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GuidesAPI ReferenceRelease NotesTutorialsBioData Catalyst powered by Seven Bridges Knowledge Center

GET STARTED

  • Before you start
  • Sign up for BioData Catalyst powered by Seven Bridges
  • Account settings
  • Manage dataset access
  • About the Payments page
    • Manage billing group members
  • Cloud infrastructure pricing
    • Compute costs
    • Storage costs
    • Data transfer costs

TUTORIALS

  • Getting started
  • Troubleshooting tutorial
  • Comprehensive user guide
  • Maintaining and versioning CWL on external tool repositories

GUIDES

  • Collaborating on the NHLBI BioData Catalyst: A Guide for Consortia
  • Estimate and Manage Your Cloud Costs
  • Using NHLBI BioData Catalyst for Workshops and Courses
  • Create a multisample VCF from Variant Store
  • Share content through Public Projects
  • Guide to Billing Groups on BioData Catalyst

ACCESS THE PLATFORM

  • Sign up for BioData Catalyst powered by Seven Bridges
  • Switch from eRA Commons to login.gov
  • Access via the visual interface
  • Access via the API
  • Set up two-factor authentication

MANAGE AN ANALYSIS ENVIRONMENT

  • Projects on BioData Catalyst powered by Seven Bridges
  • Create a project
  • View a project
  • Manage the project dashboard
  • Modify project settings
  • Delete a project
  • Leave a project
  • Manage email notifications

COLLABORATE SECURELY

  • Collaboration on BioData Catalyst powered by Seven Bridges
  • Add a collaborator to a project
  • Set permissions

