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Galaxy Newsletter September 2023
by Natalie Whitaker 13 Sep '23

13 Sep '23

September 2023 [https://lh6.googleusercontent.com/MZemkzi9MKIMf5z6tZwsnDVrmwYPMPFmB10L7CfnE…] Hello, Galaxy Community! Galaxy is excited to announce the relaunch of our Galaxy Newsletter! We are thrilled to share updates on Galaxy, including topics such as events, scientific successes, and general community announcements. ________________________________ GCC2023 Meeting Report GCC2023 was a tremendous success! Hosted by Galaxy Australia and the Australian BioCommons in Brisbane, Australia, 91 in-person and 40 virtual attendees from 21 countries came together for a week of scientific and technical discovery, collaboration, and networking. We are pleased to share the GCC2023 Meeting Report, which highlights this year’s community conference, and a playlist of all the talks from the conference. Recorded talks playlist<https://www.youtube.com/playlist?list=PLNFLKDpdM3B9PicSdtM_kKeOPvZoD1wSQ> Meeting Report<https://galaxyproject.org/blog/2023-08-14-gc-c2023-meeting-report/> One more thing - GCC2024 will be held in Brno, Czech Republic! Stay tuned for dates and updates. ________________________________ Galaxy Success Stories * MOM: A user-friendly Galaxy workflow to detect modifiers from genome sequencing data using C. elegans (Maroilley, T. et al., 2023) This brand-new paper shows how Galaxy was used to help address a significant issue in demystifying genetic modifiers: identification. Forward genetics screening and whole genome sequencing identify thousands of candidate variants at a time, making the process of identification longer than it needs to be. To contribute to the need for a broader implementation of whole genome sequencing in genetic screens for model organisms, the researchers developed a Model Organism Modifier (MOM) pipeline in Galaxy. This new Galaxy workflow analyses raw short-read whole genome sequencing data and applies personalized filtering, creating a Candidate Variant List. This list, now much shorter, can then be manually curated for easier, faster genetic modifier identification! Read the full paper: MOM: A user-friendly Galaxy workflow to detect modifiers from genome sequencing data using C. elegans | G3 Genes <https://academic.oup.com/g3journal/advance-article/doi/10.1093/g3journal/jk…> * Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy (Larivière et al., 2023) This new paper, now in preprint, presents the latest genome assembly pipeline used by the Vertebrate Genome Project in Galaxy (VGP-Galaxy pipeline 2.1). This new pipeline is freely accessible through Galaxy, which directly contributes to Galaxy’s mission of reproducible, open-source, and FAIR (Findability, Accessibility, Interoperability, and Reuse of digital assets) data analysis! Read the full paper: Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy | bioRxiv<https://www.biorxiv.org/content/10.1101/2023.06.28.546576v1.full> * PlantTribes2: Tools for comparative gene family analysis in plant genomics (Wafula et al., 2023) In an effort to address the inaccessibility of comparative genomic and phylogenomic analysis and computational resources, researchers have introduced PlantTribes2, a gene family analysis framework freely available on Galaxy! PlantTribes2 uses existing, high-quality plant genomes to assist in comparative and evolutionary studies and can improve and sort transcript models, perform downstream analysis, and customize visualizations. Perhaps most importantly, PlantTribes2 can be adapted to any organism for use in genomic and transcriptomic data! Read the full paper: PlantTribes2: Tools for comparative gene family analysis in plant genomics | Frontiers in Plant Science<https://www.frontiersin.org/articles/10.3389/fpls.2022.1011199/full> * Galaxy ASIST: A web-based platform for mapping and assessment of global standards of antimicrobial susceptibility: A case study in Acinetobacter baumannii genomes (Sharma et al., 2023) Whole-genome sequencing-based diagnosis has become the gold standard for supplementing microbiology methods for antimicrobial susceptibility testing (AST). In this study, researchers developed a freely available automated pipeline in Galaxy, Galaxy-ASIST, to characterize clinical isolates based on standards integrated into the workflow. Galaxy-ASIST indicated that only 10% of publically accessible datasets have the metadata to implement the standards presented in this paper, highlighting the need for a universal platform and framework for AST. The researchers attest that Galaxy-ASIST meets the needs presented in this paper and could provide the single globally acceptable framework for AST profiling for clinical isolates! Read the full paper: Galaxy ASIST: A web-based platform for mapping and assessment of global standards of antimicrobial susceptibility: A case study in Acinetobacter baumannii genomes | Frontiers in Microbiology <https://www.frontiersin.org/articles/10.3389/fmicb.2022.1041847/full> ________________________________ 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 The JXTX Foundation is proud to be able to sponsor six outstanding graduate students in genomics and data science to attend the 2023 CSHL Genome Informatics conference<https://meetings.cshl.edu/meetings.aspx?meet=info&year=23> at Cold Spring Harbor Laboratory. To learn more about this scholarship and to apply, please visit JXTX + CSHL 2023 Genome Informatics Scholarship<https://jxtxfoundation.org/news/2023-04-07-gi>. The application deadline is 11:59 PM (US Eastern Time) on Friday, September 15th, 2023. How to donate The JXTX Foundation 501(c)(3) application is still pending, but you can donate through Zeffy now on 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. ________________________________ Upcoming: Galaxy (v23.1) Release Stay tuned for the upcoming release of Galaxy v23.1! This release will introduce new features, such as carbon emissions reporting, a new history archive, and a new Galaxy notification system. For our Galaxy power users, you can look forward to Galaxy v23.1, allowing you to visualize HDF5 datasets, create new activity bar items, and see invocations related to specific history! ________________________________ Upcoming Events DATE EVENT VENUE/LOCATION 20-22 September 2023 International Plant and Animal Genome Conference Australia<https://intlpagaustralia.org/23/> Westin Perth, Australia 21 September 2023 Small Scale Galaxy Admins Meeting<https://galaxyproject.org/events/2023-09-small-scale/> Online, Global 4-6 October 2023 European Galaxy Days (EGD)<https://galaxyproject.org/> Freiburg, Germany 9-13 October 2023 Workshop on Single-cell Data Analysis with Galaxy<https://galaxyproject.org/events/2023-10-09-single-cell-galaxy-workshop-fre…> University of Freiburg, Germany 6-9 December 2023 Genome Informatics Conference<https://meetings.cshl.edu/meetings.aspx?meet=info&year=23> Cold Spring Harbor Laboratory, NY, USA 12-17 January 2023 International Plant and Animal Genome Conference<https://www.intlpag.org/31/> San Diego, CA, USA ________________________________ Thank you for being a part of the Galaxy Community! Get more timely info by following us on Twitter <https://twitter.com/galaxyproject?ref_src=twsrc%5Etfw%7Ctwcamp%5Eembeddedti…> and LinkedIn<https://www.linkedin.com/groups/4907635/>! If you have ideas for the type of content you’d like to see in this newsletter in the future, let us know via this short form<https://forms.gle/qV6Y3JZzsrtzxGiS9>.

