Tools and Applications

This page is our home for links to the various tools and applications we support. Check back frequently for updates and new information as our team grows.

All documentation about Data Science Lab Tools and best practices can also be found on the Fred Hutch Biomedical Data Science Wiki.

Emerging Data Infrastructure

Find out more about what data infrastructure projects we have in process in collaboration with various Fred Hutch IT groups via the “General” Data House Call.

  • Updates on ongoing Fred Hutch patient clinical data infrastructure projects
  • Updates on ongoing computing and data application projects

PROOF

PROOF (PRoduction On-ramp for Optimization and Feasibility) is a user-friendly tool designed for managing and executing WDL (Workflow Description Language) workflows using the Cromwell workflow manager, configured to run on the Fred Hutch cluster. PROOF allows users to:

  • Automate all the backend Cromwell configurations necessary to run your workflows instantly.
  • Validate, troubleshoot, assess performance, and run their workflows all under one roof.
  • Refine their workflows before potential transitions to cloud-based infrastructures, providing a “proofing” resource of sorts.

Find out more on the PROOF page on the Fred Hutch SciWiki.

cBioPortal

cBioPortal is an open-source platform for visualization, exploration, and analysis of cancer genomics data sets developed by Memorial Sloan Kettering (MSK). The Data Science Lab (DaSL) in conjunction with the Scientific Computing Group (SciComp) at Fred Hutch have launched a Fred Hutch instance of cBioPortal for research use only.

The Fred Hutch deployment of cBioPortal provides users with several advantages to enhance their research:

  • The private nature of this instance allows researchers to utilize the powerful visualization tools of the application to facilitate visualization of interim data.
  • It also provides research groups with the ability to establish controlled access to their study data, ensuring data protection.
  • Users can host and share their data through the Fred Hutch instance of cBioPortal to facilitate collaborations.
  • Additionally, this instance has been reviewed and approved by InfoSec to include up to individually identifiable research data.

For more details on what the Fred Hutch instance of cBioPortal can do for you, read our Fred Hutch cBioPortal product page and documentation on the Fred Hutch SciWiki and visit cbioportal.fredhutch.org to give it a spin.