/6f812309cd3b/reminder-5-days-left-to-submit-gcc2024-abst…> Johns Hopkins University · 3400 N Charles St · Baltimore, MD 21218-2608 · USA update your preferences<https://galaxyproject.us22.list-manage.com/profile?u=099b2f5f23bf0134dceb27…> or unsubscribe<https://galaxyproject.us22.list-manage.com/unsubscribe?u=099b2f5f23bf0134dc…>

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Invitation from Wendi Bacon: Join the Galaxy Community Board!
by Natalie Whitaker-Allen 05 Apr '24

05 Apr '24

Dear Galaxy Special Interest Groups! We are building up the Galaxy Community Board<https://galaxyproject.org/community/governance/gcb/>, which is a group of individuals representing the various communities of practice and regional communities<https://galaxyproject.org/community/sig/> across Galaxy. This board works with the Galaxy Technical Board and Executive Board to elicit global changes to support our work across Galaxy - indeed, we’ve already fed into the USA roadmap on behalf of multiple user communities coming together. Additionally, the GCB - which only meets every 3 months - provides a setting for us to exchange best practices, templates, and other helpful wisdom or resources to make running our respective groups easier. In sum, please send a representative or two to our Galaxy Community Board so we can help each other and prevent the evils of work duplication! 📪Mailing list<https://lists.galaxyproject.org/lists/sig-chairs.lists.galaxyproject.org/> 📝 Meeting notes doc<https://docs.google.com/document/d/19zv4rata-uVhFW43S8v_Fw83RVYq6jDGXy-1T8A…> ☕ Matrix Chatroom<https://matrix.to/#/#usegalaxy_commreps:matrix.org> 🗓️Galaxy Working Group GoogleCalendar<https://calendar.google.com/calendar/embed?src=f6b4dbe4aa3d7076e740e4198aa4…> Given the diversity of user base and interest across the special interest groups, we also make an effort to set clear agendas before our meetings, so only if the meeting will be useful to given SiGs do representatives show up, and you’re welcome to call a meeting topic yourself! Hope to see some of you at the next GCB meeting (May 9th!)! Wendi

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Galaxy 24.0 Release
by Natalie Whitaker-Allen 04 Apr '24

04 Apr '24

Hello Galaxy Community, We are thrilled to announce the release of Galaxy 24.0, packed with exciting new features and enhancements to improve your workflow experience. Here are some of the highlights: 1. New Workflow List and Card View: We've revamped the workflows user interface with new list and card views, along with quick access tabs for "My workflows," "Shared with me," and "Published workflows." 1. New ‘Select’ Component: A new component allows for selecting a large number of options with ease. It features a list-based layout, keyboard accessibility, and options for filtering and bulk selection. 1. Multiple Item Drag and Drop + Keyboard Navigation: You can now select multiple history items and drag them into other histories or tool forms. Keyboard navigation is also supported for easier history management. 1. Consolidated Resource Grids: Histories, visualizations, and pages are now consolidated into tab views for a more streamlined interface. 1. Move Datasets Between Storage Locations: Easily relocate datasets to new object stores using the new UI feature. The interface provides a clear visual representation of storage attributes and admin-provided details. To learn more about all that Galaxy 24.0 has to offer, please see the user release notes<https://docs.galaxyproject.org/en/master/releases/24.0_announce_user.html>. Upgrade today to take advantage of these enhancements and more! We are committed to continuously improving Galaxy to meet your needs and make your research more efficient. Your feedback is invaluable to us, so please don't hesitate to share your thoughts and suggestions. Thank you for using Galaxy! Bluesky<https://bsky.app/profile/galaxyproject.bsky.social> | Mastodon<https://mstdn.science/@galaxyproject> | LinkedIn<https://www.linkedin.com/company/galaxy-project>

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GCC2024 Updates: General Registration, Abstract Submissions, and Scholarship Reminders!
by Natalie Whitaker-Allen 07 Mar '24

