Repositories list

• 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•0•20•1•Updated Feb 21, 2025Feb 21, 2025

• docs

  Public
  User-facing, web-based documentation about the NMDC

  documentationsphinxmkdocs

  Python

  •1•1•18•2•Updated Feb 21, 2025Feb 21, 2025

• nmdc-runtime

  Public
  Runtime system for NMDC data management and orchestration

  workflownmdcmicrobiomedata

  HTML

  •

  Other

  •5•7•109•16•Updated Feb 20, 2025Feb 20, 2025

• nmdc_automation

  Public
  Prototype automation

  Python

  •2•2•49•5•Updated Feb 20, 2025Feb 20, 2025

• nmdc_mass_spectrometry_metadata_generation

  Public
  Mass spectrometry metadata generation

  Python

  •0•0•4•0•Updated Feb 20, 2025Feb 20, 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•5•11•4•Updated Feb 20, 2025Feb 20, 2025

• workflow_documentation

  Public
  This repository contains the documentation template for the NDMC workflows.

  Python

  •2•2•2•0•Updated Feb 20, 2025Feb 20, 2025

• portal_user_guide

  Public
  JavaScript

  •2•0•0•0•Updated Feb 20, 2025Feb 20, 2025

• NMDC_documentation

  Public
  Document workflows, schemas, and portal

  3•2•18•2•Updated Feb 20, 2025Feb 20, 2025

• nmdc-server

  Public
  Data portal client and server for NMDC.

  nmdc

  Python

  •

  Other

  •0•9•149•13•Updated Feb 20, 2025Feb 20, 2025

• metaT_ReadCounts

  Public
  Workflow for metatranscriptome read counting

  WDL

  •0•0•0•0•Updated Feb 20, 2025Feb 20, 2025

• nmdc-field-notes

  Public
  Mobile app for metadata collection on the go

  reactioniccapacitor

  TypeScript

  •

  Other

  •0•2•28•0•Updated Feb 19, 2025Feb 19, 2025

• ReadsQC

  Public
  WDL

  •6•3•2•1•Updated Feb 19, 2025Feb 19, 2025

• ontology-loader

  Public
  Python

  •0•0•0•0•Updated Feb 18, 2025Feb 18, 2025

• nmdc-schema

  Public
  National Microbiome Data Collaborative (NMDC) unified data model

  metadataschemagenomics+ 12standardssamplesproteomicsmetabolomicsmicrobiometranscriptomicsfair-data+ 5

  Python

  •

  Creative Commons Zero v1.0 Universal

  •8•29•362•6•Updated Feb 14, 2025Feb 14, 2025

• submission-schema

  Public
  Python

  •

  MIT License

  •1•1•50•5•Updated Feb 13, 2025Feb 13, 2025

• issues

  Public
  public repo for issues related to NMDC work

  Jupyter Notebook

  •1•2•295•2•Updated Feb 13, 2025Feb 13, 2025

• mg_annotation

  Public
  Metagenome Annotation Workflow

  WDL

  •7•4•3•3•Updated Feb 12, 2025Feb 12, 2025

• kaiko_metaproteome

  Public
  Generates sample-specific protein databases from raw peptide spectra

  Python

  •

  BSD 2-Clause "Simplified" License

  •3•2•3•1•Updated Feb 12, 2025Feb 12, 2025

• metaMS

  Public
  Metabolomics Workflows for GC-MS Metabolomics and LC-MS Lipidomics

  Python

  •

  BSD 2-Clause "Simplified" License

  •0•5•2•0•Updated Feb 11, 2025Feb 11, 2025

• metaMAGs

  Public
  Workflow for metagenome assembled genomes generation.

  Python

  •4•6•3•0•Updated Feb 11, 2025Feb 11, 2025

• metaPro

  Public
  Workflow for meta-proteomics analysis

  Python

  •

  BSD 2-Clause "Simplified" License

  •3•6•9•1•Updated Feb 5, 2025Feb 5, 2025

• nmdc-edge

  Public
  Web-based interface to the NMDC EDGE platform

  mongoexpressnode+ 2reactjscromwell

  JavaScript

  •0•4•77•0•Updated Feb 5, 2025Feb 5, 2025

• metaAssembly

  Public
  Workflow for metagenome assembly

  wdlwdl-workflowworkflow+ 2assemblymetagenome-assembly

  WDL

  •4•4•1•2•Updated Feb 5, 2025Feb 5, 2025

• sample-annotator

  Public
  NMDC Sample Annotator

  samplesmicrobiomeontologies+ 8annotatornmdcenvoenvironment-ontologysample-metadatalinkmlmicrobiomedata+ 1

  Python

  •9•5•25•11•Updated Feb 4, 2025Feb 4, 2025

• ReadbasedAnalysis

  Public
  HTML

  •6•1•0•0•Updated Feb 4, 2025Feb 4, 2025

• nmdc_notebook_tools

  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

  •0•2•1•0•Updated Feb 4, 2025Feb 4, 2025

• nmdc-status-website

  Public
  Static web page(s) used to display messages during outages and other special events

  javascriptcsshtml+ 3bootstrapmarkdownstatus

  HTML

  •0•1•2•0•Updated Feb 3, 2025Feb 3, 2025

• geoloc-tools

  Public
  Python

  •0•0•0•0•Updated Feb 3, 2025Feb 3, 2025

• refscan

  Public
  Command-line program that scans NMDC database for referential integrity violations

  mongodbreferential-integritylinkml

  Python

  •

  Other

  •0•2•3•0•Updated Feb 2, 2025Feb 2, 2025