LogoLogo
  • 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: BioData Catalyst 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
      • Seven Bridges
        • Knowledge Center
        • Getting Started Guide
        • Comprehensive Analysis Tips
        • Troubleshooting Tasks
        • GWAS with GENESIS workflows
        • Annotation Explorer
      • 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
      • Dockstore
        • Launch workflows with BioData Catalyst
        • Discover our catalog
        • Intro to Docker, WDL, CWL
        • Dockstore Forum
        • Contribute to the community
    • 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
      • 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
    • Seven Bridges Tutorials
      • Genetic Association Testing using GENESIS Workflows
      • Estimating and Managing Your Cloud Costs
    • 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 Dictionary Requirement
    • dbGaP Study Configuration Process for Submission of Data to BDC
Powered by GitBook
On this page

Was this helpful?

Export as PDF
  1. Written Documentation
  2. Community Tools & Integration
  3. Bring Your Own Tool(s)

BYOT Glossary

An introduction to terms used in this document

Each platform within BioData Catalyst may have slight variations on these definitions. You will find a more specific definition within the section of the BYOT document. Below, we highlight a few terms to introduce you to before you get started.

  • App: 1) In Seven Bridges, an app is a general term to refer to both tools and workflows. 2) App may also refer to persistent software that is integrated into a platform.

  • Container: A standard unit of software that packages up code and all its dependencies so the application runs quickly and reliably from one computing environment to another (for example, Docker).

  • Command: In workflow writing, the command specifies the literal command line run (akin to what you would run in the terminal).

  • Common Workflow Language (CWL): Simple scripting language for describing computational workflows for performing sequential operations on data. CWL is a way to describe command-line tools and connect them together to create workflows. CWL is well suited for describing large-scale workflows in cluster, cloud, and high-performance computing environments where tasks are scheduled in parallel across many nodes.

  • Docker: Software for running packaged, portable units of code, and dependencies that can be run in the same way across many computers. See also Container.

  • Dockerfile: A text document that contains all the commands a user could call on the command line to assemble an image.

  • Dockstore: An open platform developed by the Cancer Genome Collaboratory and used by the GA4GH for sharing Docker-based tools described with the Common Workflow Language (CWL), the Workflow Description Language (WDL), or Nextflow (NFL).

  • Image: In the context of containers and Docker, this refers to the resting state of the software.

  • Instance: Refers to a virtual server instance from a public or private cloud network.

  • Task: In workflow writing, the term task encompasses all of the information necessary to execute a command, such as specifying input/output files and parameters.

  • Tool: In CWL, the term tool specifies a single command. This specification is not as discrete in other languages such as WDL.

  • Workflow Description Language (WDL): Way to specify data processing workflows with a human-readable and writable syntax. Define complex analysis tasks, chain them together in workflows, and parallelize their execution.

  • Workflow: A sequence of processes, usually computational in this context, through which a user may analyze data.

  • Workspace: Areas to work on/with data within a platform. Examples: projects within Seven Bridges.

  • Wrapping: The process of describing a command-line tool or custom script in Common Workflow Language (CWL) so that it can be easily run in multiple cloud environments, dynamically scale compute requirements based on inputs, and be inserted into distinct analysis pipelines.

  • Virtual Machine (VM): An isolated computing environment with its own operating system.

PreviousBring Your Own Tool(s)NextWorking with Docker

Last updated 4 years ago

Was this helpful?

For other terms, you can reference the .

BioData Catalyst glossary