07 Mar '24

Dear Galaxy Community, General registration is now open for the 2024 Galaxy Community Conference (GCC2024) in Brno, Czech Republic! Join us for this exciting event to connect with fellow community members and developers, learn about the newest and upcoming developments in Galaxy, and contribute to the vibrant Galaxy community. Key Details: Date: June 24th*29th, 2024 Location: Brno, Czech Republic Conference Website<https://galaxyproject.org/events/gcc2024/> and Registration Link<https://register.oxfordabstracts.com/event/5248?preview=true> Abstract Submission Reminder: A friendly reminder that the deadline for submitting abstracts for talks is April 15, 2024. Share your research, insights, and experiences with the community by presenting a talk at GCC2024. Submit your abstract, here<https://galaxyproject.org/events/gcc2024/abstracts/>! JXTX + GCC2024 Scholarship Application Deadline: Don't miss the opportunity to apply for the JXTX + GCC2024 Scholarship, provided by the JXTX Foundation and the Galaxy Project. The scholarship supports graduate students in genomics and data sciences to attend GCC2024. The application deadline is March 31st, 2024. For more information and to apply, please visit the JXTX Foundation website<https://jxtxfoundation.org/news/2024-2-19-gcc/>. We look forward to welcoming you to GCC2024 and to Brno, Czech Republic, for an enriching and inspiring conference experience! Thank you for using Galaxy; see you in Brno! Bluesky<https://bsky.app/profile/galaxyproject.bsky.social> | Mastodon<https://mstdn.science/@galaxyproject> | LinkedIn<https://www.linkedin.com/company/galaxy-project>

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Last Chance for Early Registration – GCC2024 Early Bird Deadline Tomorrow!
by Natalie Whitaker-Allen 29 Feb '24

29 Feb '24

Dear Galaxy Community, This is a friendly reminder that the early registration deadline for the Galaxy Community Conference 2024 (GCC2024) is tomorrow, March 1st, 2024. This is your last chance to take advantage of the early bird registration prices. After the early registration deadline, prices will increase, so we encourage you to register today to secure the best rates and join us for this exciting event. Please visit the conference website<https://galaxyproject.org/events/gcc2024/> to register and view the conference program, speakers, and workshops. Don't miss out on this opportunity to save on your registration! We look forward to welcoming you to GCC2024. Thank you for using Galaxy; see you in Brno! Bluesky<https://bsky.app/profile/galaxyproject.bsky.social> | Mastodon<https://mstdn.science/@galaxyproject> | LinkedIn<https://www.linkedin.com/groups/4907635/>

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GCC2024 Early Registration Reminder – Register by March 1st, 2024!
by Natalie Whitaker-Allen 26 Feb '24

26 Feb '24

[A sign with black text and a yellow background Description automatically generated] Dear Galaxy Community, We hope this message finds you well. We want to remind you that the early registration deadline for the 2024 Galaxy Community Conference (GCC2024) is approaching fast! Early registration closes on March 1st, 2024. By registering early, you can take advantage of the early bird registration prices. After the early registration deadline, prices will go up, so we encourage you to register soon to secure the best rates. To register for GCC2024 and to learn more about the conference program, speakers, and workshops, please visit the conference website<https://galaxyproject.org/events/gcc2024/>. Thank you for using Galaxy; see you in Brno! Bluesky<https://bsky.app/profile/galaxyproject.bsky.social> | Mastodon<https://mstdn.science/@galaxyproject> | LinkedIn<https://www.linkedin.com/groups/4907635/>

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GCC2024 Scholarship Opportunity: JXTX + GCC2024 Scholarship
by Natalie Whitaker-Allen 21 Feb '24

