diff --git a/posts/2025-01-07-microgalaxy-preprint.md b/posts/2025-01-07-microgalaxy-preprint.md new file mode 100644 index 0000000..c31a7e1 --- /dev/null +++ b/posts/2025-01-07-microgalaxy-preprint.md @@ -0,0 +1,150 @@ +--- +media: + - mastodon-eu-freiburg + - matrix-eu-announce + #- bluesky-galaxyproject + - linkedin-galaxyproject + +mentions: + mastodon-eu-freiburg: + - galaxyproject@mstdn.science + - bebatut@piaille.fr + - bgruening@fosstodon.org + - pvanheus@mstdn.science + - nsoranzo@mstdn.science + bluesky-galaxyproject: + - galaxyproject.bsky.social + - bebatut.bsky.social + - fpsom.bsky.social + - shiltemann.bsky.social + - pratikomics.bsky.social + - pvanheus.bsky.social + - nsoranzo.bsky.social + + +--- + +Our preprint **"microGalaxy: A gateway to tools, workflows, and training for accessible, reproducible, and FAIR microbial data analysis"** is live! πŸŽ‰ +πŸ“ Read it here: https://www.biorxiv.org/content/10.1101/2024.12.23.629682v1 +#Microbiome #FAIRdata + + +🌟 What is microGalaxy? It’s a community-driven platform for microbial data analysis! + +πŸ”Ή 220+ tools +πŸ”Ή 65+ workflows +πŸ”Ή 45+ tutorials +Built with FAIR principles to empower microbiology research from genomes to multi-omics. + +Learn more below! + +![graphical abstract](https://raw.githubusercontent.com/usegalaxy-eu/galaxy-social/2025-01-07-microgalaxy-preprint/posts/images/2025-01-07-microgalaxy-preprint-graphical-abstract.png) + + +Here’s a sneak peek of what microGalaxy offers: + +πŸ” Overview of supported microbial data analysis tasks (e.g., genomics, proteomics, multi-omics) and their outputs. + +#Reproducibility + +![Figure 1](https://raw.githubusercontent.com/usegalaxy-eu/galaxy-social/2025-01-07-microgalaxy-preprint/posts/images/2025-01-07-microgalaxy-preprint-figure-1.png) + + + +πŸ”§ Galaxy has been a key player in microbial research. See how microbial-specific studies contribute to its growing impact in this citation trend analysis. + +![Attach Supplementary Figure 1: Citation trends and microbial research topics](https://raw.githubusercontent.com/usegalaxy-eu/galaxy-social/2025-01-07-microgalaxy-preprint/posts/images/2025-01-07-microgalaxy-preprint-supp-figure-1.png) + + + +🌍 Community-driven innovation! In 2023, we surveyed researchers to uncover key needs in microbial data analysis. + +πŸ”Ή Targeted tools +πŸ”Ή Challenges of Galaxy and non-Galaxy users +πŸ”Ή Deployment preferences + +Your input shaped microGalaxy! πŸ™Œ + +![Attach Supplementary Figure 2: Survey results](https://raw.githubusercontent.com/usegalaxy-eu/galaxy-social/2025-01-07-microgalaxy-preprint/posts/images/2025-01-07-microgalaxy-preprint-supp-figure-2.png) + + + + +βš™οΈ Always evolving: + +(A) Tool availability spans 220+ tool suites across various Galaxy servers. + +[Heatmap illustrating the availability of microGalaxy tool suites (x-axis) across various Galaxy servers (y-axis), grouped by EDAM topics. Tool suites may appear in multiple clusters, as they can be annotated with several topics. A logarithmic scale is applied for improved visualization.](https://raw.githubusercontent.com/usegalaxy-eu/galaxy-social/2025-01-07-microgalaxy-preprint/posts/images/2025-01-07-microgalaxy-preprint-supp-figure-3-a.png) + + +(B) Usage trends show increasing adoption of microGalaxy tools over time. + +[Scatter plots showing the usability of microGalaxy tool suites over the past five years across all Galaxy main servers, categorized by their EDAM operations. The x-axis represents the total number of tool users, while the y-axis also denotes the total number of tool users (potentially correct this redundancy).](https://raw.githubusercontent.com/usegalaxy-eu/galaxy-social/2025-01-07-microgalaxy-preprint/posts/images/2025-01-07-microgalaxy-preprint-supp-figure-3-b.png) + + +(C) The platform has gradually added hundreds of tools since its inception! + +[Cumulative number of tools added to Galaxy over time, based on the date of the first commit for each tool suite.](https://raw.githubusercontent.com/usegalaxy-eu/galaxy-social/2025-01-07-microgalaxy-preprint/posts/images/2025-01-07-microgalaxy-preprint-supp-figure-3-c.png) + +The tools and workflows are continuously evolving, driven by community needs. + + +πŸ”§ microGalaxy workflows in action! + +65+ ready-to-use workflows streamline complex analyses, from genome reconstruction to multi-omics integration. + +Here's how tools are grouped across workflows by EDAM operations: + +#Reproducibility + +[Heatmap illustrating the presence of microGalaxy tool suites within the available microGalaxy workflows, grouped by three levels of development. The tool suites are organized based on their corresponding EDAM