BROWSE DATASETS

  • Study Variable Explorer

DATASETS HUB

  • TOPMed Data overview
  • ABOUT STUDIES
    • About data access
    • Framingham Cohort
    • NHLBI TOPMed: Genomic Activities such as Whole Genome Sequencing and Related Phenotypes in the Framingham Heart Study
    • Jackson Heart Study (JHS) Cohort
    • Multi-Ethnic Study of Atherosclerosis (MESA) Cohort
    • NHLBI TOPMed Jackson Heart Study
    • NHLBI TOPMed: MESA and MESA Family AA-CAC
    • Women's Health Initiative Clinical Trial and Observational Study
    • NHLBI TOPMed: Women's Health Initiative (WHI)
    • NHLBI TOPMed: Cleveland Clinic Atrial Fibrillation (CCAF) Study
    • Cardiovascular Health Study (CHS) Cohort: an NHLBI-funded observational study of risk factors for cardiovascular disease in adults 65 years or older
    • NHLBI TOPMed: Trans-Omics for Precision Medicine (TOPMed) Whole Genome Sequencing Project: Cardiovascular Health Study
    • Massachusetts General Hospital (MGH) Atrial Fibrillation Study
    • NHLBI TOPMed: Massachusetts General Hospital (MGH) Atrial Fibrillation Study
    • Heart and Vascular Health Study (HVH)
    • NHLBI TOPMed: Heart and Vascular Health Study (HVH)
    • Atherosclerosis Risk in Communities (ARIC) Cohort
    • NHLBI TOPMed: Trans-Omics for Precision Medicine (TOPMed) Whole Genome Sequencing Project: ARIC
    • Genetic Epidemiology Network of Salt Sensitivity (GenSalt)
    • NHLBI TOPMed: Genetic Epidemiology Network of Salt Sensitivity (GenSalt)
    • GeneSTAR (Genetic Study of Atherosclerosis Risk) NextGen Consortium: Functional Genomics of Platelet Aggregation Using iPS and Derived Megakaryocytes
    • NHLBI TOPMed: GeneSTAR (Genetic Study of Atherosclerosis Risk)
    • Genetic Epidemiology Network of Arteriopathy (GENOA)
    • NHLBI TOPMed: Genetic Epidemiology Network of Arteriopathy
    • NHLBI TOPMed: San Antonio Family Heart Study
    • NHLBI TOPMed: Genetics of Cardiometabolic Health in the Amish
    • NHLBI TOPMed: Partners HealthCare Biobank
    • NHLBI TOPMed:The Vanderbilt Atrial Fibrillation Registry
    • NHLBI TOPmed: Novel Risk Factors for the Development of Atrial Fibrillation in Women
    • NHLBI TOPMed: The Vanderbilt AF Ablation Registry
    • NHLBI TOPMed: Diabetes Heart Study (DHS) African American Coronary Artery Calcification (AA CAC)
    • NHLBI TOPMed: HyperGEN - Genetics of Left Ventricular (LV) Hypertrophy
    • NHLBI TOPMed: Rare Variants for Hypertension in Taiwan Chinese (THRV)
    • NHLBI TOPMed: Genome-wide Association Study of Adiposity in Samoans
    • NHLBI TOPMed: Whole Genome Sequencing of Venous Thromboembolism (WGS of VTE)
    • NHLBI TOPMed - NHGRI CCDG: Hispanic Community Health Study/Study of Latinos
    • NHLBI TOPMed: Defining the time-dependent genetic and transcriptomic responses to cardiac injury among patients with arrhythmias
    • NHLBI TOPMed - NHGRI CCDG: The Johns Hopkins University School of Medicine Atrial Fibrillation Genetics Study
    • Coronary Artery Risk Development in Young Adults
    • NHLBI TOPMed - NHGRI CCDG: The BioMe Biobank at Mount Sinai
    • NHLBI TOPMed: Genetic Epidemiology of COPD
    • Genes-Environments and Admixture in Latino Asthmatics (GALA II) Study
    • NHLBI TOPMed - NHGRI CCDG: Genes-Environments and Admixture in Latino Asthmatics (GALA II)
    • NHLBI TOPMed: The Genetics and Epidemiology of Asthma in Barbados
    • NHLBI TOPMed: Boston Early-Onset COPD Study
    • NHLBI TOPMed: Study of African Americans, Asthma, Genes and Environment (SAGE)
    • NHLBI TOPMed: The Genetic Epidemiology of Asthma in Costa Rica
    • NHLBI TOPMed: African American Sarcoidosis Genetics Resource
    • NHLBI TOPMed: Severe Asthma Research Program
    • NHLBI TOPMed: Childhood Asthma Management Program
    • NHLBI TOPMed: GOLDN Epigenetic Determinants of Lipid Response to Dietary Fat and Fenofibrate
    • NHLBI TOPMed: Recipient Epidemiology and Donor Evaluation Study-III Brazil Sickle Cell Disease Cohort
    • NHLBI TOPMed: Walk-PHaSST Sickle Cell Disease
    • NHLBI Cleveland Family Study (CFS) Candidate Gene Association Resource (CARe)
    • NHLBI TOPMed: The Cleveland Family Study (CFS)
    • NHLBI TOPMed: Pulmonary Hypertension and the Hypoxic Response in SCD
  • ABOUT METADATA FOR STUDIES
    • NHLBI studies metadata
  • QUERY DATASETS
  • About the Data Browser
    • Data Browser features
    • Data Browser query structure
    • Data Browser query: start by searching through a study
    • Data Browser query: start by searching for an ID
    • Data Browser query: start from an existing query
  • ACCESS DATA FROM DATASETS
    • Access data from the Data Browser
    • Data Browser features
    • Data model versions

PUBLIC GALLERY

  • Overview
  • Use public datasets
  • Use public files
  • Use public apps (workflows and tools)
  • Use Interactive Web Apps

PUBLIC PROJECTS

  • Human Cell Atlas Preview Datasets
  • Data Studio Interactive Analyses

BRING YOUR PRIVATE DATA

  • Upload your data to the Platform
  • Upload from your computer
  • Upload via the command line
  • Import from an FTP or HTTP(S) server
  • Upload via the API
  • Import from a Volume
  • Import data from BioData Catalyst Powered by Gen3
  • Import from a DRS server
  • Import data from Gen3 BDC and Gen3 AnVIL

SET METADATA ASSOCIATED WITH A PRIVATE FILE

  • Metadata for your private data
    • System metadata
    • Metadata schema
  • Edit metadata using the visual interface
    • Edit metadata with a manifest
    • Export metadata to a manifest
  • Edit metadata using the command line uploader
  • Edit metadata using the API
  • Metadata manifest file format

SEARCH FILES

  • File repositories on the Platform
  • Search files on the Platform

ADD FILES TO A PROJECT

  • Copy files using the visual interface
  • Copy files using the API
  • Tag your files