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Final call: Virtual fellowships, poster and demo abstracts!
by Natalie Whitaker 30 May '23

30 May '23

Hello Galaxy Community, A friendly reminder that posters and demo session abstract submissions for the 2023 Galaxy Community Conference (GCC2023) in Brisbane, Australia, are due this Friday, June 2nd! Please use this form<https://docs.google.com/forms/d/e/1FAIpQLSejz4TgwlDZaydMhWeBSdH5C7ACc930K86…> to submit your abstract. We are excited to see all the hard work you have been putting into Galaxy! Additionally, fellowship applications for virtual attendance are also due on Friday, June 2nd. We highly encourage you to take advantage of this opportunity to participate in GCC2023 remotely! To apply, please fill out this form<https://docs.google.com/forms/d/e/1FAIpQLSdaA3EGI3LwEpWZfThSCA87DHKag7hSg1b…>. Interested in GCC2023 but not completely sure what it is about? Read on! The annual meeting of the global Galaxy community is heading to Australia in July. As well as getting up close to koalas, GCC2023 offers a great chance to network with others who are passionate about data-intensive science. There will be opportunities to hear about the latest cutting-edge improvements to the platform, as well as learn how to apply its capabilities to specialized areas. These meetings are always a fun way to connect with Galaxy developers and share your thoughts, ideas, and vision for the future of Galaxy. This friendly and inexpensive conference uniquely welcomes both biologists and software developers. Come to the conference to present your work, talk with peers, and collaborate with colleagues. As well as showcasing the latest in Galaxy advanced capabilities, you'll see demonstrations of how researchers are using Galaxy and get hands-on training in how to use of Galaxy for topics including machine learning, microbiology, structural biology and Alphafold, genomics, genome annotation, genome assembly, single cell transcriptomics and human genetics. Stay longer to deepen your involvement at the optional Collaboration Fest. Local keynote speakers include Assoc Prof Roberto Barrero Gumiel from Queensland University of Technology, who will share how he uses Galaxy to enhance Australia’s plant biosecurity. Dr Carolyn Hogg from the University of Sydney is demonstrating how Galaxy contributes to her research in biodiversity conservation genomics of Australia's native animals. University of NSW structural biologist, Dr Kate Michie, will present insights into how she uses Alphafold in Galaxy. There is a wide diversity of talks, posters, and interactive sessions to choose from in the program. Take this special trip to Australia for GCC2023 from 10-16 July 2023 and connect with the Galaxy community; or register to watch the keynote talks online from home! See you all in the land down under! Sincerely, The Galaxy Project Find us on Twitter! @galaxyproject<https://twitter.com/galaxyproject>

