Repositories list

• PineBiomeDataPaper

  Public
  Scripts and data for PineBiome fungal metabarcoding and transcriptomics

  R

  •

  Creative Commons Attribution 4.0 International

  •11 fork•00 stars•00 issues•00 pull requests•Updated Jul 21, 2026Jul 21, 2026

• DNB_Survey_Paper_OTU_processing

  Public
  Processing of PineBiome OTU tables to extract needle cast pathogen abundance for DNB survey paper

  HTML

  •11 fork•00 stars•00 issues•00 pull requests•Updated Apr 28, 2026Apr 28, 2026

• thapbi-pict

  Public
  Tree Health and Plant Biosecurity Initiative - Phytophthora ITS1 Classifier Tool

  Python

  •

  MIT License

  •22 forks•00 stars•00 issues•00 pull requests•Updated Jul 19, 2025Jul 19, 2025

• q2-thapbi-pict

  Public
  Qiime2 plugin for THAPBI PICT (q2-thapbi-pict)

  Python

  •

  MIT License

  •11 fork•00 stars•00 issues•00 pull requests•Updated Jul 19, 2025Jul 19, 2025

• pyani

  Public
  Python module for average nucleotide identity analyses, originally started within Hutton ICS

  Python

  •

  MIT License

  •5757 forks•00 stars•00 issues•00 pull requests•Updated Jul 19, 2025Jul 19, 2025

• NetLogo-tk

  Public
  Toolkit for NetLogo (various scripts)

  Python

  •

  GNU General Public License v3.0

  •11 fork•00 stars•00 issues•00 pull requests•Updated Jul 19, 2025Jul 19, 2025

• netlogo-bitstring

  Public
  A bitstring class for netlogo

  Java

  •

  GNU General Public License v3.0

  •22 forks•00 stars•00 issues•00 pull requests•Updated Jul 19, 2025Jul 19, 2025

• gridscore-next-server

  Public
  GridScore server implementation for sharing GridScore configurations.

  Java

  •

  Apache License 2.0

  •11 fork•00 stars•00 issues•00 pull requests•Updated Jul 19, 2025Jul 19, 2025

• gridscore-next-client

  Public
  GridScore is a field phenotyping app for trials data.

  Vue

  •

  Apache License 2.0

  •22 forks•00 stars•00 issues•00 pull requests•Updated Jul 19, 2025Jul 19, 2025

• get-germinate

  Public
  CSS

  •

  Apache License 2.0

  •22 forks•00 stars•00 issues•00 pull requests•Updated Jul 19, 2025Jul 19, 2025

• germinate-vue

  Public
  Germinate is an open source plant database infrastructure and application programming platform on which complex data from genetic resource collections can be st…

  Vue

  •

  Apache License 2.0

  •77 forks•00 stars•00 issues•00 pull requests•Updated Jul 19, 2025Jul 19, 2025

• germinate-server

  Public
  The generic plant genetic resources database

  Java

  •

  Apache License 2.0

  •33 forks•00 stars•00 issues•00 pull requests•Updated Jul 19, 2025Jul 19, 2025

• germinate-importer

  Public
  Java

  •

  Apache License 2.0

  •22 forks•00 stars•00 issues•00 pull requests•Updated Jul 19, 2025Jul 19, 2025

• germinate-codegen

  Public
  Java

  •

  Apache License 2.0

  •11 fork•00 stars•00 issues•00 pull requests•Updated Jul 19, 2025Jul 19, 2025

• germinate-brapi

  Public
  BrAPI implementation for Germinate

  Java

  •

  Apache License 2.0

  •22 forks•00 stars•00 issues•00 pull requests•Updated Jul 19, 2025Jul 19, 2025

• gatekeeper-vue

  Public
  Vue

  •

  Apache License 2.0

  •22 forks•00 stars•00 issues•00 pull requests•Updated Jul 19, 2025Jul 19, 2025

• gatekeeper-server

  Public
  User management system for Germinate.

  Java

  •

  Apache License 2.0

  •22 forks•00 stars•00 issues•00 pull requests•Updated Jul 19, 2025Jul 19, 2025

• BrAPI

  Public
  Repository for version control of the BrAPI specifications

  Python

  •

  MIT License

  •3535 forks•00 stars•00 issues•00 pull requests•Updated Jul 19, 2025Jul 19, 2025

• biopython

  Public
  Various James Hutton Institute staff contribute to Biopython

  Python

  •

  Other

  •1.9k1.9k forks•00 stars•00 issues•00 pull requests•Updated Jul 19, 2025Jul 19, 2025

• galaxy_blast

  Public
  Galaxy wrappers for NCBI BLAST+ and related BLAST tools.

  Python

  •7070 forks•00 stars•00 issues•00 pull requests•Updated May 1, 2025May 1, 2025

• sgone

  Public
  Easily identify possible duplicates in your data.

  Vue

  •

  Apache License 2.0

  •11 fork•00 stars•00 issues•00 pull requests•Updated Apr 4, 2025Apr 4, 2025

• germinate-i18n

  Public
  Apache License 2.0

  •11 fork•00 stars•00 issues•00 pull requests•Updated Jan 30, 2025Jan 30, 2025

• germinate-data-templates

  Public
  Germinate data template Excel spreadsheets

  Apache License 2.0

  •11 fork•00 stars•00 issues•00 pull requests•Updated Jan 30, 2025Jan 30, 2025

• pick-a-mix-server

  Public
  Java

  •

  Apache License 2.0

  •11 fork•00 stars•00 issues•00 pull requests•Updated Nov 1, 2024Nov 1, 2024

• humbug

  Public
  Humbug is a multi-platform barcode generator which can be used alongside our Germinate Scan application to generate sheets of user-defined barcodes to aid in th…

  Vue

  •

  Apache License 2.0

  •11 fork•00 stars•00 issues•00 pull requests•Updated Nov 1, 2024Nov 1, 2024

• picobio

  Public
  Miscellaneous Bioinformatics scripts etc mostly in Python by Peter Cock

  Python

  •

  MIT License

  •1212 forks•00 stars•00 issues•00 pull requests•Updated Oct 18, 2024Oct 18, 2024

• brapi-java

  Public
  A Breeding Api (BrAPI) implementation written in Java. Contains all data objects, client and server interfaces for all modules.

  Java

  •

  Apache License 2.0

  •44 forks•00 stars•00 issues•00 pull requests•Updated Aug 31, 2024Aug 31, 2024

• agmicrobiomebase

  Public
  UK Crop Microbiome Cryobank

  R

  •33 forks•11 star•00 issues•11 pull request•Updated Aug 13, 2024Aug 13, 2024

• flapjack

  Public
  Flapjack

  Java

  •

  BSD 2-Clause "Simplified" License

  •99 forks•00 stars•00 issues•00 pull requests•Updated Jul 18, 2024Jul 18, 2024

• ncfp

  Public
  Program to pull NCBI nucleotide sequences coding for proteins in a protein multiple sequence file

  Python

  •

  MIT License

  •22 forks•00 stars•00 issues•00 pull requests•Updated Jun 28, 2024Jun 28, 2024