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How-To Guides

  • Access Data in the Open Science Data Repository (OSDR)
    • Searching for data within the OSDR
    • General Search Filters
      • Data Source
      • Data Type
      • Study Search Filters
    • Example Search
  • Navigate an OSDR Study Page
    • Navigation panel
    • Study Overview: OSD ID, Title, GeneLab ID, ALSDA ID and DOI
    • Description: Factor(s), organism, assay(s), project and contact information.
    • Experiments
    • Payloads
    • Missions
    • Protocols
    • Samples
      • Selecting sample(s) metadata for export
    • Assays
      • Selecting assay metadata for export
    • Publications
    • Files
    • Version History
    • Visualization
  • Request Controlled Access Datasets from OSDR
    • Step 1: Identify the Dataset
    • Step 2: Investigator Submits Data Access Request (DAR)
    • Step 3: Verify Affiliation
    • Step 4: Request Reviewed by OSDR Curation Team
    • Step 5: Data Access Committee Reviews Request
    • Step 6: Access Data
    • Step 7: Report Progress
    • Step 8: Close Out
    • Step 9: Questions?
  • Use the OSDR Public AWS S3 Bucket
    • Getting Started with AWS and OSDR Data
    • Introduction to OSDR Data on AWS
    • Installing the AWS CLI
    • Exploring OSDR Data
    • Copying Data Locally
    • Additional Resources
  • Create a Login.gov Account
    • Step 1: Sign Up
    • Step 2: Verify Email
    • Step 3: Set Password
    • Step 4: Registration Complete
    • Step 5: Log In
    • Step 6: Select ‘Submission Portal’ or ‘Workspace’
    • Step 7: BDME Dashboard (Submission Portal)
    • Step 8: Access the Workspace
    • Troubleshooting Steps
  • Use the OSDR Workspace
    • The OSDR Workspace
    • Workspace Console
    • Add New Folder
    • Download Files
  • Data Submission Guide
    • Prior to starting the data submission process please do the following:
    • Data Submission Tutorial
      • Download and Complete the Sample Metadata Files
      • Download and Complete the Assay Metadata Files
      • Create a Login.gov Account and Upload Files to Workspace
      • Login to BDME and Create a New Study
      • Input Study Information, Sample and Assay Metadata, and Associate Data Files
      • Preview Your Study and Submit to OSDR
  • Use the Biological Data API
    • The ISA model
    • Hierarchical metadata in the Biological Data API
    • Additional fields
    • Query endpoints vs. REST endpoints
    • Obtaining metadata tables
    • Obtaining data tables
    • Output formats
  • Explore Data Visualizations
    • About Data Visualization
    • Metadata Dashboard
      • Filters
      • Studies Table
    • Single Study Visualization Portal
      • Sidebar Functions
      • Plotly
      • PCA Plots
      • Pair Plots
      • Volcano Plots
      • Heatmap
      • DGE Table
      • GSEA
      • Ideogram
    • Multi-Study
      • Exploring the Multi-Study Page
      • Multi-Study PCA Plot
      • Factor Selection for Gene Expression Analysis
      • Sample Selection for Gene Expression Analysis
      • Normalize Using Only Selected Samples and/or Factors
      • Visualizing and Downloading Results
      • Exploring Visualization Plots
  • View and Download Environmental Data
    • Telemetry data
    • Radiation data
    • Mission comparison
    • Data Tables
  • Use the RadLab Portal and Data API
    • Data Overview Page
    • RadLab Time Series Line Plots
    • Data Comparison
    • Geospatial Plots
    • Knowledgebase
    • Data API
    • Settings
  • Report Issues to OSDR
    • Visit the OSDR Contact Page
    • Complete the Contact OSDR Form

Portals

  • Data Repository
  • Data Visualization Portal
  • EDA
  • RadLab
  • Explore NBISC

GitHub Repos

  • OSDR Curation
  • GeneLab Sample Processing
  • GeneLab Data Processing

Reference

  • Open Science Abbreviations
    • General Abbreviations
    • Data Systems Abbreviations
    • Sample Abbreviations
OSDR Tutorials
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