Repositories list

• docs

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

  documentationsphinx

  HTML

  •0•0•24•0•Updated Nov 19, 2024Nov 19, 2024

• ReadbasedAnalysis

  Public
  HTML

  •6•0•0•0•Updated Nov 19, 2024Nov 19, 2024

• mg_annotation

  Public
  Metagenome Annotation Workflow

  WDL

  •7•4•3•3•Updated Nov 19, 2024Nov 19, 2024

• metaT

  Public
  Metatranscriptomics workflow

  transcriptomicsmetatranscriptomicsworkflow

  WDL

  •2•4•6•1•Updated Nov 19, 2024Nov 19, 2024

• metaT_Assembly

  Public
  workflow for metatranscriptome assembly

  WDL

  •0•0•1•1•Updated Nov 19, 2024Nov 19, 2024

• metaT_ReadsQC

  Public
  Workflow for metatranscriptome quality control

  WDL

  •0•0•0•1•Updated Nov 19, 2024Nov 19, 2024

• metaT_ReadCounts

  Public
  WDL

  •0•0•0•1•Updated Nov 19, 2024Nov 19, 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•12•3•Updated Nov 18, 2024Nov 18, 2024

• nmdc_automation

  Public
  Prototype automation

  Python

  •2•2•31•1•Updated Nov 18, 2024Nov 18, 2024

• metaAssembly

  Public
  Workflow for metagenome assembly

  wdlwdl-workflowworkflow+ 2assemblymetagenome-assembly

  WDL

  •4•4•1•1•Updated Nov 18, 2024Nov 18, 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 Nov 18, 2024Nov 18, 2024

• ReadsQC

  Public
  WDL

  •6•3•2•1•Updated Nov 18, 2024Nov 18, 2024

• nmdc-server

  Public
  Data portal client and server for NMDC.

  nmdc

  Python

  •

  Other

  •0•9•166•13•Updated Nov 18, 2024Nov 18, 2024

• nmdc-runtime

  Public
  Runtime system for NMDC data management and orchestration

  workflownmdcmicrobiomedata

  HTML

  •

  Other

  •3•7•109•13•Updated Nov 18, 2024Nov 18, 2024

• metaMAGs

  Public
  Workflow for metagenome assembled genomes generation.

  Python

  •4•6•1•0•Updated Nov 18, 2024Nov 18, 2024

• nmdc-edge

  Public
  Web-based interface to the NMDC EDGE platform

  mongoexpressnode+ 2reactjscromwell

  JavaScript

  •0•4•69•0•Updated Nov 18, 2024Nov 18, 2024

• geoloc-tools

  Public
  Python

  •0•0•0•0•Updated Nov 18, 2024Nov 18, 2024

• nmdc-schema

  Public
  National Microbiome Data Collaborative (NMDC) unified data model

  metadataschemagenomics+ 12standardssamplesproteomicsmetabolomicsmicrobiometranscriptomicsfair-data+ 5

  Python

  •

  Creative Commons Zero v1.0 Universal

  •8•27•362•10•Updated Nov 15, 2024Nov 15, 2024

• metaMS

  Public
  GC-MS Based Metabolomics Workflow

  Python

  •

  BSD 2-Clause "Simplified" License

  •0•4•10•0•Updated Nov 15, 2024Nov 15, 2024

• submission-schema

  Public
  Python

  •

  MIT License

  •1•1•57•8•Updated Nov 15, 2024Nov 15, 2024

• issues

  Public
  public repo for issues related to NMDC work

  Jupyter Notebook

  •1•2•329•1•Updated Nov 14, 2024Nov 14, 2024

• 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•2•1•Updated Nov 14, 2024Nov 14, 2024

• workflow_documentation

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

  Python

  •2•2•0•1•Updated Nov 14, 2024Nov 14, 2024

• NMDC_documentation

  Public
  Document workflows, schemas, and portal

  3•2•20•2•Updated Nov 14, 2024Nov 14, 2024

• nmdc-aggregator

  Public
  Scripts that periodically aggregate data related to KEGG search

  Python

  •0•0•2•1•Updated Nov 12, 2024Nov 12, 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•5•0•4•Updated Nov 11, 2024Nov 11, 2024

• 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 10, 2024Nov 10, 2024

• enviroMS

  Public
  Python

  •

  BSD 2-Clause "Simplified" License

  •0•4•3•0•Updated Oct 24, 2024Oct 24, 2024

• refscan

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

  mongodbreferential-integritylinkml

  Python

  •0•1•4•0•Updated Oct 22, 2024Oct 22, 2024

• 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 Oct 17, 2024Oct 17, 2024