21 Feb '24

[cid:image001.png@01DA64B1.A3FB10E0] Hello, Galaxy Community! We are thrilled to announce the JXTX + GCC2024 Scholarship, a collaboration between the JXTX Foundation<https://jxtxfoundation.org/> and the Galaxy Project<https://galaxyproject.org/>. This scholarship will support six outstanding graduate students in genomics and data sciences and offers a unique opportunity for students to attend the 2024 Galaxy Community Conference in Brno, Czech Republic, furthering their knowledge and networking within the field! The scholarship will be awarded in two tiers: • The first tier will be awarded to three individuals and will cover conference registration plus transportation to and from the conference (up to 1,000€). • The second tier will be awarded to three individuals and will cover conference registration only. Key Dates: • Deadline for application: March 31, 2024 • Winners announced: April 10, 2024 Applicants should plan to present their work at the conference as a talk or a poster. This scholarship presents an excellent opportunity for students to showcase their research and engage with a diverse community of professionals and researchers. For more information on how to apply, please visit the JXTC + GCC2024 Scholarship page<https://jxtxfoundation.org/news/2024-2-19-gcc/>. We encourage all eligible students to apply and look forward to receiving your applications and abstracts! Thank you for using Galaxy; see you in Brno! Bluesky<https://bsky.app/profile/galaxyproject.bsky.social> | Mastodon<https://mstdn.science/@galaxyproject> | LinkedIn<https://www.linkedin.com/groups/4907635/>

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Announcing Galaxy 23.2: Exciting New Features and Enhancements!
by Natalie Whitaker-Allen 06 Feb '24

06 Feb '24

Hello, Galaxy Community! We are happy to announce the release of Galaxy 23.2, packed with exciting new features and enhancements to elevate your Galaxy skills and experience! Here are some the highlights of what's included in this release: * InvenioRDM Integration: We're excited to announce the integration of InvenioRDM into Galaxy! Import files directly from InvenioRDM repositories into Galaxy, and effortlessly publish Galaxy records, including Histories and datasets, to InvenioRDM. This integration streamlines data import and export processes, enhancing your overall Galaxy experience. * Introducing Workflow Comments: Collaborate like never before with our brand-new Workflow Comments feature in the Galaxy Workflow Editor. Now, you can visually explain and structure your workflows with ease, facilitating better communication and organization among team members. [Example of a structured workflow.] * Revamped Published Workflow Sharing Page: Experience a more informative, visually appealing, and user-friendly Published Workflow Sharing page. With new features such as a read-only mode, embedded interactive editor view, additional workflow information, and enhanced responsiveness for smaller screens, sharing and navigating workflows has never been smoother. [The new Workflow Sharing page.] Be sure to upgrade to Galaxy 23.2 to take advantage of these fantastic new features and upgrades! For detailed information on the full release, please refer to our user release notes<https://docs.galaxyproject.org/en/master/releases/23.2_announce_user.html>. We look forward to your continued support and feedback as we strive to continuously improve Galaxy! Thank you for being a part of Galaxy! Bluesky<https://bsky.app/profile/galaxyproject.bsky.social> | Mastodon<https://mstdn.science/@galaxyproject> | LinkedIn<https://www.linkedin.com/groups/4907635/>

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GCC2024: Early bird registration now open!
by Natalie Whitaker-Allen 17 Jan '24

17 Jan '24

[A black and white image of a city Description automatically generated] Hello, Galaxy Community! We are thrilled to announce that early bird registration for the 2024 Galaxy Community Conference (GCC2024) is now open! Join us in the beautiful city of Brno, Czech Republic, from June 24th to 29th, 2024, for an unforgettable experience of learning, collaboration, and networking. We encourage you to take advantage of our early bird registration discounted rates; for more information and to register or submit an abstract, please see the GCC2024 website<https://galaxyproject.org/events/gcc2024/>. Why Attend GCC2024? * Learn from experts in your field * Collaborate with like-minded users and researchers * Stay updated on the latest developments in Galaxy * Ample opportunities for networking Stay Tuned for Exciting Updates: We have more in store for our community! Keep an eye out for upcoming announcements on: * Keynote speakers who will inspire and share insights * Training and workshop opportunities to enhance your skills * Networking and social events to connect with fellow participants Don't miss out on this opportunity to join a diverse community of researchers, developers, and Galaxy users from around the world! Thank you for being a part of Galaxy; see you in Brno! Get more timely info by following us on Mastodon<https://mastodon.social/@galaxyproject@mstdn.science>, Bluesky<https://bsky.app/profile/galaxyproject.bsky.social>, and LinkedIn<https://www.linkedin.com/groups/4907635/>!