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GCC2023 Schedule Announcement and Early Bird Registration!
by Natalie Whitaker 08 May '23

08 May '23

Hello Galaxy Community, We are elated to share the schedule for the 2023 Galaxy Community Conference (GCC2023) in Brisbane, Australia! GCC2023 will consist of the main meeting, interactive training, and a collaboration fest (CoFest)<https://galaxyproject.org/events/gcc2023/cofest/>. The main meeting and the training are interleaved on the same days (July 10th*July 13th) with the CoFest following (July 14th*16th). Each day of the meeting, there will be three sessions, morning talks, mid-day training, and afternoon talks, with breaks and lunch in between. Training events will consist of five parallel tracks, each session being 2.5 hours long. More details for each of the trainings will be provided as we approach the conference. CoFest is a community gathering by the members who are interested in contributing to Galaxy's tool set, documentation, training materials, code base, and anywhere else that expands the Galaxy ecosystem. CoFest participants will coalesce around shared interests and address common topics related to those interests. These clusters form before, at the beginning of, and throughout CoFest and will be fluid and highly interactive with each other. To see a full outline of the GCC2023 schedule, a list of talks and accompanying abstracts, and an overview of our three fabulous keynote speakers, please visit the GCC2023 website<https://galaxyproject.org/events/gcc2023/schedule/>! A friendly reminder, early bird registration, along with the accompanying early bird discount, ends this Friday, May 12th! Register today, here<https://www.eventbrite.com.au/e/galaxy-community-conference-2023-tickets-54…>! We look forward to seeing you all in Brisbane! Sincerely, The Galaxy Project Find us on Twitter! @galaxyproject<https://twitter.com/galaxyproject>

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GCC2023: Final Keynote Speaker Announcement!
by Natalie Whitaker 28 Apr '23

28 Apr '23

Hello Galaxy Community, The time has come, we are excited to announce our third and final Keynote Speaker for the 2023 Galaxy Community Conference (GCC2023)! It’s our pleasure to share that Dr. Barrero, Associate Professor at Queensland University, will be showcasing his research in agriculture, plant biosecurity, and human health. Please see more about our fantastic final Keynote Speaker, below! [2jhmDNgAAAABJRU5ErkJggg==] Associate Professor Roberto Barrero Gumiel Senior Bioinformatics Solutions Architect Academic Division, Research Portfolio, eResearch “A/Professor Roberto Barrero has joined the Queensland University of Technology bringing his Bioinformatics expertise to contribute tackling real world problems in Agriculture, Plant Biosecurity and Human Health. He has led the bioinformatics analysis of a range of projects with applications in both the agricultural and biomedical domains. He has formal training in molecular biology and developed bioinformatics skills over 15 years working as part of large international collaboration consortia including Human Invitational Consortium, Rice Annotation Project, Cattle tick Genome Sequencing Consortium, and the International Barley Genome Consortium. He has conducted analysis and comparative genomics in crop plants, pathogenic bacteria, viruses, animal genomics and human diseases. He has devised innovative strategies in experimental design in a range of large genomics initiatives in model and non-model species. He led the implementation of customized computational workflows to data analysis to enable advanced research applications, run bioinformatics workshops, and mentored and supervised other bioinformaticians and PhD students. More recently, he led a multidisciplinary team at the Plant Biosecurity Cooperative Research Centre to develop a plant diagnostic toolkit that accurately detects a range of viruses and viroids in a single test. Dr. Barrero and the team were awarded the ‘Biosecurity Impact Award 2018’ recognizing their measurable change to plant biosecurity by delivering research outcomes to end-users and change in policy for the quarantine screening of viruses in ornamental grasses. He has been invited to be the Project Coordinator of an international collaboration involving National Plant Protection Organizations from nine countries to harmonize standards and best practices for regulatory application of high throughput technologies for phytosanitary diagnostics.” We hope you are as excited as we about our three amazing Keynote Speakers for GCC2023! See you all in Brisbane! Sincerely, The Galaxy Project Find us on Twitter! @galaxyproject<https://twitter.com/galaxyproject>

