AGB: Software for Breeding Management

AGB is now available via github:

agb repositry: https://github.com/maizeatlas/agb
latest release: https://github.com/maizeatlas/agb/releases
reference documentation: https://github.com/maizeatlas/agb/tree/master/AccreteGB/Reference_Docs

Overview: Accrete Genetics & Breeding (AGB) is an open source laboratory information management system with an accompanying multi-user interface for plant genetics & breeding programs. AGB supports the complete workflow for managing genetics and breeding projects (from selecting stocks for a given planting to inventorying seed stocks from a harvest). AGB uses a modular design. A project manager module provides an active memory of the workflow for different projects and allows collaborators to share/transfer responsibility in executing breeding and trialing activities across seasons and locations. Projects and data are preserved as users advance through modules to choose germplasm, create experimental designs, organize and plant genetic/breeding stocks and produce row or plant tags, create data collection files and upload phenotype or weather data, track tissue samples, record mating types and pedigrees when harvesting, inventory seed stocks created, and more. AGB does not handle sequence or genotype data or perform data analysis. There are plans to add a module for users to export datasets in formats for downstream analysis with other tools.

AGB was designed based on a maize genetics and breeding program but should be compatible with other programs.

Programing design: This system is fully integrated in the Eclipse programming environment and is platform-independent. AGB is programmed in Java Swing using the Spring framework for control of software interface components and the Hibernate framework for mapping data from two relational databases, AGB-Manager and AGB-Data. AGB also connects to R providing extensibility for AGB through the he vast collection of packages available via R. Currently, the R API is only used for the experimental design module, calling functions from the agricolae package for randomizing trials.

Developers: Ningjing Tian, Naveen Kumar, Matthew Saponaro, Chinmay Pednekar, Teclemariam Weldekidan, Randy Wisser

Funding: This material is based upon work supported by the National Institute of Food and Agriculture, U.S. Department of Agriculture, including (i) Conservation, Management, Enhancement and Utilization of Plant Genetic Resources, Hatch 0227433 and (ii) Climate Variability and Change Challenge Area, AFRI 2011-67003-30342.

AGB includes two databases. AGB-Manager is like an active memory of your projects. It stores information about edits made to a project that collaborators can also access at different points in the breeding management process, allowing parts of the workflow to be transferred to members of a team. AGB-Data serves as the datastore for all breeding related information ranging from the inventory of seed stocks to experimental designs to planting events to phenotype/weather data to harvesting and pedigree records. The schema for AGB-Data was adapted from the GDPDM schema of the Panzea database

Graphical Schemas:

AGB-Manager

AGB-Data

Project Manager module. Allows users to create projects, add/remove collaborators, and load projects into the explorer for editing. A conservatively programmed but robust checkout/checkin system is used to work collaboratively on projects. After a project is created or checked out the user is assigned a token to freely edit the project while invited collaborators can view but not edit the same project. Once returned collaborators can then check out and advance the project.

ProjectManager

Stock Search/Selection module. Users can search existing stocks and create separate “carts” containing sets of stocks intended for an experiment or planting event. Search functions and filters are used to assist users in rapidly accumulating available seed stocks for breeding and trialing.

StockSearch

Planting module. After pushing carts of stocks from the stock selection module or stocks from the experimental design module to a planting, users can order planting rows, note planned activities for the nursery (delays, mating method, etc.), access an interactive field map, and generate row/plant tags.

Planting