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    34 repositories

    • aced_etl_pod

      Public
      etl worker pod
      Python
      •
      MIT License
      •1•2•3•2•Updated Dec 30, 2025Dec 30, 2025

    • gen3_util

      Public
      Collection of command line tools to interact with a Gen3 instance
      Python
      •
      MIT License
      •1•4•19•7•Updated Dec 17, 2025Dec 17, 2025

    • submission

      Public
      Submit FHIR based data into a Gen3 Commons
      Python
      •0•1•7•0•Updated Nov 10, 2025Nov 10, 2025

    • guppy

      Public
      Server that supports GraphQL queries on data from Elasticsearch
      JavaScript
      •
      Apache License 2.0
      •13•0•0•0•Updated Nov 3, 2025Nov 3, 2025

    • image_viewer

      Public
      create urls for image viewer, coverts object_id to signed url
      Python
      •
      MIT License
      •0•0•6•3•Updated Aug 18, 2025Aug 18, 2025

    • gen3-tests

      Public archive
      Framework for release testing of Gen3 instances
      Apache License 2.0
      •0•0•0•0•Updated Jul 8, 2025Jul 8, 2025

    • .github

      Public
      ACED-IDP repository for default templates
      0•0•0•0•Updated May 23, 2025May 23, 2025

    • fhir_server

      Public
      A FHIR server built for direct integration with Gen3
      Python
      •0•0•0•0•Updated May 15, 2025May 15, 2025

    • g3t_etl

      Public
      Transform submissions into FHIR
      Python
      •0•1•6•0•Updated Apr 8, 2025Apr 8, 2025

    • gecko

      Public
      A http server for wielding frontend configurations for dynamic data loading
      Go
      •
      MIT License
      •0•1•1•1•Updated Apr 4, 2025Apr 4, 2025

    • gen3-frontend-framework

      Public
      A Frontend Framework for Gen3 data portals
      TypeScript
      •
      Apache License 2.0
      •14•1•4•0•Updated Mar 26, 2025Mar 26, 2025

    • status-monitor

      Public archive
      Uptime/downtime monitor and status page for ACED data commons
      uptime-monitorstatus-pageupptime
      Markdown
      •
      MIT License
      •0•1•0•0•Updated Jan 29, 2025Jan 29, 2025

    • viv

      Public
      Library for multiscale visualization of high-resolution multiplexed bioimaging data on the web. Directly renders Zarr and OME-TIFF.
      JavaScript
      •
      MIT License
      •57•0•0•1•Updated Oct 17, 2024Oct 17, 2024

    • arborist_users

      Public
      Extract arborist entities[resource, role, policy, etc.] from current k8s context, create user.yaml
      Python
      •0•1•3•0•Updated May 10, 2024May 10, 2024

    • graph-benchmark

      Public
      Python
      •0•0•0•0•Updated May 5, 2024May 5, 2024

    • synapse-sync

      Public
      Extract teams from synapse
      Python
      •0•1•0•0•Updated Apr 16, 2024Apr 16, 2024

    • cloud-automation

      Public
      Automation for standing up Gen3 commons
      Shell
      •
      Apache License 2.0
      •69•1•0•0•Updated Jan 10, 2024Jan 10, 2024

    • dictionaryutils

      Public
      python wrapper and metaschema for datadictionary
      Python
      •
      Apache License 2.0
      •9•0•0•0•Updated Dec 12, 2023Dec 12, 2023

    • data_model

      Public
      Schema and synthetic data
      Python
      •1•2•18•1•Updated Nov 30, 2023Nov 30, 2023

    • UCL-certs

      Public
      Add UCL Certs to linux / python environment
      Shell
      •0•0•0•0•Updated Oct 6, 2023Oct 6, 2023

    • nvidia-collaboration

      Public
      OHSU CEDAR Cyclic IF and H&E images
      Python
      •0•0•5•0•Updated Jul 19, 2023Jul 19, 2023

    • minio-deploy

      Public
      A collection of Ansible playbooks and instructions on Minio deployment
      Apache License 2.0
      •0•2•3•0•Updated Jul 6, 2023Jul 6, 2023

    • data-portal

      Public
      Windmill: data portal for metadata submission and query
      JavaScript
      •
      Apache License 2.0
      •54•0•0•0•Updated May 25, 2023May 25, 2023

    • gen3sdk-python

      Public
      Gen3 SDK for Python
      Python
      •
      Apache License 2.0
      •27•0•0•0•Updated May 5, 2023May 5, 2023

    • MCF10A

      Public
      LINCS MCF10A Molecular Deep Dive (MDD)
      Python
      •0•0•5•1•Updated May 2, 2023May 2, 2023

    • dir_to_study

      Public
      A utility to create a "bare bones" ResearchStudy with DocumentReference
      0•1•0•1•Updated Apr 12, 2023Apr 12, 2023

    • devops

      Public
      Playbooks and scripts
      0•1•4•0•Updated Mar 3, 2023Mar 3, 2023

    • aced_queries

      Public
      Worked examples of ACED queries
      MIT License
      •0•0•1•1•Updated Mar 3, 2023Mar 3, 2023

    • fhir-example

      Public
      A standalone FHIR service
      Python
      •0•1•2•0•Updated Feb 28, 2023Feb 28, 2023

    • compose-services-training

      Public
      Learn about Gen3 using Docker compose
      Python
      •
      Apache License 2.0
      •39•1•11•3•Updated Feb 24, 2023Feb 24, 2023