Compatible Software
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The Crop Ontology
From Alliance of Bioversity & CIAT
Created in 2008 by the CGIAR, the Crop Ontology is an essential source of traits and variables to support the standardization of the breeding databases
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ShinyBrAPPs
From CIRAD
The ShinyBrAPPs package contains shiny applications designed for plant breeders: TDxPLOR (the trial data explorer), STABrAPP (an application for single trial mixed model analysis, BrAVISE (a decision support application including GxE analysis) and more.
ToolPhenotypingGenotypingGermplasmBrAPI V2 -
Sugarcane Crossing Tool (SCT)
From Sugarcane Integrated Breeding System
The Sugarcane Crossing Tool (SCT) is a lightweight R-Shiny dashboard application designed to receive, process, and visualize data from a linked BreedBase11 instance.
ToolGermplasmBrAPI V2 -
G-Crunch
From Robbins Lab, Cornell University
G-Crunch is an upcoming user-facing tool to make simple, repeatable analysis requests.
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MGIS
From Alliance Bioversity - CIAT
The Musa Germplasm Information System (MGIS) contains key information on Musa germplasm diversity, including passport data, botanical classification, morpho-taxonomic descriptors, molecular studies, plant photographs and GIS information
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Florilège
From CIRAD
Florilège is a web portal designed primarily for the general public to access public plant genetic resources held by Biological Resource Centers across France. Through this portal, users can browse accessions from over 50 plant genera, spread across 19 genebanks.
DatabasePhenotypingGermplasmBrAPI V2 -
AGENT
AGENT aims to unlock the full potential of the biological material stored in gene banks around the globe by using FAIR international data standards and an open digital infrastructure for the management of plant genetic resources.
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Practical Haplotype Graph (PHG)
From Buckler Lab, Cornell University
The Practical Haplotype Graph (PHG) is a graph-based computational framework that represents large-scale genetic variation and is optimized for plant breeding and genetics.
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DArTView
From Diversity Arrays Technology
DArTView is a desktop application for marker data curation via metadata filtering. DArTView enables genotype variant data visualization designed such that users can easily identify trends or correlations within their data.
ToolGenotypingBrAPI V2 -
Trait Selector BrAPP
From Alliance Bioversity - CIAT
The BrAPI Trait Selector application provides a user interface to filter germplasm according to their trait. The user interface is composed by an SVG image representing a plant of interest and a javascript application that manages user actions.
ToolPhenotypingBrAPI V2 -
ImageBreed
From Robbins Lab, Cornell University
ImageBreed helps you manage field trials, process imaging events, and perform genotypically informed predictions.
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ClimMob
From Alliance Bioversity - CIAT
ClimMob is software for agricultural citizen science with the following features: 1) Organize large-scale experiments. 2) Invite participation of thousands of volunteering citizen scientists: farmers, consumers and others. 3) Test different technology options, such as crop varieties, food products, or agronomic practices. 4) Streamline the experimental cycle with electronic forms and barcodes. 5) Get quick insights from extensive automatic reports. 6) Use a suite of open-source tools to gain in-depth understanding trends and patterns.
ServicePhenotypingBrAPI V2 -
BrAPI Germplasm Search Tool
Enter a list of germplasm names and find matching germplasm records on a BrAPI-compliant database using different search routines that can find matches with variations in spelling, punctuation, etc in the database names and/or synonyms. The user can then select matches and download lists of the matches and/or missing records.
ToolGermplasmBrAPI V2 -
qrlabelr: Generate Machine- And Human-Readable Plot Labels for Experiments
From Crop Adaptation Lab
A no-frills open-source solution for designing plot labels affixed with QR codes. It features 'EasyQrlabelr', a 'shiny' app that simplifies the process of plot label design for non-R users.
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BrAPIMapper
From The Alliance Bioversity - CIAT (bioinformatics team)
A docker (compose) project that enables a complete BrAPI implementation on almost any type of data source once a data mapping is set on the included mapping interface.
Code LibraryToolDatabasePhenotypingGenotypingGermplasmBrAPI V2 -
DivBrowse
DivBrowse is a software for interactive visualization and analysis of the diversity of genomic variants. It uses VCF and GFF3 files as data input and consists of a web server written in Python and a GUI written in Javascript. It is available as a Python package on PyPI.org and also as Docker image.
ToolGenotypingBrAPI V2 -
MIRA
Phenotyping datasets are often available as MIAPPE compliant ISA Tab in repositories. However, the programmatic use of those datasets is limited. To enable access to such data products, MIRA is transforming them and provides BrAPI endpoints accordingly. This allows developers to use the data products in their applications.
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GIGWA
From CIRAD, IRD and Alliance Bioversity CIAT
Gigwa, a web-based tool which provides an easy and intuitive way to explore large amounts of genotyping data by filtering the latter based not only on variant features, including functional annotations, but also on genotype patterns. GIGWA can work as a BrAPI source and client.
DatabaseGenotypingBrAPI V2 -
DeltaBreed
From Breeding Insight, Cornell University
DeltaBreed is a user friendly interface designed to support USDA-ARS specialty crop and animal breeders to load, view, and retrieve breeding data.
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Helium
From The James Hutton Institute (JHI)
Helium provides a BrAPI enabled visualization platform for plant pedigree data.
ToolGermplasmBrAPI V2 -
GridScore
From The James Hutton Institute (JHI)
GridScore is a cross-platform open-source plant phenotyping app combining a visual view of the field layout with barcode system compatibility and a guided data collection approach allowing step-by-step collection of phenotypic data, supported by a set of powerful visualizations.
