Projects in Awesome Lists by DataBiosphere
A curated list of projects in awesome lists by DataBiosphere .
https://github.com/databiosphere/toil
A scalable, efficient, cross-platform (Linux/macOS) and easy-to-use workflow engine in pure Python.
aws common-workflow-language cwl gridengine kubernetes mesos pipeline python slurm wdl workflow workflow-description-language
Last synced: 29 Apr 2025
https://github.com/DataBiosphere/toil
A scalable, efficient, cross-platform (Linux/macOS) and easy-to-use workflow engine in pure Python.
aws common-workflow-language cwl gridengine kubernetes mesos pipeline python slurm wdl workflow workflow-description-language
Last synced: 07 Apr 2025
https://github.com/databiosphere/dsub
Open-source command-line tool to run batch computing tasks and workflows on backend services such as Google Cloud.
Last synced: 27 Jun 2025
https://github.com/databiosphere/terra-ui
Web user interface for the Terra platform
Last synced: 11 Mar 2026
https://github.com/databiosphere/job-manager
Job Manager API and UI for interacting with asynchronous batch jobs and workflows.
Last synced: 27 Jun 2025
https://github.com/DataBiosphere/job-manager
Job Manager API and UI for interacting with asynchronous batch jobs and workflows.
Last synced: 08 Apr 2025
https://github.com/databiosphere/terra-interoperability-model
Common data model proposal for biomedical research intended to facilitate and encourage data sharing and reuse
Last synced: 27 Jun 2025
https://github.com/databiosphere/jade-data-repo
The Terra Data Repository built by the Jade team.
Last synced: 27 Jun 2025
https://github.com/databiosphere/topmed-workflows
a place for topmed workflows
Last synced: 27 Jan 2026
https://github.com/databiosphere/consent
Broad Institute Data Use Oversight System
Last synced: 27 Jun 2025
https://github.com/databiosphere/duos-ui
Broad Institute Data Use Oversight System
Last synced: 11 Jun 2025
https://github.com/databiosphere/azul
Metadata indexer and query service used for AnVIL, HCA, LungMAP, and CGP
Last synced: 27 Jun 2025
https://github.com/databiosphere/consent-ontology
Broad Institute Data Use Oversight System
Last synced: 27 Jun 2025
https://github.com/databiosphere/terra-examples
Examples for use in data analysis.
Last synced: 27 Jun 2025
https://github.com/databiosphere/analysis_pipeline_wdl
Collection of WDL workflows based off the University of Washington TOPMed DCC Best Practices for GWAS. The WDL structure was based upon CWLs written by the Seven Bridges development team.
pipeline topmed topmed-pipeline wdl workflow
Last synced: 27 Jun 2025
https://github.com/databiosphere/getm
Concurrent reads of HTTP URL addressed data
Last synced: 21 Jun 2025
https://github.com/databiosphere/sync-github-labels
Synchronize Github issue and PR labels between two repositories
Last synced: 27 Jun 2025
https://github.com/databiosphere/fhir
Broad FHIR is a FHIR Server that powers applications for Genomics research.
Last synced: 27 Jul 2025
https://github.com/databiosphere/herzog
Version control, test, and CI/CD your Python Jupyter notebooks.
Last synced: 27 Jun 2025
https://github.com/databiosphere/terra-axon-examples
Example notebooks and documentation for working with the Terra Axon UI.
Last synced: 27 Jun 2025
https://github.com/databiosphere/jade-data-repo-ui
UI for the Jade Data Repo
Last synced: 31 Jul 2025
https://github.com/databiosphere/terra-resource-buffer
Terra Resource Buffering Service
Last synced: 26 Feb 2026
https://github.com/databiosphere/encode-ingest
Batch ETL pipeline to mirror ENCODE data into the Jade Data Repository.
Last synced: 08 Aug 2025
https://github.com/databiosphere/xsamtools
Lightly modified versions of htslib and bcftools to merge VCF streams.
Last synced: 27 Jun 2025
https://github.com/databiosphere/clinvar-ingest
Batch ETL pipeline to mirror ClinVar releases into the Jade Data Repository.
Last synced: 27 Jun 2025
https://github.com/databiosphere/terra-resource-janitor
Janitor service to cleanup resources created by Cloud Resource Library (CRL)
Last synced: 20 Feb 2026
https://github.com/databiosphere/ssds
Simple data storage system for AWS and GCP
Last synced: 27 Jun 2025
https://github.com/databiosphere/saturn-ui-prod-deploy
Terra UI automated prod deploy service
Last synced: 30 Jan 2026
https://github.com/databiosphere/tanagra
Repo for the Tanagra service being developed by the All of Us DRC
Last synced: 27 Jun 2025
https://github.com/databiosphere/github-actions
Data Biosphere GitHub Actions
Last synced: 27 Jun 2025
https://github.com/databiosphere/stairway
Stairway saga transaction processor library
Last synced: 27 Jun 2025
https://github.com/databiosphere/terra-axon-ui
Repository for the Terra "Axon" UI
Last synced: 27 Jun 2025
https://github.com/databiosphere/data-platforms
Components of the Commons Alliance
Last synced: 27 Jun 2025
https://github.com/databiosphere/bard-client
JavaScript library for shared client-side analytics across DSP
Last synced: 27 Jun 2025
https://github.com/databiosphere/wdl-parsers
A package that provides the generated ANTLR4 WDL parsers for Python.
Last synced: 27 Jun 2025
https://github.com/databiosphere/bdcat-integration-tests
This supports integration testing between components for the biodata catalyst grant.
Last synced: 27 Jun 2025
https://github.com/databiosphere/saturn-terraform
Terraform definitions for all Saturn-managed repos and GCS projects
Last synced: 08 Feb 2026
https://github.com/databiosphere/hca-import-validation
A utility to validate a staging area before it is imported.
Last synced: 27 Jun 2025
https://github.com/databiosphere/app-schema
A place to document "app" definitions
Last synced: 27 Jan 2026
https://github.com/databiosphere/terra-test-runner-dashboard
Test Runner Dashboard.
Last synced: 22 Oct 2025
https://github.com/databiosphere/terra-gradle-plugin
Reusable Gradle plugin for Terra backend services
Last synced: 28 Jan 2026
https://github.com/databiosphere/mf-soundcheck-testing
This is mf-soundcheck-testing
Last synced: 08 Jul 2026
https://github.com/databiosphere/terra-axon-server
Backend-for-frontend server for the Terra Axon UI and other Terra clients
Last synced: 22 Jul 2025
https://github.com/databiosphere/toolbox
Repository for various helper tools used by supported workflows
Last synced: 28 Jan 2026
https://github.com/databiosphere/gitlab-in-google
Google Cloud Based Gitlab CI/CD Platform with Kubernetes in Terraform.
Last synced: 30 Jan 2026
https://github.com/databiosphere/cwl-tool-wrapper-workflow
A CWL workflow template for use in wrapping a CWL tool so that it can be registered on Dockstore as a workflow
Last synced: 31 Jan 2026
https://github.com/databiosphere/xvcfview
A WDL workflow to subset, subsample, and filter VCF files using bcftools.
Last synced: 27 Jun 2025
https://github.com/databiosphere/terra-app-manager
This is terra-app-manager
Last synced: 27 Jun 2025
https://github.com/databiosphere/data-portal-summary-stats
Generate descriptive figures of cell by gene matrices.
Last synced: 27 Jun 2025