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@cape-ph Center for Applied Pathogen Epidemiology and Outbreak Control

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    20 repositories

    • cape-cod

      Public
      This is the main repository for the CAPE infrastructure as code.
      Python
      •
      Apache License 2.0
      •0•2•51•1•Updated Feb 3, 2025Feb 3, 2025

    • arlog

      Public
      Package to process files for AR Log database creation.
      R
      •
      MIT License
      •0•0•0•0•Updated Jan 31, 2025Jan 31, 2025

    • etl-tnl-genome-report

      Public
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Jan 28, 2025Jan 28, 2025

    • etl-gphl-cre-alert

      Public
      Repo containing the Epi/HAI ETL for a GDPH CRE alert
      Python
      •
      Apache License 2.0
      •0•0•2•0•Updated Jan 28, 2025Jan 28, 2025

    • etl-template

      Public template
      Template repository for creating ETL scripts for the CAPE COD system
      Python
      •
      Apache License 2.0
      •0•0•3•0•Updated Jan 28, 2025Jan 28, 2025

    • etl-tnl-alert

      Public
      Repo containing the Epi/HAI ETL for a Tennessee Lab alert
      Python
      •
      Apache License 2.0
      •0•0•1•0•Updated Jan 28, 2025Jan 28, 2025

    • etl-gphl-sequencing-alert

      Public
      Python
      •
      Apache License 2.0
      •0•0•1•0•Updated Jan 28, 2025Jan 28, 2025

    • capepy

      Public
      A collection of utility functions useful for developing on and interacting with the CAPE infrastructure
      Python
      •
      Apache License 2.0
      •0•0•3•0•Updated Jan 23, 2025Jan 23, 2025

    • haiarlogdb

      Public archive
      R
      •
      MIT License
      •0•0•0•0•Updated Dec 5, 2024Dec 5, 2024

    • aws-jupyterhub-tljh-ami

      Public
      AMI for TLJH Ubuntu 24.04.
      HCL
      •
      Apache License 2.0
      •0•0•4•0•Updated Nov 20, 2024Nov 20, 2024

    • .github

      Public
      CAPE organization shared github configuration
      0•0•0•1•Updated Nov 8, 2024Nov 8, 2024

    • nvim

      Public
      A Neovim configuration based on AstroNvim for development within the CAPE organization
      Lua
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Oct 29, 2024Oct 29, 2024

    • aws-batch-ecs-ami

      Public
      Shell
      •
      Apache License 2.0
      •0•0•0•1•Updated Oct 4, 2024Oct 4, 2024

    • public-docs

      Public
      Markdown documents for public consumption
      Apache License 2.0
      •1•0•0•0•Updated Sep 9, 2024Sep 9, 2024

    • cape-policy-agent

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated May 9, 2024May 9, 2024

    • bell-lapadula

      Public
      Bell-LaPadula model for confidentiality of public health data stored in information systems
      Python
      •
      MIT License
      •0•0•1•0•Updated Feb 28, 2024Feb 28, 2024

    • cape-baby-steps

      Public
      Repo containing a phased architecture test for CAPE AWS stacks
      0•1•0•2•Updated Feb 23, 2024Feb 23, 2024

    • bactopia-baseline

      Public
      A vagrant VM to provide a baseline for running the bactopia pipeline
      Shell
      •0•0•0•0•Updated Oct 25, 2023Oct 25, 2023

    • r-nextflow-template

      Public
      R
      •
      Other
      •0•0•0•0•Updated Jul 14, 2023Jul 14, 2023

    • nf-tower

      Public
      Nextflow Tower system
      Groovy
      •
      Mozilla Public License 2.0
      •52•0•0•0•Updated Feb 2, 2023Feb 2, 2023