Repositories list

• COPO-production

  Public
  COPO is a Django-based platform that serves as a metadata broker to describe research data per FAIR principles. It supports community-recognised metadata standards, ensuring data is discoverable, interoperable, and accessible. Submitted data is accessible via public repositories, promoting long-term preservation and reuse across systems.

  researchgenomicsomics+ 3biodiversitylife-sciencesmetadata-broker

  JavaScript

  •

  MIT License

  •2•4•0•0•Updated Dec 11, 2025Dec 11, 2025

• rfparser

  Public
  Parse ResearchFish publications to update CKAN

  Python

  •

  MIT License

  •0•0•0•0•Updated Dec 11, 2025Dec 11, 2025

• eista

  Public
  A single-cell spatial transcriptomics pipeline aimed at covering all analysis stages from quantification and clustering to tertiary analyses.

  Python

  •

  MIT License

  •0•0•0•0•Updated Dec 9, 2025Dec 9, 2025

• eisca

  Public
  A single-cell RNA-seq pipeline aimed at covering all analysis stages from quantification and clustering to tertiary analyses.

  Nextflow

  •

  MIT License

  •1•2•2•0•Updated Dec 9, 2025Dec 9, 2025

• grassroots-service-field-trial

  Public
  A Grassroots service for storing the data for field trials

  C

  •

  Apache License 2.0

  •0•2•0•0•Updated Dec 8, 2025Dec 8, 2025

• earlham-galaxytools

  Public
  Galaxy tools and workflows developed at the Earlham Institute

  Python

  •

  MIT License

  •15•14•7•3•Updated Dec 8, 2025Dec 8, 2025

• COPO-documentation

  Public
  COPO documentation was created using the Sphinx reStructuredText (reST) markup language which is hosted on readthedocs.io. The documentation uses Sphinx.

  metadatasphinxreadthedocs+ 4sphinx-documentationcopocopo-projectcopo-docs

  Python

  •

  Apache License 2.0

  •0•2•0•2•Updated Dec 6, 2025Dec 6, 2025

• COPO-schemas

  Public
  This repository provides a collection of schemas, or data objects, for representing different types of metadata.

  metadatavalidationschemas+ 7data-standardsresearch-datachecklistscopolife-sciencecopo-projectmetadata-submission

  MIT License

  •0•1•0•0•Updated Dec 3, 2025Dec 3, 2025

• SingleCellSchemas

  Public
  For resources related to the EI Cellgen ISP, including metadata mappings and schemas for Single Cell Genomics and Spatial Transcriptomics experiments.

  sequencingschemassingle-cell+ 3single-cell-rna-seqspatial-transcriptomicsearlham-institute

  Python

  •

  Other

  •0•1•0•0•Updated Dec 3, 2025Dec 3, 2025

• COPO-ansible-deployment

  Public
  COPO - ansible deployment

  MIT License

  •0•0•0•0•Updated Dec 1, 2025Dec 1, 2025

• nanopore-mod-course-2024

  Public
  Contains materials used for the nanopore base modification course at the Earlham Institute that ran in 2024

  CSS

  •

  Other

  •117•1•0•0•Updated Nov 25, 2025Nov 25, 2025

• reposyncer

  Public
  GitHub workflow to sync various repo mirrors

  MIT License

  •2•0•0•0•Updated Nov 24, 2025Nov 24, 2025

• grassroots-installer

  Public
  Tools to automate the installation of Grassroots

  Shell

  •

  Apache License 2.0

  •0•0•0•0•Updated Nov 24, 2025Nov 24, 2025

• MARTi

  Public
  Metagenomic Analysis in Real Time

  Java

  •

  MIT License

  •3•0•0•0•Updated Nov 23, 2025Nov 23, 2025

• JP_PhD

  Public
  Additional material for Jess Peers' PhD thesis

  Python

  •0•0•0•0•Updated Nov 20, 2025Nov 20, 2025

• grassroots-lucene

  Public
  Lucene engine customised for Grassroots data

  Java

  •

  Apache License 2.0

  •0•0•0•0•Updated Nov 11, 2025Nov 11, 2025

• grassroots_services_django_web

  Public
  JavaScript

  •1•0•0•10•Updated Oct 31, 2025Oct 31, 2025

• 2025-11-04-earlham

  Public
  HTML

  •

  Other

  •0•0•0•0•Updated Oct 31, 2025Oct 31, 2025

• grassroots-core

  Public
  The core libraries of the Grassroots infratructure

  C

  •

  Apache License 2.0

  •0•1•0•0•Updated Oct 27, 2025Oct 27, 2025

• Aequatus

  Public
  Earlham Institute's Synteny Browser

  JavaScript

  •

  GNU General Public License v3.0

  •0•7•1•30•Updated Oct 26, 2025Oct 26, 2025

• grassroots-client-qt-desktop

  Public
  The desktop Grassroots client application for running services on Grassroots servers

  C++

  •

  Apache License 2.0

  •0•0•0•0•Updated Oct 25, 2025Oct 25, 2025

• TGACBrowser

  Public
  TGAC's Genome Browser

  JavaScript

  •0•11•1•42•Updated Oct 22, 2025Oct 22, 2025

• cvanmf

  Public
  (bi)crossvalidation for NMF rank selection, and visualisation/analysis tools

  Python

  •

  GNU General Public License v2.0

  •2•1•0•0•Updated Sep 21, 2025Sep 21, 2025

• grassroots-service-search

  Public
  A service to search across all of the Grassroots data and tools

  C

  •

  Apache License 2.0

  •0•0•0•0•Updated Sep 16, 2025Sep 16, 2025

• grassroots-parental-genotype-service

  Public
  A Grassroots service to give parental cross information for given markers

  C

  •

  Apache License 2.0

  •0•0•0•0•Updated Sep 16, 2025Sep 16, 2025

• grassroots-service-gene-trees

  Public
  C

  •

  Apache License 2.0

  •0•0•0•0•Updated Sep 16, 2025Sep 16, 2025

• grassroots-build-tools

  Public
  Scripts to manage the building of the different Grassroots infrastructure components

  Shell

  •

  Apache License 2.0

  •0•0•0•0•Updated Sep 16, 2025Sep 16, 2025

• grassroots-brapi-module

  Public
  A wrapper for the Grassroots DFW Field Trial Service to give a BrAPI interface

  C

  •

  Apache License 2.0

  •0•0•0•0•Updated Sep 7, 2025Sep 7, 2025

• 2025-11-05-earlham

  Public
  HTML

  •

  Other

  •0•0•0•0•Updated Sep 5, 2025Sep 5, 2025

• grassroots-geocoder

  Public
  The Grassroots library to use for making requests to get GPS coordinates for addresses and vice versa

  C

  •

  Apache License 2.0

  •0•0•0•0•Updated Sep 3, 2025Sep 3, 2025