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Galaxy Newsletter December 2023: End-of-year Wrap-up!
by Natalie Whitaker-Allen 19 Dec '23

19 Dec '23

December 2023 [https://lh7-us.googleusercontent.com/AiAsl1Jc_HEGctLGVW6Si8dMJpV-hETvan7mOG…] Hello, Galaxy Community! Firstly, the Galaxy team would like to extend our warmest wishes to you and all your loved ones this holiday season! With the New Year rapidly approaching, we wanted to thank you all for being a part of the Galaxy Community in 2023; we couldn’t do it without you, and we are excited for what is to come! As a part of the final newsletter for 2023, we are including an end-of-year wrap-up to highlight some of Galaxy's successes and updates over the past year. We also are including a preview of what is to come in 2024, and we hope you are as excited as we are! ________________________________ Galaxy 2023 End-of-year Wrap-up: Another Year Around the Galaxy To celebrate Galaxy’s 18th year, we have put together an infographic highlighting the top Galaxy events, features, and scientific drivers of 2023! To view the infographic, please view this PDF<https://drive.google.com/file/d/1QhMWQ3JHJNtoUB169adcfb_788uo9hqT/view?usp=…>. ________________________________ Galaxy 2023 Success Stories We are excited to share just a few of the Galaxy's scientific success stories in 2023. This year, we are thrilled to have been a part of over 1,400 papers, which brings our total to over 16,000! Check out our “Citations per year” graph from Google Scholar<https://scholar.google.com/citations?hl=en&user=3tSiRGoAAAAJ>. The success of our users helps drive Galaxy to adapt and improve its features, and we cannot wait to see the continued success of our users over the next year! [https://lh7-us.googleusercontent.com/VX24V7DsFCJYJuDAc2yLmo1AJE6x3lpqUfjXof…] See below for a brief highlight on each story, and view the full paper for each article to learn more! While there are many more success stories from 2023, each of these articles was chosen by our users and developers who wished to highlight specific features or advances in Galaxy. * A Galaxy of informatics resources for MS-based proteomics (Mehta et al., 2023) As mass spectrometry (MS) technology progresses, there is a growing demand for bioinformatics tools that can effectively analyze complex MS-based proteomic data. The Galaxy bioinformatics ecosystem is designed to meet these analysis needs by providing a diverse range of open-source tools tailored for MS-based proteomics applications. This ecosystem operates on a flexible, scalable, and easily accessible computing platform. Galaxy's distinctive feature, provenance tracking, enables users to save and share comprehensive analysis histories and workflows. This capability extends to various MS-based proteomics techniques, including shotgun proteomics, data-independent acquisition MS-based quantitation, multi-omics, MS imaging, as well as results visualization and interpretation. Researchers have successfully employed existing workflows within the Galaxy ecosystem in diverse fields such as COVID-19 pandemic research, proteogenomics, metaproteomics, MS imaging, and clinical studies involving MS-based proteomics with patient-derived samples. Additionally, Galaxy provides access to training resources, fostering awareness and facilitating the widespread adoption of these tools within the research community. Read the full paper!<https://www.tandfonline.com/doi/abs/10.1080/14789450.2023.2265062> * Sequential and directional insulation by conserved CTCF sites underlies the Hox timer in stembryos (Rekaik et al., 2023) In this study, the researchers aim to understand better the mechanism governing the Hox gene timer, in which the activation of Hox genes occurs in a temporal sequence based on their positions within gene clusters. To address this, stembryos derived from mouse embryonic stem cells were obtained, and various next-generation sequencing (NGS) analyses and figure-generation techniques were applied. These techniques included RNA-seq, single-cell RNA-seq, ChIP and ChIP-M, CHi-C, and HiChIP. Galaxy was utilized for all NGS analyses, excluding single-cell RNA-seq. The findings indicated that the precision and pace of the Hox gene timer are regulated by the presence of evolutionarily conserved and regularly spaced intergenic CTCF sites. Read the full paper!