SUMMARY.md

Table of contents

• NHLBI BioData Catalyst® (BDC) Documentation

Community

• Who We Are
• BDC Glossary
• Citation and Acknowledgement
• Strategic Planning
• Request for Comments
  • NHLBI BioData Catalyst Ecosystem Security Statement
  • NHLBI DICOM Medical Image De-Identification Baseline Protocol
• BDC Video Content Guidance
• Contributing User Resources to BDC

Written Documentation

• Getting Started
• Data Access
  • Data Interoperability
  • Understanding Access
  • Submitting a dbGaP Data Access Request
  • Checking Access
• Explore Available Data
  • Dug Semantic Search
    • Search and Results
  • PIC-SURE User Guide
    • Getting Started
      • Requirements and Login
      • Available Data and Managing Data Access
        • TOPMed and TOPMed related datasets
        • BioLINCC Datasets
        • CONNECTS Dataset
    • Data Organization in PIC-SURE
    • PIC-SURE Features and General Layout
    • PIC-SURE Open Access vs. PIC-SURE Authorized Access
      • PIC-SURE Open Access
      • PIC-SURE Authorized Access
    • Data Analysis Using the PIC-SURE API
    • Additional Resources
    • PIC-SURE API Documentation
    • Appendix 1: BDC Identifiers - dbGaP, TOPMed, and PIC-SURE
    • Appendix 2: Table of Harmonized Variables
  • Discovering Data Using Gen3
    • Dictionary
    • Exploration
    • Query
    • Workspace
    • Profile
    • PFB Files
    • Current Projects
• Analyze Data
  • Transferring Files Between Seven Bridges and Terra
  • BDC-Seven Bridges
    • Knowledge Center
    • Getting Started Guide
    • Comprehensive Analysis Tips
    • Troubleshooting Tasks
    • GWAS with GENESIS workflows
    • Annotation Explorer
  • BDC-Terra
    • Account Setup
      • Billing
      • Managing Costs
    • Workspace Setup
      • Data Storage & Management
      • Collaboration
      • Security
    • Bring Data into a Workspace
      • Bring in Data from Gen3
      • From Terra’s Data Library
      • Use Your Own Data with Terra
    • Run Analyses
      • Batch Processing with Workflows
      • Interactive Analysis
      • Genome-Wide Association Studies
    • Troubleshooting & Support
• Community Tools & Integration
  • Bring Your Own Tool(s)
    • BYOT Glossary
    • Working with Docker
    • Creating, testing & scaling WDL workflows
    • Creating, testing & scaling CWL workflows
    • Version Control, Publishing & Validation of Workflows
    • Advanced Topics
  • Import a Dockstore App With Seven Bridges
• Writing BDC into a Grant Proposal
• Incurring Cloud Costs
• Release Notes
  • 2026-04-15 BDC Ecosystem Release Notes
  • 2026-01-15 BDC Ecosystem Release Notes
  • 2025-11-15 BDC Ecosystem Release Notes
  • 2025-07-15 BDC Release Notes
  • 2025-04-15 BDC Release Notes
  • 2025-01-15 NHLBI BioData Catalyst Ecosystem Release Notes
  • 2024-10-21 NHLBI BioData Catalyst Ecosystem Release Notes
  • 2024-07-02 NHLBI BioData Catalyst Ecosystem Release Notes
  • 2024-04-01 NHLBI BioData Catalyst Ecosystem Release Notes
  • 2024-01-08 NHLBI BioData Catalyst Ecosystem Release Notes
  • 2023-10-04 NHLBI BioData Catalyst Ecosystem Release Notes
  • 2023-07-11 NHLBI BioData Catalyst Ecosystem Release Notes
  • 2023-04-04 BioData Catalyst Ecosystem Release Notes
  • 2023-01-09 BioData Catalyst Ecosystem Release Notes
  • 2022-10-03 BioData Catalyst Ecosystem Release Notes
  • 2022-07-11 BioData Catalyst Ecosystem Release Notes
  • 2022-04-04 BioData Catalyst Ecosystem Release Notes
  • 2022-01-24 BioData Catalyst Ecosystem Release Notes
  • 2021-10-04 BioData Catalyst Ecosystem Release Notes
  • 2021-07-09 BioData Catalyst Ecosystem Release Notes
  • 2021-04-02 BioData Catalyst Ecosystem Release Notes
  • 2021-01-15 BioData Catalyst Ecosystem Release Notes
  • 2020-10-23 BioData Catalyst Ecosystem Release Notes
  • 2020-08-24 BioData Catalyst Ecosystem Release Notes
  • 2020-04-02 BioData Catalyst Ecosystem Release Notes
• Data Versioning Release Notes
• NIH RECOVER Release Notes

Tutorials: Videos & Modules

• BDC-Seven Bridges Tutorials
  • Genetic Association Testing using GENESIS Workflows
  • Estimating and Managing Your Cloud Costs
• BDC-Terra Tutorials
  • Getting Started with Gen3 Data on Terra Tutorial
  • Genome Wide Association Study with 1000 Genomes Data Tutorial
  • Genome Wide Association Study with TOPMed Data Tutorial
  • TOPMed Aligner, or, How to Import Data From Gen3 into Terra and Run a Workflow on It

Data Management

• Data Management Strategy
• Instructions for Data Submission to BDC
  • De-identification Readme
  • Data Submission FAQs
• dbGaP Study Configuration Process for Submission of Data to BDC