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@microbiomedata National Microbiome Data Collaborative

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    83 repositories

    • nmdc-mcp

      Public
      Python
      •2•1•3•0•Updated Jul 15, 2025Jul 15, 2025

    • nmdc-runtime

      Public
      Runtime system for NMDC data management and orchestration
      workflownmdcmicrobiomedata
      Jupyter Notebook
      •
      Other
      •5•7•113•15•Updated Jul 15, 2025Jul 15, 2025

    • nmdc_notebooks

      Public
      Jupyter Notebooks demonstrating R and Python-based access to NMDC metadata and data
      Jupyter Notebook
      •
      Creative Commons Zero v1.0 Universal
      •0•6•9•4•Updated Jul 15, 2025Jul 15, 2025

    • nmdc-schema

      Public
      National Microbiome Data Collaborative (NMDC) unified data model
      metadataschemagenomicsstandardssamplesproteomicsmetabolomicsmicrobiometranscriptomicsfair-data
      Python
      •
      Creative Commons Zero v1.0 Universal
      •9•43•389•19•Updated Jul 15, 2025Jul 15, 2025

    • submission-schema

      Public
      Python
      •
      MIT License
      •2•1•54•9•Updated Jul 14, 2025Jul 14, 2025

    • nmdc_automation

      Public
      Prototype automation
      Python
      •2•2•51•4•Updated Jul 14, 2025Jul 14, 2025

    • nmdc-field-notes

      Public
      Mobile app for metadata collection on the go
      reactioniccapacitor
      TypeScript
      •
      Other
      •0•2•29•2•Updated Jul 14, 2025Jul 14, 2025

    • refscan

      Public
      Command-line program that scans NMDC database for referential integrity violations
      mongodbreferential-integritylinkml
      Python
      •
      Other
      •0•2•3•0•Updated Jul 14, 2025Jul 14, 2025

    • metadata-for-user-facility-template-transformations

      Public
      CLI tool to convert metadata submissions from the NMDC submission portal to user facility Excel templates
      Python
      •0•< 10000 /span>0•11•1•Updated Jul 14, 2025Jul 14, 2025

    • docs

      Public
      User-facing, web-based documentation about the NMDC
      documentationsphinxmkdocs
      Dockerfile
      •1•2•20•1•Updated Jul 14, 2025Jul 14, 2025

    • nmdc-server

      Public
      Data portal client and server for NMDC.
      nmdc
      Python
      •
      Other
      •0•12•131•17•Updated Jul 14, 2025Jul 14, 2025

    • enviroMS

      Public
      Python
      •
      BSD 2-Clause "Simplified" License
      •0•5•5•0•Updated Jul 14, 2025Jul 14, 2025

    • geoloc-tools

      Public
      Python
      •0•0•1•0•Updated Jul 14, 2025Jul 14, 2025

    • metaPro

      Public
      Workflow for meta-proteomics analysis
      Python
      •
      BSD 2-Clause "Simplified" License
      •3•6•10•1•Updated Jul 11, 2025Jul 11, 2025

    • issues

      Public
      public repo for issues related to NMDC work
      Jupyter Notebook
      •1•2•303•2•Updated Jul 11, 2025Jul 11, 2025

    • nmdc_mass_spectrometry_metadata_generation

      Public
      Mass spectrometry metadata generation
      Python
      •
      Other
      •0•2•9•0•Updated Jul 10, 2025Jul 10, 2025

    • nmdc-edge

      Public
      Web-based interface to the NMDC EDGE platform
      mongoexpressnodereactjscromwell
      JavaScript
      •1•4•81•1•Updated Jul 9, 2025Jul 9, 2025

    • nmdc_api_utilities

      Public
      A library designed to simplify various research tasks for users looking to leverage the NMDC (National Microbiome Data Collaborative) APIs. The library provides a collection of general-purpose functions that facilitate easy access, manipulation, and analysis of microbiome data.
      Python
      •
      Other
      •0•3•1•0•Updated Jul 3, 2025Jul 3, 2025

    • ontology-loader

      Public
      Python
      •0•0•1•0•Updated Jul 2, 2025Jul 2, 2025

    • w3id.org

      Public
      w3id purl redirections for NMDC schema files and per-term help pages
      HTML
      •1.4k•0•0•0•Updated Jul 1, 2025Jul 1, 2025

    • ReadbasedAnalysis

      Public
      HTML
      •6•2•0•0•Updated Jun 26, 2025Jun 26, 2025

    • metaAssembly

      Public
      Workflow for metagenome assembly
      wdlwdl-workflowworkflowassemblymetagenome-assembly
      WDL
      •4•4•3•0•Updated Jun 26, 2025Jun 26, 2025

    • ReadsQC

      Public
      WDL
      •6•3•2•1•Updated Jun 26, 2025Jun 26, 2025

    • nmdc-orcid-creditor

      Public
      Web app NMDC team members use to credit ambassadors and champions via ORCID
      Python
      •0•1•3•0•Updated Jun 25, 2025Jun 25, 2025

    • nmdc-metrics-fetcher

      Public
      Tools used to collect metrics-related data about the NMDC system
      google-apps-script
      JavaScript
      •0•1•0•0•Updated Jun 25, 2025Jun 25, 2025

    • metaMS

      Public
      Metabolomics Workflows for GC- and LC-MS Metabolomics and LC-MS Lipidomics
      Python
      •
      BSD 2-Clause "Simplified" License
      •0•5•2•0•Updated Jun 25, 2025Jun 25, 2025

    • docs-dev

      Public
      Temporary, non-production deployments of docs.microbiomedata.org
      0•0•0•0•Updated Jun 25, 2025Jun 25, 2025

    • mg_annotation

      Public
      Metagenome Annotation Workflow
      WDL
      •7•5•1•1•Updated Jun 19, 2025Jun 19, 2025

    • nmdc-aggregator

      Public
      Scripts that periodically aggregate data related to KEGG search
      Python
      •0•0•1•0•Updated Jun 4, 2025Jun 4, 2025

    • metaT_Assembly

      Public
      workflow for metatranscriptome assembly
      WDL
      •0•0•1•0•Updated Jun 4, 2025Jun 4, 2025
    0