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GCC2023 Keynote Speaker Announcement: Dr. Kate Michie!
by Natalie Whitaker 26 Apr '23

26 Apr '23

Hello Galaxy Community, Ready to know our second keynote speaker? We are ecstatic to share that Dr. Kate Michie from the University of New South Wales will joining us at the 2023 Galaxy Community Conference (GCC2023) in Brisbane, Australia! Dr. Michie will be showcasing her work in Structural Biology; please see more about Dr. Michie’s astounding background and her exceptional research, below! [w9ESElC8hVejgAAAABJRU5ErkJggg==] Dr. Kate Michie Senior Lecturer Structural Biology Facility Mark Wainwright Analytical Centre University of New South Wales “Dr. Michie is a Senior Lecturer at the University of New South Wales (in BABS and the Structural Biology Facility MWAC) with over two decades of expertise in Protein Structural Biology. She has completed her doctoral degree from the University of Sydney and received prestigious fellowships from L'Oréal-UNESCO and Marie Curie to continue her research at the Laboratory of Molecular Biology in Cambridge, UK (2006-2010). Her research primarily focuses on molecular biology of filament forming proteins, with a particular interest in structural biology. Dr. Michie has published papers in top scientific journals, including Nature, Molecular Cell, and PNAS, and has made significant contributions to the field of bacterial cell division, in the field of filament forming proteins and more recently in light harvesting proteins from algae. Dr. Michie has also been involved in various community roles within the field of structural biology. She established the Structural Biology Facility at UNSW in 2019, which provides state-of-the-art resources for researchers in the field. She is the coordinator for the Greater Sydney Collaborative Access Program for MX beamtime at the Australian Synchrotron, the President of the Sydney Protein Group, and established the Computational Structural Biology Workgroup at UNSW, bringing together researchers across campus who use computational structural biology resources. Aside from her research, Dr. Michie also uses Alphafold2 extensively, which she has helped set up in the cloud at UNSW within 2 weeks of the code being publicly released. She has worked closely with a wide range of researchers to teach them how to use this powerful tool to advance their research and has already had several successful collaborative grants awarded for projects impacted by Alphafold2. Dr. Michie's drive and leadership in this area have been instrumental in providing UNSW researchers with access to the computing resources they need to stay competitive on a world stage.” We cannot wait to showcase Dr. Michie and learn more about her research at GCC2023! Sincerely, The Galaxy Project Find us on Twitter! @galaxyproject<https://twitter.com/galaxyproject>

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GCC2023 Keynote Speaker Announcement: Dr. Carolyn Hogg!
by Natalie Whitaker 24 Apr '23

24 Apr '23

Hello Galaxy Community, We are excited to announce the first of our three keynote speakers who will be joining us at the 2023 Galaxy Community Conference (GCC2023) in Brisbane, Australia! Our first phenomenal speaker is the Senior Research Manager for the Australasian Wildlife Genomics Group and uses Galaxy to address biodiversity challenges and promote species’ resilience in Australia. See more about the fantastic Dr. Carolyn Hogg below! Dr. Carolyn Hogg Senior Research Manager Australasian Wildlife Genomics Group School of Life and Environmental Sciences University of Sydney [cid:a8aac929-8dde-4588-8989-f26fd1662cc9] “I have been working on the conservation of threatened species for over 25 years, both in Australia and overseas. I am currently the Senior Research Manager for the Australasian Wildlife Genomics Group in the Faculty of Science. I have been working with the Save the Tasmanian Devil Program for the past 10 years, in addition to other species such as orange-bellied parrots, koalas, bilbies, and woylies. Working closely with both my academic and conservation management partners, my vision is to create a conservation legacy for Australia by changing the way we integrate science, management, and policy to proactively promote species’ resilience in the face of a changing world. We are achieving this by developing better tools and technologies to integrate molecular genetics into real-time conservation management decisions.” We are thrilled to showcase Dr. Hogg and her research at GCC2023! Stay tuned for more information on this year’s keynote speakers! Sincerely, The Galaxy Project Find us on Twitter! @galaxyproject<https://twitter.com/galaxyproject>

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Themes & fonts & tool search, oh my! Galaxy 23.0 is here!
by Natalie Whitaker 14 Apr '23

