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@HuttonICS Information & Computational Sciences (ICS), James Hutton Institute

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    73 repositories

    • thapbi-pict

      Public
      Tree Health and Plant Biosecurity Initiative - Phytophthora ITS1 Classifier Tool
      Python
      •
      MIT License
      •2•0•0•0•Updated Jul 19, 2025Jul 19, 2025

    • q2-thapbi-pict

      Public
      Qiime2 plugin for THAPBI PICT (q2-thapbi-pict)
      Python
      •
      MIT License
      •1•0•0•0•Updated Jul 19, 2025Jul 19, 2025

    • pyani

      Public
      Python module for average nucleotide identity analyses, originally started within Hutton ICS
      Python
      •
      MIT License
      •57•0•0•0•Updated Jul 19, 2025Jul 19, 2025

    • NetLogo-tk

      Public
      Toolkit for NetLogo (various scripts)
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Jul 19, 2025Jul 19, 2025

    • netlogo-bitstring

      Public
      A bitstring class for netlogo
      Java
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated Jul 19, 2025Jul 19, 2025

    • gridscore-next-server

      Public
      GridScore server implementation for sharing GridScore configurations.
      Java
      •
      Apache License 2.0
      •1•0•0•0•Updated Jul 19, 2025Jul 19, 2025

    • gridscore-next-client

      Public
      GridScore is a field phenotyping app for trials data.
      Vue
      •
      Apache License 2.0
      •1•0•0•0•Updated Jul 19, 2025Jul 19, 2025

    • get-germinate

      Public
      CSS
      •
      Apache License 2.0
      •2•0•0•0•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 stored, queried and visualized.
      Vue
      •
      Apache License 2.0
      •5•0•0•0•Updated Jul 19, 2025Jul 19, 2025

    • germinate-server

      Public
      The generic plant genetic resources database
      Java
      •
      Apache License 2.0
      •3•0•0•0•Updated Jul 19, 2025Jul 19, 2025

    • germinate-importer

      Public
      Java
      •
      Apache License 2.0
      •1•0•0•0•Updated Jul 19, 2025Jul 19, 2025

    • germinate-codegen

      Public
      Java
      •
      Apache License 2.0
      •1•0•0•0•Updated Jul 19, 2025Jul 19, 2025

    • germinate-brapi

      Public
      BrAPI implementation for Germinate
      Java
      •
      Apache License 2.0
      •2•0•0•0•Updated Jul 19, 2025Jul 19, 2025

    • gatekeeper-vue

      Public
      Vue
      •
      Apache License 2.0
      •2•0•0•0•Updated Jul 19, 2025Jul 19, 2025

    • gatekeeper-server

      Public
      User management system for Germinate.
      Java
      •
      Apache License 2.0
      •2•0•0•0•Updated Jul 19, 2025Jul 19, 2025

    • BrAPI

      Public
      Repository for version control of the BrAPI specifications
      Python
      •
      MIT License
      •32•0•0•0•Updated Jul 19, 2025Jul 19, 2025

    • biopython

      Public
      Various James Hutton Institute staff contribute to Biopython
      Python
      •
      Other
      •1.8k•0•0•0•Updated Jul 19, 2025Jul 19, 2025

    • galaxy_blast

      Public
      Galaxy wrappers for NCBI BLAST+ and related BLAST tools.
      Python
      •70•0•0•0•Updated May 1, 2025May 1, 2025

    • sgone

      Public
      Easily identify possible duplicates in your data.
      Vue
      •
      Apache License 2.0
      •1•0•0•0•Updated Apr 4, 2025Apr 4, 2025

    • germinate-i18n

      Public
      Apache License 2.0
      •1•0•0•0•Updated Jan 30, 2025Jan 30, 2025

    • germinate-data-templates

      Public
      Germinate data template Excel spreadsheets
      Apache License 2.0
      •1•0•0•0•Updated Jan 30, 2025Jan 30, 2025

    • pick-a-mix-server

      Public
      Java
      •
      Apache License 2.0
      •1•0•0•0•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 the recording of data in the field or glasshouse.
      Vue
      •
      Apache License 2.0
      •1•0•0•0•Updated Nov 1, 2024Nov 1, 2024

    • picobio

      Public
      Miscellaneous Bioinformatics scripts etc mostly in Python by Peter Cock
      Python
      •
      MIT License
      •13•0•0•0•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
      •3•0•0•0•Updated Aug 31, 2024Aug 31, 2024

    • agmicrobiomebase

      Public
      UK Crop Microbiome Cryobank
      R
      •3•1•0•1•Updated Aug 13, 2024Aug 13, 2024

    • flapjack

      Public
      Flapjack
      Java
      •
      BSD 2-Clause "Simplified" License
      •8•0•0•0•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
      •2•0•0•0•Updated Jun 28, 2024Jun 28, 2024

    • pico_galaxy

      Public
      Galaxy tools and wrappers for sequence analysis
      Python
      •25•0•0•0•Updated Jun 12, 2024Jun 12, 2024

    • ThreeDRNAseq

      Public
      A shiny App for differential expression and differential alternative splicing analysis
      GNU General Public License v3.0
      •28•0•0•0•Updated Apr 27, 2024Apr 27, 2024