ServiceToolPhenotypingBrAPI V2 -
PHIS
From OpenSILEX
The open-source Phenotyping Hybrid Information System (PHIS), based on OpenSILEX, manages and collects data from Phenotyping and High Throughput Phenotyping experiments on a day to day basis. It can store, organize and manage highly heterogeneous (e.g. images, spectra, growth curves) and multi-spatial and temporal scale data (leaf to canopy level) originating from multiple sources (field, greenhouse). It unambiguously identifies all objects and traits in an experiment and establishes their relations via ontologies and semantics that apply to both field and controlled conditions. Its ontology-driven architecture is a powerful tool for integrating and managing data from multiple experiments and platforms, for creating relationships between objects and enriching datasets with knowledge and metadata. It is MIAPPE and BrAPI compliant, and naming conventions are recommended for users to declare their resources. Several experimental platforms use PHIS to manage their data, and PHIS instances dedicated to sharing resources (projects, genetic resources, variables) also exist to allow the sharing of studied concepts.
DatabasePhenotypingGermplasmBrAPI V2 -
Flapjack
From The James Hutton Institute (JHI)
Flapjack is a multi-platform application providing interactive visualizations of high-throughput genotype data, allowing for rapid navigation and comparisons between lines, markers and chromosomes.
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DArT Genotyping Services
From Diversity Arrays Technology
You can order DNA analysis and laboratory services from DArT through BrAPI
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Cornell Genotyping Services
You can order DNA analysis and laboratory services from Cornell BRC through BrAPI
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Germinate
From The James Hutton Institute (JHI)
Germinate provides a fully featured open-source plant genetic resources platform.
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BIMS
From Main Lab Bioinformatics at WSU
Breeding Information Management System (BIMS) is a free, open-source, secure and online breeding management system which allows breeders to store, manage, archive and analyze their private breeding program data.
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QBMS
From ICARDA
Breeders can use this R package to Query Breeding Management Systems such as BMS, BreedBase, EBS, Germinate, and GIGWA (using BrAPI calls), enabling them to retrieve phenotypic and genotypic data directly into their analysis pipelines developed in the R statistical environment.
Code LibraryPhenotypingGenotypingBrAPI V2 -
HortControl
From Phenospex
HortControl is the central software to setup, visualize and analyze your PlantEye measurements. Designed to be used by staff with any professional background with a user friendly interface. You can access HortControl from your office or in the field.
DatabasePhenotypingBrAPI V2 -
BrAPI Node Server
From Forest Biotech Lab
This is an implementation of BrAPI using NodeJS. It is being developed by the Portuguese Node within the context of ELIXIR-EXCELERATE.
Code LibraryPhenotypingGenotypingGermplasmBrAPI V1 -
JHI BrAPI Java
From The James Hutton Institute (JHI)
BrAPI Java is a Breeding API (BrAPI) implementation written in Java. It contains all data objects as well as a client interface that can be utilized using Retrofit and server interfaces that are designed to be used with the Restlet library.
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GRIN-Global
From USDA-ARS
The GRIN-Global project's mission is to provide a scalable version of the Germplasm Resource Information Network (GRIN) suitable for use by any interested genebank in the world.
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FAIDARE
From INRAe - URGI
FAIR Data-finder for Agronomic REsearch
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GLIS DOI Registration Service
From Food and Agriculture Organization of the United Nations
The DOI Registration Service of the GLobal Information System (GLIS) assigns Digital Object Identifiers (DOIs) to Plant Genetic Resources for Food and Agriculture (PGRFA) for reference in third party systems and scientific literature.
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Field Book
From PhenoApps
Field Book is a simple app for taking phenotypic notes. Field Book was created to replace paper field books and to enable increased collection speed with greater data integrity.
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Breeding Management System (BMS)
From The Integrated Breeding Platform (IBP)
The Breeding Management System (BMS) is a data management software specifically designed to meet the needs of modern plant breeders.
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Mr.Bean
From Alliance Bioversity - CIAT
Mr.Bean is an easy to use R-Shiny web-app that simplifies the analysis of large-scale plant breeding experimental analysis by using the power and versatility of Linear Mixed Models (LMM).
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BrAPI-Sync
From The Integrated Breeding Platform (IBP)
Built by the IBP Team, this tool allows for the automated transfer of data between BrAPI compliant systems.
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Flapjack-Bytes
From The James Hutton Institute (JHI)
Flapjack-Bytes is a graphical genotype visualization library. The visualization is modelled on the pre-existing Java desktop application Flapjack.
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BrAPI Fieldmap
From The Integrated Breeding Platform (IBP)
Built by the IBP Team, this is a fully BrAPI compliant tool for editing field spatial layout using GeoJson information.
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Graphical Filtering Tool
From BreedBase
Built by BreedBase, this is a fully BrAPI compliant tool for graphically building complex search and filter queries of Observational Data.
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Variable Ontology Widget
From INRAe - URGI
Built by URGI - INRA, this is a JavaScript widget displaying all the observation variables of a BrAPI endpoint.
ToolPhenotypingBrAPI V1 -
Study Comparison Tool
From BreedBase
Built by BreedBase, this is a fully BrAPI compliant tool for comparing the performance of germplasm across studies.
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Pedigree Viewer
From BreedBase
Built by BreedBase, this is a fully BrAPI compliant tool for viewing and exploring germplasm pedigrees.
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Beegmac
From South Green
Brapi-Enabled Embeddable Genomic-Marker Allele Client
ToolGenotypingBrAPI V1 -
Comparative Map Viewer
From BreedBase
Comparative Map Viewer, this is a fully BrAPI compliant tool for viewing and comparing genetic maps
ToolGenotypingBrAPI V1 -
BijMantra
From Denish Dholaria
Cross-Domain Agricultural Intelligence Platform (Under Development)
ToolServicePhenotypingGenotypingGermplasmBrAPI V2
