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@microbiomedata National Microbiome Data Collaborative

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    83 repositories

    • metaMS

      Public
      Metabolomics Workflows for GC- and LC-MS Metabolomics and LC-MS Lipidomics
      Python
      •
      BSD 2-Clause "Simplified" License
      •1•6•2•0•Updated Jul 10, 2026Jul 10, 2026

    • nmdc-runtime

      Public
      Runtime system for NMDC data management and orchestration
      workflownmdcmicrobiomedata
      workflownmdcmicrobiomedata
      Python
      •
      Other
      •7•7•144•13•Updated Jul 10, 2026Jul 10, 2026

    • nmdc_notebooks

      Public
      Jupyter Notebooks demonstrating R and Python-based access to NMDC metadata and data
      Jupyter Notebook
      •
      Creative Commons Zero v1.0 Universal
      •1•7•6•1•Updated Jul 10, 2026Jul 10, 2026

    • nmdc-schema

      Public
      National Microbiome Data Collaborative (NMDC) unified data model
      metadataschemagenomics
      metadataschemagenomicsstandardssamplesproteomicsmetabolomicsmicrobiometranscriptomicsfair-data
      Python
      •
      Creative Commons Zero v1.0 Universal
      •13•48•439•13•Updated Jul 10, 2026Jul 10, 2026

    • external-metadata-awareness

      Public
      MongoDB + Parquet analytics for NCBI BioSample/BioProject/SRA and NMDC submission-portal metadata. Environmental triad annotation, harmonized-attribute counts, …
      Jupyter Notebook
      •1•2•90•2•Updated Jul 10, 2026Jul 10, 2026

    • nmdc-metadata-suggestor-ai-tool

      Public
      A repository to that holds the code for the NMDC Submission portal metadata suggestor tool, powered by AI
      Python
      •
      Other
      •1•1•48•6•Updated Jul 10, 2026Jul 10, 2026

    • nmdc-server

      Public
      Data portal client and server for NMDC.
      nmdc
      nmdc
      Python
      •
      Other
      •1•12•124•9•Updated Jul 10, 2026Jul 10, 2026

    • nmdc_mass_spectrometry_metadata_generation

      Public
      Mass spectrometry metadata generation
      Python
      •
      Other
      •1•2•5•1•Updated Jul 10, 2026Jul 10, 2026

    • nmdc_automation

      Public
      Prototype automation
      Python
      •4•2•59•8•Updated Jul 10, 2026Jul 10, 2026

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

      Public
      CLI tool to convert metadata submissions from the NMDC submission portal to DOE user facility Excel templates
      Python
      •1•1•12•1•Updated Jul 9, 2026Jul 9, 2026

    • nmdc-client

      Public
      A python client for interacting with the NMDC (National Microbiome Data Collaborative) runtime API.
      Python
      •
      Other
      •1•7•1•1•Updated Jul 9, 2026Jul 9, 2026

    • nmdc-ai-eval

      Public
      Framework and data for performing evaluations for AI-powered NMDC tools.
      Python
      •0•2•37•1•Updated Jul 9, 2026Jul 9, 2026

    • nmdc-mass-spec-automation

      Public
      Python
      •1•1•4•2•Updated Jul 8, 2026Jul 8, 2026

    • nmdc-ingest-agent

      Public
      AI-agent-assisted workflows for translating external metadata sources into NMDC-schema-compliant JSON
      Python
      •
      Other
      •0•3•14•1•Updated Jun 29, 2026Jun 29, 2026

    • ReadsQC

      Public
      This workflow is a replicate of the QA protocol implemented at JGI for Illumina reads
      WDL
      •8•3•3•4•Updated Jun 26, 2026Jun 26, 2026

    • submission-schema

      Public
      The NMDC submission schema
      Python
      •
      MIT License
      •4•1•29•0•Updated Jun 25, 2026Jun 25, 2026

    • docs

      Public
      User-facing, web-based documentation about the NMDC
      documentationsphinxmkdocs
      documentationsphinxmkdocs
      Dockerfile
      •5•3•33•2•Updated Jun 8, 2026Jun 8, 2026

    • ontology-loader

      Public
      Suite of tools to configure and load an ontology from the OboFoundary into the data object for OntologyClass as specified by NMDC schema
      Python
      •1•0•17•1•Updated Jun 5, 2026Jun 5, 2026

    • metaMAGs

      Public
      Workflow for metagenome assembled genomes generation.
      Python
      •7•8•2•0•Updated May 29, 2026May 29, 2026

    • nmdc-aggregator

      Public
      Scripts that periodically aggregate data related to KEGG search
      Python
      •1•0•3•1•Updated May 26, 2026May 26, 2026

    • ReadbasedAnalysis

      Public
      The pipeline takes in sequencing files (single- or paired-end) and profiles them using multiple taxonomic classification tools
      HTML
      •9•2•1•0•Updated May 26, 2026May 26, 2026

    • refscan

      Public
      Command-line program that scans NMDC database for referential integrity violations
      mongodbreferential-integritylinkml
      mongodbreferential-integritylinkml
      Python
      •
      Other
      •1•3•3•3•Updated May 22, 2026May 22, 2026

    • mg_annotation

      Public
      Metagenome Annotation Workflow
      WDL
      •8•5•2•2•Updated May 22, 2026May 22, 2026

    • DataHarmonizer

      Public
      A standardized browser-based spreadsheet editor and validator that can be run offline and locally, which works of of LinkML data specifications.
      JavaScript
      •
      MIT License
      •39•1•0•5•Updated May 22, 2026May 22, 2026

    • nmdc-lakehouse

      Public
      Jupyter Notebook
      •0•0•30•1•Updated May 22, 2026May 22, 2026

    • enviroMS

      Public
      EnviroMS is a workflow for natural organic matter data processing and annotation
      Python
      •
      BSD 2-Clause "Simplified" License
      •1•5•0•0•Updated May 22, 2026May 22, 2026

    • nmdc-mcp

      Public
      A fastmcp-based tool for writing prompts against data in the NMDC database
      Python
      •
      Other
      •3•2•21•1•Updated May 22, 2026May 22, 2026

    • streams-agent

      Public
      Python
      •1•0•0•5•Updated May 22, 2026May 22, 2026

    • metaT

      Public
      Metatranscriptomics workflow
      workflowtranscriptomicsmetatranscriptomics
      workflowtranscriptomicsmetatranscriptomics
      WDL
      •4•4•6•0•Updated May 21, 2026May 21, 2026

    • metaT_ReadCounts

      Public
      Workflow for metatranscriptome read counting
      WDL
      •2•0•0•0•Updated May 21, 2026May 21, 2026
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