14 Apr '23

[cid:05aad615-b16b-4cf1-b1ca-65a4eadea69d] Hello, Galaxy Community! We are ecstatic to announce the release of Galaxy 23.0! Now more accessible, inclusive, speedy, and lively, Galaxy 23.0 brings out the best of Galaxy while honing the features that make Galaxy the success it is! This release includes significant user interface changes that enhance accessibility and usability. New features include a new tool search, a modernized multi-history view, new tag displays, theme support, and better drag-and-drop handling across the application. There are also brand new 'Datatypes' and 'About This Galaxy' interfaces. Interactive Tools are now more seamlessly integrated into the user interface, and now Galaxy also includes a new MGnify Notebook IT. In addition, the workflow editor has been completely overhauled with significant improvements to usability and extensibility, including new conditional workflow step functionality. Want to see a complete overview of the new release? Visit the Galaxy Release 23.0 Highlights here<https://docs.galaxyproject.org/en/master/releases/23.0_announce_user.html>! Sincerely, The Galaxy Project Find us on Twitter! @galaxyproject<https://twitter.com/galaxyproject>

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GCC2023 Fellowship Applications and Abstracts Due Friday!
by Natalie Whitaker 10 Apr '23

10 Apr '23

[cid:0bf31bd7-4f04-4673-a8f7-a6b0fc47bb56] Hello, Galaxy Community! A friendly reminder that fellowship applications and presentation abstracts for the 2023 Galaxy Community Conference<https://galaxyproject.org/events/gcc2023/> (GCC2023) are due this Friday, April 14th! Submit your abstract here<https://docs.google.com/forms/d/e/1FAIpQLSejz4TgwlDZaydMhWeBSdH5C7ACc930K86…>. Apply for one of the two offered fellowships (both in-person and virtual attendance) here<https://docs.google.com/forms/d/e/1FAIpQLSdaA3EGI3LwEpWZfThSCA87DHKag7hSg1b…>. The GCC2023 gathering will bring together scientists, software developers, and trainers of Galaxy from a variety of disciplines to share their experiences, knowledge, and skills. The Galaxy Project is passionate about open-source science, making your work with the platform essential to our community! We look forward to learning about your research with Galaxy and encourage you to take this opportunity to network and connect with the Galaxy Community. Sincerely, The Galaxy Project Find us on Twitter! @galaxyproject<https://twitter.com/galaxyproject>

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GCC2023 Abstract Deadline Extended!
by Natalie Whitaker 04 Apr '23

04 Apr '23

Hello, Galaxy Community! In response to requests from members of the Galaxy Community needing more time to prepare for the 2023 Galaxy Community Conference (GCC2023) in Brisbane, Australia, we have extended the abstract submission deadline until April 14th, 2023! Please use this form to submit your abstract<https://docs.google.com/forms/d/e/1FAIpQLSejz4TgwlDZaydMhWeBSdH5C7ACc930K86…>. A friendly reminder for those interested in attending, fellowships are now available thanks to a generous anonymous donor! Submit your application via this form<https://docs.google.com/forms/d/e/1FAIpQLSdaA3EGI3LwEpWZfThSCA87DHKag7hSg1b…>; we are rooting for you! · 2 in-person fellowships: covers conference and CoFest registration, conference dinner, 4 nights accommodation, and up to AU$500 in travel costs (applicant must also submit a talk abstract). · 10 virtual fellowships: covers virtual conference registration (applicant must submit an abstract for a poster or demo and present online). For more information on GCC2023, please visit our website<https://galaxyproject.org/events/gcc2023/>! Best of luck to you all, and we are excited to meet you all in Brisbane! Many thanks, The Galaxy Project Find us on Twitter! @galaxyproject<https://twitter.com/galaxyproject>

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GCC2023 abstracts are due TODAY!
by Natalie Whitaker 03 Apr '23

03 Apr '23

Hello, Galaxy Community! Today is the day! Abstracts are due today, April 3rd, for the 2023 Galaxy Community Conference (GCC2023) in Brisbane, Australia! If you haven’t already, please submit your abstracts here<https://docs.google.com/forms/d/e/1FAIpQLSejz4TgwlDZaydMhWeBSdH5C7ACc930K86…>. An exciting reminder, fellowships are now available for virtual and in-person attendance and participation at GCC2023! For your application to be considered, your abstract must be submitted. Please fill out this form<https://docs.google.com/forms/d/e/1FAIpQLSdaA3EGI3LwEpWZfThSCA87DHKag7hSg1b…> to apply for one of this year’s fellowship opportunities. We look forward to reviewing your abstracts and learning about the fantastic work you are all accomplishing with Galaxy! See you soon! Sincerely, The Galaxy Project [cid:e9c07d82-e143-41b1-9d38-716bf6b3e989] Find us on Twitter! @galaxyproject<https://twitter.com/galaxyproject>

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