diff --git a/content/news/2023-12-23-galaxy-sc-2023-in-review/2023_dec_sc.png b/content/news/2023-12-23-galaxy-sc-2023-in-review/2023_dec_sc.png new file mode 100644 index 0000000000..0cb7d25e75 Binary files /dev/null and b/content/news/2023-12-23-galaxy-sc-2023-in-review/2023_dec_sc.png differ diff --git a/content/news/2023-12-23-galaxy-sc-2023-in-review/index.md b/content/news/2023-12-23-galaxy-sc-2023-in-review/index.md new file mode 100644 index 0000000000..68e32abe83 --- /dev/null +++ b/content/news/2023-12-23-galaxy-sc-2023-in-review/index.md @@ -0,0 +1,77 @@ +--- +title: "Galaxy Single-cell Community: Year in Review" +date: '2023-12-23' +tease: 'The Galaxy Single-cell Community provides a 2023 review!' +authors: Wendi Bacon, Pavankumar Videm, Mehmet Tekman +authors_structured: +- github: nomadscientist +- github: pavanvidem +- github: mtekman +tags: [gtn, communications, single-cell] +subsites: [all-eu,global,esg] +--- + +
+ +![swirled cluster dots surround a circle of people all holding hands, looking towards the bright center (future)](./2023_dec_sc.png) + +
+ +🚀Embarking on a cosmic journey, the Galaxy Single-cell Community has clustered together to unveil a constellation of tools, making strides in +RNA-stellar discoveries and creating out-of-this-world workflows. With a commitment to battling work duplication across the multiverse, +this community is boldly charting a course for global domination, proving that when it comes to bioinformatics, the Galaxy is the limit!✨ + +# Tools & Workflows + +The past year has been a spectacular journey in advancing tools and workflows within the Galaxy Single-cell Community. +Breaking free from the confines of scRNA-seq, we've expanded our horizons to include tools for analyzing data from other modalities such +as single-cell ATAC-seq and CITE-Seq. Dive into our updated scRNA-seq analysis tools, now featuring more downstream analysis options for +trajectory analysis. We've even thrown in advanced analysis tools for estimating cell type proportions from bulk RNA-seq data! + +**RNA STARSolo** just got a makeover to version 2.7.10b, boasting a revamped UI, Velocyto-like UMI counting, and nifty alternatives for +quantifying single nuclei data. Analyzing single-cell ATAC-seq data on Galaxy is now a breeze with the introduction of +the **EpiScanpy** tool suite, built on the renowned **Scanpy** toolkit. Plus, we've added some powerful tools from the **Sinto** toolkit +for preprocessing scATAC-seq data on Galaxy. And that's not all! The **MuSiC** tool suite in Galaxy now unveils deconvolution tools +for discovering cell type composition in bulk RNA-seq using cell types within scRNA-seq. Multi-faceted comparisons are now at your fingertips with the **MuSiC Compare** tool. + +Seurat fans, rejoice! Updates have rolled in, offering additional functionalities and optional CITE-seq capabilities at runtime. + +# Community Infrastructure + +Our efforts in community building have seen the unification of single-cell subdomains into [https://singlecell.usegalaxy.eu/](https://singlecell.usegalaxy.eu/), +the creation of the Single Cell Community of Practice hub page ([https://galaxyproject.org/projects/singlecell/](https://galaxyproject.org/projects/singlecell/)), +and a user-focused Matrix channel. Testing brilliant widgets, automated updates, and the latest addition of automated help request updates onto +Matrix channels have made community collaboration a breeze. + +# Global Connections + +Down under, the Australian BioCommons launched their [Single Cell and Spatial Omics Analysis Infrastructure Roadmap for Australia](https://zenodo.org/records/10368976), complementing our endeavors to unite across timezones. Collaboration, including international tool adventures across three continents, +proves that team work does, in fact, make the dream work. + +## Training + +Get ready for a thrilling journey through the [Single Cell Training](https://training.galaxyproject.org/training-material/topics/single-cell/)'s latest updates! +The **Case Study Reloaded** tutorial, fueled by three remote-working undergrads, introduces parallel trajectory analysis in R, Python, and the Galaxy GUI. + +Sustainability shines as we've revamped numerous tutorials with hands-on and video re-recordings. New tools bring new tutorials, such as +[Pre-processing of 10X Single-Cell ATAC-seq Datasets](https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scatac-preprocessing-tenx/tutorial.html) +and [Comparing inferred cell compositions using MuSiC deconvolution](https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/bulk-music-4-compare/tutorial.html). + +Tackling user hurdles, our data ingest and conversion tutorials in the **Changing data formats & preparing objects** section await exploration. + +Dive into the unique **Tips, tricks & other hints** section, offering analysis options like [parameter iteration](https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scanpy_parameter_iterator/tutorial.html) +for swift optimization or [Removing the effects of the cell cycle](https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-case_cell-cycle/tutorial.html) for precise clustering analysis. + +And don't miss our inaugural [Learning Pathway](https://training.galaxyproject.org/training-material/learning-pathways/intro_single_cell.html), guiding Galaxy +novices to becoming single-cell analysis experts! + + +# Fighting Work Duplication + +Our mission: No more work duplication! We've consolidated single-cell instances and are diligently preventing tool and infrastructure duplication, +creating smoother pathways across servers. We value efficiency here at single-cell, so we'd like to thank ChatGPT (free version) for adding in +Galaxy puns to this post, as per our request. + +# What a Year! + +What's next on our list? World domination or global collaboration? You decide. Stay tuned for another exciting year with the Galaxy Single-cell Community!