DASH Release Notes

2024_06_03

In this quarter's installment of the DASH release notes we are happy to again report tremendous progress.

  • An incredibly successful Hackathon event, with some 50 registrants across 5 TeamLabs coming together May 20-21 at MSKCC for: 6 training workshops on emerging scRNA, spatial, TCR, and bulkDNA+RNA pipelines in Cirro, coupled with hands-on data analysis and real-time tool construction to explore scientific hypotheses. Each of the working groups performed valuable pipeline, analysis, and exploratory data work; with the winning team taking home a $150 prize for developing a novel approach to using the pool of doublet cells in GBM single-cell RNA data (about 10% of cell population) as markers for strong cell-cell interaction, confirming one such interaction in matched GBM spatial data, then using L-R gene vector analysis to identify a marked gradient effect in a separate, public GBM dataset. Finally, we'd like to thank the MSKCC and BTC organizing, events, and Program Management teams for tremendous catalyzing effort and helping create the sense that this inaugural hackathon is but the first of many to come.
  • The scRNA, spatial, and TCR development teams have released multiple versions of their pipelines, applied in conjunction with disease TeamLabs to emerging data.
  • By way of 6 internal data releases, the total quantity of data shared to DASH has more than doubled since March and number of files nearly tripled; the current 2024-05-21 data version includes over 20TB across some 1200 samples: DASH-counts-2024-06
  • Thanks to Henry Dewhurst and the Cirro team (especially Nathan Thorpe), we now have an operational, BTC-specific Cirro tenant. This provides additional security sandboxing and configuration flexibility, was used in the aforementioned hackathon, and is the final major step towards production-grade, multi-modal analyses workspaces for each disease TeamLab to be rolled out in Q2 through Q4 of 2024.
  • Multiple software releases of the DASH Board, Browse and Curate APPs
    • Reflecting new metadata export, annotations, and filtering capabilities
    • Improved UI, phone home, and metadata collection, towards self-service by data coordinators

2024_03_04

Welcome to the inaugural edition of the DASH Release Notes, through which we'll provide regular, BTC-wide updates as new datasets, analysis methods & pipelines, infrastructure, and more emerge. With this first installment we're happy to relay:

  • A meeting of the Data Science TeamLab (DST) last week at MD Anderson, with thanks to Kadir Akdemir & MDA colleagues for hosting. This 2-day event showcased considerable progress in the development of analysis methods & pipelines (notably single-cell and bulkRNA, TCR, spatial, and classical bulkDNA approaches); and how they're being woven into an increasingly capable data analysis system for the entire BTC portfolio. Leading to energetic discussion of future science, cross-team interaction, and trainee development.

  • Data snapshot version 2024-02-20, with over 1K samples and 9TB of data across several TeamLabs:

    • OV-IOC:
      • 335 STIC histoPath images from the Shih Lab @ JHU (courtesy of Yen-Wei Chien)
      • Over 200 files of methylation data from the Cope Lab at JHU
    • Pancreatic: over 450 files including
      • Flow, RNASeq, and path images of MRTX1133-treated mice & cell lines from Dougan Lab @ DFCI (courtesy of Li Qiang)
      • Visium spatialTranscriptomics mouse data from Kalluri Lab @ MDA (courtesy of Kate McAndrews)
      • Cell surface proteomics from Oni Lab @ MIT (courtesy of Salome Shubitidze)

    • More than 4,400 files of GBM data comprising 101 samples and 8 assay data types

      Contact the DASH team if you still do not have an account for accessing or analyzing data, but please keep in mind that until embargo periods have passed the data created by a TeamLab will generally be accessible only to members of that TeamLab.

    • Data shared to DASH is summarized for easy perusal in the Board app ... DASH-Board ... may be browsed/downloaded from the Browse app or programmatically (e.g. see here or here) DASH-Board ... analyzed with any of the 20+ pipeline configurations available in Cirro Cirro ... with all easily accessed from the DASH home page at dash.breakthroughcancer.org DASH-HomePage