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@CU-DBMI University of Colorado Department of Biomedical Informatics

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    46 repositories

    • set-website

      Public
      Website for the software engineering team (SET)
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •380•1•2•1•Updated Jul 10, 2025Jul 10, 2025

    • template-uv-python-research-software

      Public
      A template for Pythonic research software with environment management through uv.
      Jinja
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Jun 12, 2025Jun 12, 2025

    • hetionet-analysis

      Public
      Various data analysis performed using Hetionet, a hetnet of biomedical knowledge.
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•1•0•Updated Jun 5, 2025Jun 5, 2025

    • mends-on-fhir

      Public
      Python
      •2•6•0•0•Updated May 27, 2025May 27, 2025

    • onesentence

      Public
      A pre-commit check for semantic line breaks.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated May 27, 2025May 27, 2025

    • wall-of-software

      Public
      A list of tools, packages, workflows, resources, and other software developed at or in collaboration with DBMI
      JavaScript
      •14•2•1•1•Updated Apr 25, 2025Apr 25, 2025

    • word-spot

      Public
      Search for words or phrases in text, with exact or loose matching
      Vue
      •0•0•0•0•Updated Apr 21, 2025Apr 21, 2025

    • pmc-crawler

      Public
      Crawls PMC for publications by specified authors
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •2•0•0•0•Updated Apr 3, 2025Apr 3, 2025

    • redirects-website

      Public template
      Test out "chatroom" redirection link below:
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •2•1•0•0•Updated Feb 19, 2025Feb 19, 2025

    • redirects

      Public template
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •0•5•1•0•Updated Feb 19, 2025Feb 19, 2025

    • state-cancer-profile-scraper

      Public
      State cancer profiles scraper
      Python
      •
      MIT License
      •1•0•0•0•Updated Feb 10, 2025Feb 10, 2025

    • PONG

      Public
      C++
      •
      Other
      •2•0•0•0•Updated Feb 8, 2025Feb 8, 2025

    • .github

      Public
      A special GitHub repository for setting the organization profile and default community health files.
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Dec 10, 2024Dec 10, 2024

    • set-presentations

      Public
      A repository for presentations from the DBMI Software Engineering Team (SET)
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•2•1•0•Updated Nov 1, 2024Nov 1, 2024

    • screensaver

      Public
      Fun visualization that can be used as a background
      HTML
      •
      MIT License
      •0•1•0•0•Updated Oct 8, 2024Oct 8, 2024

    • demo-python-software-testing

      Public
      A project to help demonstrate Python software testing.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Oct 1, 2024Oct 1, 2024

    • set-intake

      Public
      Request support from the Software Engineering Team
      0•0•9•0•Updated Sep 10, 2024Sep 10, 2024

    • dbmi_seminar

      Public
      @CU-DBMI seminar committee material
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Aug 16, 2024Aug 16, 2024

    • rootstock

      Public
      TEST for Manubot AI Editor
      HTML
      •
      Other
      •192•0•0•1•Updated Jul 17, 2024Jul 17, 2024

    • rtx-kg2-gateway

      Public
      Enabling RTX-KG2 data access through various means.
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•2•0•Updated May 17, 2024May 17, 2024

    • gc-cloud-storage-bucket

      Public
      Template for creating Cloud Storage bucket on Google Cloud.
      templatecloud-resourcesterraformgoogle-cloudcloud-storagebucketcookiecutter-templategsutil
      CUE
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•10•0•Updated Apr 11, 2024Apr 11, 2024

    • healthcare-data-harmonization

      Public
      This is an engine that converts data of one structure to another, based on a configuration file which describes how. There is an accompanying syntax to make writing mappings easier and more robust.
      Java
      •
      Apache License 2.0
      •73•1•0•0•Updated Mar 24, 2024Mar 24, 2024

    • action-pr-test-3

      Public
      A test repo to see why workflows submitted from forked PRs weren't running, please ignore
      1•0•1•1•Updated Mar 7, 2024Mar 7, 2024

    • set-effort-analysis

      Public
      Data analysis on DBMI Software Engineering Team efforts.
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•1•0•Updated Feb 22, 2024Feb 22, 2024

    • demo-python-memory-reference-accounting

      Public
      Demonstrating Python memory allocator reference counting and debug.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•3•0•Updated Feb 22, 2024Feb 22, 2024

    • demo-poetry-dynamic-semver-with-docker-hub-push

      Public
      A demonstrational repository showing how Python Poetry dynamic versioning can be used to distribute Docker container images on Docker Hub for Python packages.
      pythonpoetrydocker-hubsemver-releasedynamic-versioningdocker
      Dockerfile
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Jan 2, 2024Jan 2, 2024

    • RTX-KG2

      Public
      Build system for the RTX-KG2 biomedical knowledge graph, part of the ARAX reasoning system (https://github.com/RTXTeam/RTX)
      Python
      •
      MIT License
      •8•0•0•0•Updated Dec 7, 2023Dec 7, 2023

    • CCPM-IO.github

      Public
      A special GitHub repository for setting the CCPM-IO organization profile and default community health files.
      2•0•0•0•Updated Nov 13, 2023Nov 13, 2023

    • omop-fhir-data

      Public
      Python
      •1•3•0•0•Updated Sep 28, 2023Sep 28, 2023

    • example-hpc-alpine-python

      Public
      Demonstrating the use of Python on Alpine, a High Performance Compute (HPC) cluster hosted by the University of Colorado Boulder's Research Computing.
      Shell
      •
      Apache License 2.0
      •1•0•1•0•Updated Sep 15, 2023Sep 15, 2023