operations, highlighting the breadth of tools utilized for different workflows.](https://raw.githubusercontent.com/usegalaxy-eu/galaxy-social/2025-01-07-microgalaxy-preprint/posts/images/2025-01-07-microgalaxy-preprint-supp-figure-4.png) + + + +πŸ“š Training is a core focus of microGalaxy! + +45+ materials support researchers of all levels bridging the gap between learning and doing! πŸ§‘β€πŸ«βœ¨ + +Tools integrated into training contexts, grouped by EDAM operations: + + +[Heatmap illustrating the presence of microGalaxy tool suites within the available microGalaxy training materials, grouped by EDAM topics. The tool suites are organized based on their corresponding EDAM operations, highlighting the breadth of tools utilized for different training contexts.](https://raw.githubusercontent.com/usegalaxy-eu/galaxy-social/2025-01-07-microgalaxy-preprint/posts/images/2025-01-07-microgalaxy-preprint-supp-figure-5.png) + + + + +πŸ” How does microGalaxy compare? + +We reviewed 44 microbial data analysis platforms, comparing: + + General characteristics (e.g., free/open-source) + Accessibility (e.g., user-friendly interfaces, automatable APIs) + Supported methods (e.g., taxonomy profiling, MAGs, multi-omics) + +πŸ“Š See Supplementary Table 1 for full comparisons! + + + + +microGalaxy wouldn’t exist without our amazing global community! + +From tool developers to educators, this is a testament to the power of collaboration in bioinformatics. + +Big thanks to everyone who made this possible! πŸ™ + +#Community #Collaboration + + + +🌟 Beyond tools, microGalaxy empowers researchers to tackle global challenges like antimicrobial resistance, biodiversity loss, and food security. 🌱🍎 + +πŸ“ Read the preprint: https://www.biorxiv.org/content/10.1101/2024.12.23.629682v1 + + + +🌐 Explore microGalaxy platform: https://microgalaxy.usegalaxy.eu +πŸ‘₯ Join the microGalaxy community: https://galaxyproject.org/community/sig/microbial +πŸ’¬ Share your thoughts on Matrix: https://matrix.to/#/#galaxyproject_microGalaxy:gitter.im + +Let's build the future of microbial data analysis together! 🀝 + diff --git a/posts/images/2025-01-07-microgalaxy-preprint-figure-1.png b/posts/images/2025-01-07-microgalaxy-preprint-figure-1.png new file mode 100644 index 0000000..eb8c8d2 Binary files /dev/null and b/posts/images/2025-01-07-microgalaxy-preprint-figure-1.png differ diff --git a/posts/images/2025-01-07-microgalaxy-preprint-graphical-abstract.png b/posts/images/2025-01-07-microgalaxy-preprint-graphical-abstract.png new file mode 100644 index 0000000..3a67a55 Binary files /dev/null and b/posts/images/2025-01-07-microgalaxy-preprint-graphical-abstract.png differ diff --git a/posts/images/2025-01-07-microgalaxy-preprint-supp-figure-1.png b/posts/images/2025-01-07-microgalaxy-preprint-supp-figure-1.png new file mode 100644 index 0000000..24d0bdd Binary files /dev/null and b/posts/images/2025-01-07-microgalaxy-preprint-supp-figure-1.png differ diff --git a/posts/images/2025-01-07-microgalaxy-preprint-supp-figure-2.png b/posts/images/2025-01-07-microgalaxy-preprint-supp-figure-2.png new file mode 100644 index 0000000..1f454ad Binary files /dev/null and b/posts/images/2025-01-07-microgalaxy-preprint-supp-figure-2.png differ diff --git a/posts/images/2025-01-07-microgalaxy-preprint-supp-figure-3-a.png b/posts/images/2025-01-07-microgalaxy-preprint-supp-figure-3-a.png new file mode 100644 index 0000000..481b0da Binary files /dev/null and b/posts/images/2025-01-07-microgalaxy-preprint-supp-figure-3-a.png differ diff --git a/posts/images/2025-01-07-microgalaxy-preprint-supp-figure-3-b.png b/posts/images/2025-01-07-microgalaxy-preprint-supp-figure-3-b.png new file mode 100644 index 0000000..e3380a9 Binary files /dev/null and b/posts/images/2025-01-07-microgalaxy-preprint-supp-figure-3-b.png differ diff --git a/posts/images/2025-01-07-microgalaxy-preprint-supp-figure-3-c.png b/posts/images/2025-01-07-microgalaxy-preprint-supp-figure-3-c.png new file mode 100644 index 0000000..569d0a5 Binary files /dev/null and b/posts/images/2025-01-07-microgalaxy-preprint-supp-figure-3-c.png differ diff --git a/posts/images/2025-01-07-microgalaxy-preprint-supp-figure-4.png b/posts/images/2025-01-07-microgalaxy-preprint-supp-figure-4.png new file mode 100644 index 0000000..4c79778 Binary files /dev/null and b/posts/images/2025-01-07-microgalaxy-preprint-supp-figure-4.png differ diff --git a/posts/images/2025-01-07-microgalaxy-preprint-supp-figure-5.png b/posts/images/2025-01-07-microgalaxy-preprint-supp-figure-5.png new file mode 100644 index 0000000..fc9e7ff Binary files /dev/null and b/posts/images/2025-01-07-microgalaxy-preprint-supp-figure-5.png differ