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@microbiomedata National Microbiome Data Collaborative

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    76 repositories

    • 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•5•1•3•Updated Sep 30, 2024Sep 30, 2024

    • nmdc-aggregator

      Public
      Scripts that periodically aggregate data related to KEGG search
      Python
      •0•0•4•1•Updated Sep 30, 2024Sep 30, 2024

    • nmdc_automation

      Public
      Prototype automation
      Python
      •2•2•37•2•Updated Sep 30, 2024Sep 30, 2024

    • berkeley-schema-fy24

      Public
      A fork of the nmdc-schema, for refactoring based on Monterey insights
      Python
      •
      Creative Commons Zero v1.0 Universal
      •8•6•0•14•Updated Sep 30, 2024Sep 30, 2024

    • nmdc-runtime

      Public
      Runtime system for NMDC data management and orchestration
      workflownmdcmicrobiomedata
      HTML
      •
      Other
      •3•5•103•10•Updated Sep 30, 2024Sep 30, 2024

    • nmdc-server

      Public
      Data portal client and server for NMDC.
      nmdc
      Python
      •
      Other
      •0•9•161•13•Updated Sep 30, 2024Sep 30, 2024

    • issues

      Public
      public repo for issues related to NMDC work
      Jupyter Notebook
      •0•1•315•1•Updated Sep 30, 2024Sep 30, 2024

    • nmdc-edge

      Public
      Web-based interface to the NMDC EDGE platform
      mongoexpressnodereactjscromwell
      JavaScript
      •0•3•67•0•Updated Sep 30, 2024Sep 30, 2024

    • ReadsQC

      Public
      WDL
      •6•3•3•1•Updated Sep 30, 2024Sep 30, 2024

    • kaiko_metaproteome

      Public
      Generates sample-specific protein databases from raw peptide spectra
      Python
      •
      BSD 2-Clause "Simplified" License
      •3•1•6•2•Updated Sep 26, 2024Sep 26, 2024

    • geoloc-tools

      Public
      Python
      •0•0•0•0•Updated Sep 26, 2024Sep 26, 2024

    • nmdc-schema

      Public
      National Microbiome Data Collaborative (NMDC) unified data model
      metadataschemagenomicsstandardssamplesproteomicsmetabolomicsmicrobiometranscriptomicsfair-data
      Python
      •
      Creative Commons Zero v1.0 Universal
      •8•27•365•27•Updated Sep 26, 2024Sep 26, 2024

    • metaT

      Public
      Metatranscriptomics workflow
      transcriptomicsmetatranscriptomicsworkflow
      WDL
      •2•4•6•0•Updated Sep 25, 2024Sep 25, 2024

    • external-metadata-awareness

      Public
      Tools for fetching and processing external schemas, ontologies and metadata records. Includes value set maintenance and some GitHub org exploration.
      Python
      •0•0•11•1•Updated Sep 25, 2024Sep 25, 2024

    • metaMS

      Public
      GC-MS Based Metabolomics Workflow
      Python
      •
      BSD 2-Clause "Simplified" License
      •0•4•16•0•Updated Sep 24, 2024Sep 24, 2024

    • metaPro

      Public
      Workflow for meta-proteomics analysis
      Python
      •
      BSD 2-Clause "Simplified" License
      •3•6•8•1•Updated Sep 24, 2024Sep 24, 2024

    • nmdc-field-notes

      Public
      Mobile app for metadata collection on the go
      reactioniccapacitor
      TypeScript
      •
      Other
      •0•1•36•0•Updated Sep 17, 2024Sep 17, 2024

    • metaT_Assembly

      Public
      workflow for metatranscriptome assembly
      WDL
      •0•0•0•0•Updated Sep 17, 2024Sep 17, 2024

    • NMDC_documentation

      Public
      Document workflows, schemas, and portal
      3•2•21•2•Updated Sep 13, 2024Sep 13, 2024

    • refscan

      Public
      Command-line program that scans NMDC database for referential integrity violations
      mongodbreferential-integritylinkml
      Python
      •0•1•4•0•Updated Sep 12, 2024Sep 12, 2024

    • 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•17•0•Updated Sep 9, 2024Sep 9, 2024

    • docs

      Public
      User-facing, web-based documentation about the NMDC
      documentationsphinx
      Python
      •0•0•1•0•Updated Sep 4, 2024Sep 4, 2024

    • submission-schema

      Public
      Python
      •
      MIT License
      •1•1•44•5•Updated Aug 29, 2024Aug 29, 2024

    • metaMAGs

      Public
      Workflow for metagenome assembled genomes generation.
      Python
      •4•5•0•0•Updated Aug 26, 2024Aug 26, 2024

    • metaT_ReadsQC

      Public
      Workflow for metatranscriptome quality control
      WDL
      •0•0•0•0•Updated Aug 23, 2024Aug 23, 2024

    • metaT_ReadCounts

      Public
      WDL
      •0•0•0•0•Updated Aug 20, 2024Aug 20, 2024

    • nmdc-datasets

      Public archive
      Datasets that are stored in the central NMDC database.
      MIT License
      •0•0•0•1•Updated Aug 19, 2024Aug 19, 2024

    • mg_annotation

      Public
      Metagenome Annotation Workflow
      WDL
      •7•4•2•2•Updated Aug 9, 2024Aug 9, 2024

    • enviroMS

      Public
      Python
      •
      BSD 2-Clause "Simplified" License
      •0•4•4•0•Updated Jul 24, 2024Jul 24, 2024

    • ReadbasedAnalysis

      Public
      HTML
      •6•0•0•0•Updated Jul 23, 2024Jul 23, 2024