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    208 repositories

    • funnel

      Public
      Funnel is a toolkit for distributed task execution via a simple, standard API.
      dockerkubernetesgoogle-cloudslurmgridenginega4ghaws-batchpbs-torque
      Go
      •
      MIT License
      •40•131•129•3•Updated Nov 1, 2025Nov 1, 2025

    • helm-charts

      Public
      Helm Charts for deploying various projects in Kubernetes!
      Smarty
      •1•1•0•0•Updated Nov 1, 2025Nov 1, 2025

    • embedding-kit

      Public
      Python
      •2•0•0•2•Updated Oct 28, 2025Oct 28, 2025

    • meeting-summarizer

      Public
      Summarizer for meeting transcripts
      0•0•0•0•Updated Oct 15, 2025Oct 15, 2025

    • indexd

      Public
      Prototype index service server.
      Python
      •
      Apache License 2.0
      •21•0•1•0•Updated Oct 14, 2025Oct 14, 2025

    • regulon-enrichment

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •2•5•0•0•Updated Sep 2, 2025Sep 2, 2025

    • .github

      Public template
      0•0•0•0•Updated Aug 19, 2025Aug 19, 2025

    • fhir

      Public
      FHIR Protocol Buffers
      C++
      •
      Apache License 2.0
      •203•0•0•0•Updated Aug 18, 2025Aug 18, 2025

    • homebrew-formula

      Public
      homebrew tap for OHSU Comp Bio tools
      Ruby
      •
      MIT License
      •1•1•0•2•Updated Jul 12, 2025Jul 12, 2025

    • fence

      Public
      AuthN/AuthZ OIDC Service
      Python
      •
      Apache License 2.0
      •49•0•1•0•Updated Jul 9, 2025Jul 9, 2025

    • indexclient

      Public
      Prototype index service client.
      Python
      •
      Apache License 2.0
      •3•0•0•0•Updated Jul 9, 2025Jul 9, 2025

    • pypfb

      Public
      Python library & CLI to create, view and edit PFB files
      Python
      •
      Apache License 2.0
      •13•0•0•0•Updated Jul 2, 2025Jul 2, 2025

    • gen3-workflow

      Public
      Gen3 service for GA4GH TES integration
      Python
      •
      Apache License 2.0
      •1•1•0•0•Updated Jun 4, 2025Jun 4, 2025

    • funnel-plugins

      Public
      Golang Plugin development + testing using go-plugin from Hashicorp
      bioinformaticsauthenticationworkflows
      Go
      •
      Apache License 2.0
      •2•1•0•1•Updated May 15, 2025May 15, 2025

    • compbio-galaxy-wrappers

      Public archive
      OHSU Galaxy wrappers.
      Python
      •10•6•0•0•Updated Apr 24, 2025Apr 24, 2025

    • py-tes

      Public
      Python SDK for the GA4GH Task Execution API
      Python
      •
      MIT License
      •12•5•18•0•Updated Apr 9, 2025Apr 9, 2025

    • caliper-design

      Public
      Design docs for the CALIPER components and tools ⚙️
      Apache License 2.0
      •1•1•7•1•Updated Mar 26, 2025Mar 26, 2025

    • pycascades

      Public
      PyCascdes 2025 Demo
      Python
      •
      Apache License 2.0
      •0•2•0•0•Updated Feb 9, 2025Feb 9, 2025

    • example-repo

      Public
      Test Repo!
      HTML
      •
      Apache License 2.0
      •0•0•0•0•Updated Jan 31, 2025Jan 31, 2025

    • HTAN-FHIR

      Public
      python scripts to transform HTAN metadata to FHIR
      Python
      •0•0•0•0•Updated Jan 14, 2025Jan 14, 2025

    • fence-multipart

      Public
      AuthN/AuthZ OIDC Service
      Python
      •
      Apache License 2.0
      •49•0•0•0•Updated Dec 9, 2024Dec 9, 2024

    • awesome-tes

      Public
      A curated list of awesome GA4GH TES projects and programs
      workflowbioinformaticsreproducible-researchworkflow-enginega4gh
      Creative Commons Zero v1.0 Universal
      •0•2•1•0•Updated Dec 7, 2024Dec 7, 2024

    • vrs-annotator

      Public
      Annotates VCF Variants with VRS IDs
      Jupyter Notebook
      •3•2•0•0•Updated Nov 22, 2024Nov 22, 2024

    • syntheVAEiser

      Public
      Jupyter Notebook
      •
      Apache License 2.0
      •0•2•0•0•Updated Oct 18, 2024Oct 18, 2024

    • docker-centos-slurm

      Public archive
      Slurm Docker Container on CentOS 7
      Shell
      •
      MIT License
      •4•0•0•0•Updated Oct 1, 2024Oct 1, 2024

    • idp-backups

      Public
      Steps for backing up, migrating, and restoring IDP data
      Apache License 2.0
      •0•0•0•0•Updated Aug 29, 2024Aug 29, 2024

    • project-template

      Public template
      Example Repo Template for OHSU Comp Bio projects
      Apache License 2.0
      •0•0•0•0•Updated Aug 12, 2024Aug 12, 2024

    • load-testing

      Public
      Browser load testing using k6s
      JavaScript
      •1•1•2•0•Updated Aug 12, 2024Aug 12, 2024

    • gatk4_xml_prepare

      Public archive
      Tools to auto-create XML files from GATK4 json descriptions.
      Python
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated Jul 30, 2024Jul 30, 2024

    • glasswing-status

      Public
      Uptime/downtime monitor and status page for CBDS
      uptime-monitorstatus-pageupptime
      Markdown
      •
      MIT License
      •0•0•0•0•Updated Jul 22, 2024Jul 22, 2024