September 2023
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.
One more thing - GCC2024 will be held in Brno, Czech Republic! Stay tuned for dates and updates.
Galaxy Success Stories
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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
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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
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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
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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!
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 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 at Cold Spring Harbor Laboratory. To learn more about this scholarship and to apply, please visit JXTX + CSHL 2023 Genome Informatics Scholarship.
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! 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
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