<https://www.nature.com/articles/s41588-023-01426-7> * Galaxy Training: A powerful framework for teaching! (Hiltemann et al., 2023) Bioinformatics has assumed a pivotal role in the realm of research studies across the natural sciences due to the continuous generation of scientific datasets resulting from numerous technological advancements. Despite the significant influx of knowledge and scientific progress facilitated by the proliferation of datasets, there exists a substantial gap in basic computational skills and data analysis. To bridge this skill gap and empower researchers, the Galaxy Training Network introduced the Galaxy Training Platform. This platform, a community-driven framework accessible to all, compiles FAIR (Findable, Accessible, Interoperable, and Reusable) training materials tailored for data analyses within the Galaxy environment. Since its launch, the Galaxy Training Platform has surpassed expectations, emerging as a reliable repository featuring hundreds of tutorials from numerous contributors worldwide. Initially rooted in the natural sciences, the platform has expanded its scope to encompass diverse subjects such as climatology, cheminformatics, and machine learning. Furthermore, the Galaxy Training Platform has transcended its original purpose of supporting researchers, now serving as a valuable resource for educators. This paper highlights the recent advancements in the Galaxy Training Platform and explores how the Galaxy Training Network has evolved to facilitate the integration of its materials into classroom settings. Read the full paper!<https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1010…> * MetaboLights: open data repository for metabolomics (Yurekten et al., 2023) MetaboLights serves as a global database for metabolomics studies, encompassing both the raw experimental data and associated metadata. It stands as the recommended repository for metabolomics by several prominent journals and the European Infrastructure for Life Science Information (ELIXIR). This paper delves into the notable progress made by MetaboLights in recent years, emphasizing the introduction of MetaboLights Labs, a new instance within Galaxy. The objectives of this Galaxy instance are threefold: 1) to streamline the reuse of MetaboLights data through high-quality analysis tools, 2) to empower users to analyze their own data, and 3) to foster collaboration with researchers for the contribution of community tools and workflows. Galaxy is enthusiastic about being a part of MetaboLight's recent advancements in FAIR data science and is looking forward to seeing what they do next! Read the full paper!<https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkad1045/74244…> * Training Infrastructure as a Service (Rasche et al., 2023) Instructors often face significant hurdles when planning and organizing training courses, such as a lack of needed technical resources and expertise, complications with queue contention and managing resources, and adapting to the rise of virtual and hybrid teaching. To help make training more accessible and adaptable, a collaboration between Galaxy Europe, the Gallantries, and the Galaxy community has developed Training Infrastructure-as-a-Service (TIaaS) with the goal of delivering user-friendly training infrastructure to the global training community. TIaaS is designed to offer dedicated training resources specifically for Galaxy-based courses and events. TIaaS represents a substantial enhancement for instructors, learners, and infrastructure administrators alike. The instructor dashboard facilitates the feasibility and simplicity of remote events, and students benefit from a seamless learning experience, as all training occurs on Galaxy, a platform they can continue to utilize post-event. The success of TIaaS has been substantial, as over the past 60 months, 504 training events, engaging more than 24,000 learners, have utilized this infrastructure for Galaxy training. Read the full paper!