National Microbiome Data Collaborative

Pinned Repositories

berkeley-schema-fy24
A fork of the nmdc-schema, for refactoring based on Monterey insights
Language:Python6 0 00
metaMAGs
Workflow for metagenome assembled genomes generation.
Language:Python5 7 184
metaPro
Workflow for meta-proteomics analysis
Language:Python6 5 513
mixs-6-2-release-candidate
Proposed, Harmonized MIxS 6.2
Language:Python5 4 1250
nmdc-schema
National Microbiome Data Collaborative (NMDC) unified data model
Language:Python27 9 1.2k8
nmdc-server
Data portal client and server for NMDC.
Language:Python8 8 6300
NMDC_documentation
Document workflows, schemas, and portal
2 4 363
nmdc_notebooks
Jupyter Notebooks demonstrating R and Python-based access to NMDC metadata and data
Language:Jupyter Notebook5 5 290
sample-annotator
NMDC Sample Annotator
Language:Python5 4 689
WorkflowPlanning
This is primarily a repo for capturing policies and discussions around the different workflows for NMDC. This is also used for project management related pieces.
Language:WDL7 4 166

National Microbiome Data Collaborative's Repositories

microbiomedata/nmdc-schema
National Microbiome Data Collaborative (NMDC) unified data model
Language:Python27 9 1.2k8
microbiomedata/nmdc-server
Data portal client and server for NMDC.
Language:Python8 8 6300
microbiomedata/berkeley-schema-fy24
A fork of the nmdc-schema, for refactoring based on Monterey insights
Language:Python6 0 00
microbiomedata/metaMAGs
Workflow for metagenome assembled genomes generation.
Language:Python5 7 184
microbiomedata/nmdc_notebooks
Jupyter Notebooks demonstrating R and Python-based access to NMDC metadata and data
Language:Jupyter Notebook5 5 290
microbiomedata/enviroMS
Language:Python4 8 80
microbiomedata/metaAssembly
Workflow for metagenome assembly
Language:WDL4 7 84
microbiomedata/metaMS
GC-MS Based Metabolomics Workflow
Language:Python4
microbiomedata/metaT
Metatranscriptomics workflow
Language:WDL4 5 282
microbiomedata/nmdc-runtime
Runtime system for NMDC data management and orchestration
Language:HTML4 11 3623
microbiomedata/mg_annotation
Metagenome Annotation Workflow
Language:WDL3 6 177
microbiomedata/nmdc-edge
Web-based interface to the NMDC EDGE platform
Language:JavaScript3 6 1740
microbiomedata/ReadsQC
Language:WDL3 7 156
microbiomedata/nmdc_automation
Prototype automation
Language:Python2 5 1402
microbiomedata/NMDC_documentation
Document workflows, schemas, and portal
2 4 363
microbiomedata/workflow_documentation
This repository contains the documentation template for the NDMC workflows.
Language:Python22
microbiomedata/DataHarmonizer
Our dev interface is available via github pages:
Language:JavaScript1 3 1230
microbiomedata/issues
public repo for issues related to NMDC work
Language:Jupyter Notebook1 4 8080
microbiomedata/nmdc-field-notes
Mobile app for metadata collection on the go
Language:TypeScript1 4 72
microbiomedata/refscan
Command-line program that scans NMDC database for referential integrity violations
Language:Python10
microbiomedata/SRA_submit
ncbi export
Language:Python1 4 0
microbiomedata/submission-schema
Language:Python1 5 1121
microbiomedata/ReadbasedAnalysis
Language:HTML0 7 96
microbiomedata/sheets_and_friends
Enhance a LinkML model with imported and optionally modified slots
Language:Python0 3 1480
microbiomedata/metadata-for-user-facility-template-transformations
CLI tool to convert metadata submissions from the NMDC submission portal to user facility Excel templates
Language:Python
microbiomedata/metaT_Assembly
workflow for metatranscriptome assembly
Language:WDL5 4
microbiomedata/metaT_ReadCounts
Language:WDL
microbiomedata/metaT_ReadsQC
Workflow for metatranscriptome quality control
Language:WDL
microbiomedata/nmdc-aggregator
Scripts that periodically aggregate data related to KEGG search
Language:Python4 3
microbiomedata/nmdc-datasets
Datasets that are stored in the central NMDC database.