ORGANIZE FILES

  • Available actions

ARCHIVE FILES

  • File archiving overview
  • Archive a file
  • Restore a file
  • Delete an archived file

BRING YOUR TOOLS

  • About the SDK
  • About the Common Workflow Language
  • CWL v1.0 improvements over sbg:draft-2
  • CWL v1.2 conditional execution
  • About Docker
  • Install Docker
  • The BioData Catalyst Image Registry
  • Core Docker commands
  • Create and upload your Docker image
  • Create and upload your Docker image with a Dockerfile
  • Manage Docker repositories
  • Bring Nextflow apps to the Platform
  • Bring WDL apps to the Platform

EDIT AN APP

  • About the editor
  • The tool editor
    • About the tool editor
    • Introduction to tool wrapping
    • Create a tool
    • Tool editor tutorial
    • Input file options
    • Advanced practices
    • Dynamic expressions in tool descriptions
    • Javascript Cookbook
  • The workflow editor
    • About the workflow editor
    • Create a workflow
    • Workflow editor tutorial

RUN AN ANALYSIS

  • About analyses
  • Run a task
  • Define app settings
  • About batch analyses
  • Project and file locations (Multi-cloud)
  • Import a Dockstore app
  • About secondary (index) files

TASK EXECUTION

  • About Spot/Preemptible Instances
  • Set execution hints at task level
  • Use Spot/Preemptible Instances
  • List of execution hints
  • List of available Amazon Web Services US East instances
  • List of available Google Cloud Platform instances
  • About Memoization (WorkReuse)

REVIEW A TASK

  • Review the task page
  • View Task stats
  • View Task logs
  • Job retry
  • View instance metrics
  • Real-time job monitoring
  • Troubleshoot a failed task

INTERACTIVE ANALYSIS

  • Interactive analysis on the Platform
  • Seven Bridges Genome Browser
  • CummeRbundQC RNA-Seq Visualization
  • FastQC
  • Picard Alignment Summary metrics
  • The Seven Bridges Coverage app
  • TOPMed Annotation Explorer
  • Annotation Explorer

DOWNLOAD RESULTS

  • Download results

DEVELOPER TOOLS

  • Get your authentication token

CONNECT CLOUD STORAGE

  • Connect cloud storage overview
  • Volumes
  • Aliases
  • Supported cloud storage providers
  • Amazon Web Services Simple Storage Service (AWS S3) Volumes
  • Google Cloud Storage (GCS) Volumes
  • Enabling cross-origin resource sharing (CORS)
  • Security concerns when working with volumes
  • About volumes on the visual interface
  • Attach an Amazon Web Services (AWS) volume
  • Attach a Google Cloud Storage volume
  • Manage members for a volume
  • Browse and add files to a project from a volume
  • Deactivate a volume
  • API Cloud storage tutorials
    • AWS Cloud storage tutorial
    • Google Cloud Storage tutorial

API Hub

  • API Overview
  • API Quickstart
  • Client libraries
  • Seven Bridges Command Line Interface
  • R library
  • Python Library
  • Java library
  • Java library Quickstart

API CLIENTS

  • Seven Bridges Command Line Interface Reference
    • General commands
    • Billing
    • Projects and members
    • Upload and download files
    • Apps
    • Tasks
    • Volumes

DATA STUDIO

  • About Data Studio
  • JupyterLab quick reference
  • RStudio quick reference
  • SAS Viya/Studio quick reference
  • Run a Data Studio analysis
  • Data Studio analysis details
  • Copy a Data Studio analysis
  • Data Studio analysis charging
  • Data Studio environments and libraries
  • Data Studio analysis editor

SBFS (Beta)

  • About SBFS
  • Install SBFS manually
  • Install SBFS automatically
  • Configure SBFS credentials
  • List available projects for SBFS
  • Mount a project
  • Unmount a project
  • SBFS Log
  • Upgrade SBFS
  • Uninstall SBFS

SBFS Command Reference

  • Overview
  • Configure
  • List
  • Mount
  • Actions after mounting
  • Unmount
  • General commands

Python Library

Suggest Edits

The Seven Bridges API Python client for the API is available from the Python Package Index at https://pypi.python.org/pypi/sevenbridges-python. Documentation is available at Readthedocs.

The code is available on Github at https://github.com/sbg/sevenbridges-python

Updated less than a minute ago


Any Questions?

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