<https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giad04…> Finally, we would like to direct your attention to our running list of publications that cite Galaxy on Zotero<https://www.zotero.org/groups/1732893/galaxy> and Google Scholar<https://scholar.google.com/citations?user=3tSiRGoAAAAJ&hl=en&authuser=1>! Galaxy tries to keep up with all publications from our users, but if you have a paper you would like to see highlighted either in a Galaxy Newsletter or on social media, please use this form<https://docs.google.com/forms/d/e/1FAIpQLSemRJuFm_C8NASuCeWuWtlcYVp6BVd9NRs…> to let us know! We would love to see all the amazing work you have been doing with Galaxy, as this not only helps us know what our users are accomplishing but also helps guide us in developing new features! ________________________________ Looking Ahead: Galaxy in 2024 There is much to look forward to from Galaxy in 2024! Most notably, the 2024 Galaxy Community Conference<https://galaxyproject.org/events/gcc2024/> (GCC2024) is scheduled for June 24–29th in Brno, Czech Republic. While we are rapidly planning for this year's fantastic keynote speakers, workshops, and networking opportunities, we encourage you to sign up to receive GCC2024-specific announcements here<https://gaggle.email/join/gcc2024-announce@gaggle.email>! Additionally, Galaxy is ecstatic to be once again participating at the International Plant & Animal Genome (PAG 31)<https://intlpag.org/31/> conference set to be held from January 12–17th in San Diego, CA, USA! Galaxy will be hosting a workshop titled “Galaxy for NGS Data Analysis: A Hands-on Workshop”, where we will be sharing a brief introduction to Galaxy and working with participants to walk through an advanced microbiome tutorial. Additionally, this year we are thrilled to also include two users, Katherine Ulbricht and Nia Davis from Spelman College, in our workshop, who will share their personal Galaxy user success stories! Finally, Galaxy has a lineup of some incredible new features to be introduced to the interface in 2024. From a new Galaxy Help Tool to user-interface simplifications, users can expect Galaxy to continue to grow and advance throughout 2024! See the Galaxy Roadmap<https://galaxyproject.org/roadmap/> for a detailed listing of features planned for the next 6 to 12 months. ________________________________ Upcoming Events DATE EVENT VENUE/LOCATION 12–17 January 2024 International Plant & Animals Genome Conference<https://intlpag.org/31/> San Diego, CA, USA 4–8 March 2024 Workshop on High-Throughput Data Analysis with Galaxy<https://galaxyproject.org/events/2024-03-04-galaxy-workshop-freiburg/> University of Freiburg, Germany 7-11 May 2024 CSHL Biology of Genomes<https://meetings.cshl.edu/meetings.aspx?meet=GENOME&year=24> Cold Spring Harbor, NY 24–29 June 2024 2024 Galaxy Community Conference<https://galaxyproject.org/events/gcc2024/> Brno, Czech Republic ________________________________ JXTX Foundation “The most important job of senior faculty is to mentor junior faculty and students.” - JXTX In memory of James P. Taylor, one of the original founders of the Galaxy Project, the JXTX Foundation<https://jxtxfoundation.org/> was created to enable and support ongoing mentoring of young and diverse faculty and students to the best Open Science computational biology. JXTX + CSHL 2023 Genome Informatics Scholarship Awardees Congratulations to this year’s JXTX + CSHL 2023 Genome Informatics scholarship awardees! We cannot wait to see what they bring to this year's conference. Check out our awardees below: [https://lh7-us.googleusercontent.com/IxahNkBcDlcFks9rQKH5OZXqBs8wlWKMj0KVz9…] How to donate The JXTX Foundation is now proudly a 501(c)(3)! Please consider donating online through the foundation’s website<https://jxtxfoundation.org/donate/>! Your contribution will support the foundation's efforts by providing graduate student scholarships, academic mentorship, and sponsoring student outreach. ________________________________ To conclude, Galaxy is going to be increasing communications on the ‘galaxy-dev’ mailing list! Anyone running a local installation, wrapping tools, and otherwise expanding the Galaxy ecosystem is encouraged to join the galaxy-dev mailing list<https://lists.galaxyproject.org/lists/galaxy-dev.lists.galaxyproject.org/>. Typical discussions regard features, bugs, and new ideas. Announcements from the Galaxy Team are also sent to this list. Subscription is open to all! Thank you for being a part of the Galaxy Community, and happy holidays! Get more timely info by following us on Mastodon<https://mastodon.social/@galaxyproject@mstdn.science>, Twitter (X)<https://twitter.com/galaxyproject?ref_src=twsrc%5Etfw%7Ctwcamp%5Eembeddedti…>, Bluesky<https://bsky.app/profile/galaxyproject.bsky.social>, and LinkedIn<https://www.linkedin.com/groups/4907635/>!

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