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@microbiomedata National Microbiome Data Collaborative

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    80 repositories

    • docs

      Public
      User-facing, web-based documentation about the NMDC
      documentationsphinxmkdocs
      Dockerfile
      •3•2•37•2•Updated Dec 23, 2025Dec 23, 2025

    • nmdc-server

      Public
      Data portal client and server for NMDC.
      nmdc
      Python
      •
      Other
      •0•12•126•24•Updated Dec 23, 2025Dec 23, 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•0•15•2•Updated Dec 22, 2025Dec 22, 2025

    • nmdc-status-website

      Public
      Static web page(s) used to display messages during outages and other special events
      javascriptcsshtmlbootstrapmarkdownstatus
      HTML
      •0•1•3•0•Updated Dec 20, 2025Dec 20, 2025

    • nmdc_mass_spectrometry_metadata_generation

      Public
      Mass spectrometry metadata generation
      Python
      •
      Other
      •0•2•5•1•Updated Dec 19, 2025Dec 19, 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•7•5•0•Updated Dec 19, 2025Dec 19, 2025

    • nmdc_automation

      Public
      Prototype automation
      Python
      •2•2•62•8•Updated Dec 18, 2025Dec 18, 2025

    • nmdc-schema

      Public
      National Microbiome Data Collaborative (NMDC) unified data model
      metadataschemagenomicsstandardssamplesproteomicsmetabolomicsmicrobiometranscriptomicsfair-data
      Python
      •
      Creative Commons Zero v1.0 Universal
      •9•44•356•12•Updated Dec 18, 2025Dec 18, 2025

    • nmdc-aggregator

      Public
      Scripts that periodically aggregate data related to KEGG search
      Python
      •0•0•4•1•Updated Dec 17, 2025Dec 17, 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•4•3•1•Updated Dec 17, 2025Dec 17, 2025

    • nmdc-edge

      Public
      Web-based interface to the NMDC EDGE platform
      mongoexpressnodereactjscromwell
      JavaScript
      •1•4•83•1•Updated Dec 16, 2025Dec 16, 2025

    • nmdc-runtime

      Public
      Runtime system for NMDC data management and orchestration
      workflownmdcmicrobiomedata
      Python
      •
      Other
      •6•7•129•8•Updated Dec 15, 2025Dec 15, 2025

    • ReadbasedAnalysis

      Public
      The pipeline takes in sequencing files (single- or paired-end) and profiles them using multiple taxonomic classification tools
      HTML
      •6•2•0•0•Updated Dec 12, 2025Dec 12, 2025

    • metaMAGs

      Public
      Workflow for metagenome assembled genomes generation.
      Python
      •4•8•1•1•Updated Dec 10, 2025Dec 10, 2025

    • metaT_ReadsQC

      Public
      Workflow for metatranscriptome quality control
      WDL
      •0•0•0•0•Updated Dec 10, 2025Dec 10, 2025

    • submission-schema

      Public
      The NMDC submission schema
      Python
      •
      MIT License
      •3•1•25•3•Updated Dec 8, 2025Dec 8, 2025

    • mixs

      Public
      Minimum Information about any (X) Sequence” (MIxS) specification
      Python
      •
      Creative Commons Zero v1.0 Universal
      •22•0•41•3•Updated Dec 8, 2025Dec 8, 2025

    • issues

      Public
      public repo for issues related to NMDC work
      Jupyter Notebook
      •1•2•293•1•Updated Dec 3, 2025Dec 3, 2025

    • 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
      •33•1•0•2•Updated Dec 1, 2025Dec 1, 2025

    • geoloc-tools

      Public
      Library to request information about a location regarding the elevation, soil type, and landuse
      Python
      •0•1•0•0•Updated Nov 24, 2025Nov 24, 2025

    • refscan

      Public
      Command-line program that scans NMDC database for referential integrity violations
      mongodbreferential-integritylinkml
      Python
      •
      Other
      •0•2•3•0•Updated Nov 23, 2025Nov 23, 2025

    • ReadsQC

      Public
      This workflow is a replicate of the QA protocol implemented at JGI for Illumina reads
      WDL
      •6•3•2•3•Updated Nov 19, 2025Nov 19, 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 Nov 19, 2025Nov 19, 2025

    • metaT_Assembly

      Public
      workflow for metatranscriptome assembly
      WDL
      •0•0•0•0•Updated Nov 19, 2025Nov 19, 2025

    • metaT_ReadCounts

      Public
      Workflow for metatranscriptome read counting
      WDL
      •0•0•0•0•Updated Nov 4, 2025Nov 4, 2025

    • streams-agent

      Public
      Python
      •0•0•0•5•Updated Nov 3, 2025Nov 3, 2025

    • nmdc-mcp

      Public
      A fastmcp-based tool for writing prompts against data in the NMDC database
      Python
      •
      Other
      •2•2•21•1•Updated Oct 23, 2025Oct 23, 2025

    • metaMS

      Public
      Metabolomics Workflows for GC- and LC-MS Metabolomics and LC-MS Lipidomics
      Python
      •
      BSD 2-Clause "Simplified" License
      •0•6•3•0•Updated Oct 23, 2025Oct 23, 2025

    • external-metadata-awareness

      Public
      Tools for fetching and processing external schemas, ontologies and metadata records. Includes value set maintenance and some GitHub org exploration.
      Jupyter Notebook
      •0•2•74•1•Updated Oct 21, 2025Oct 21, 2025

    • metaPro

      Public
      Workflow for meta-proteomics analysis
      Python
      •
      BSD 2-Clause "Simplified" License
      •2•7•12•0•Updated Oct 17, 2025Oct 17, 2025