BMS 9.0 Manual


  • Breeding Management System Server v9.0

    Breeding Management System Server v9.0

    Breeding Management System (BMS) is an information management system developed by the Integrated Breeding Platform to help breeders manage the breeding process, from programme planning to decision-making. The BMS is customizable for most crop breeding programs, and comes pre-loaded with curated ontology terms for: bean, cassava, chickpeacowpea, groundnut, maize, rice, sorghum, soybean, and wheat. The BMS Server v9.0 is available as a cloud application, which can be installed on local or remote servers and accessed by multiple users.

    BMS Tools

    The Breeding Management System (BMS) contains database-integrated tools that seamlessly connect to the crop database when launched from an established Workbench program.  Database integration minimizes the need to manually create, save, and import files. Some functionality, like adding ontology terms, may be restricted by user roles and permissions.

    Manage Germplasm

    • Browse and search for germplasm and germplasm lists
    • Customize lists with germplasm attributes
    • Build lists for upcoming activities, like nurseries and trials
    • Import new germplasm into the database
    • Manage seed inventory: Review, add, commit, and withdraw

    Manage Nurseries

    • Specify nursery germplasm and checks
    • Create field maps and planting labels
    • Design and record crosses
    • Create a nursery field book for data collection
    • Track genealogies as nursery germplasm is advanced by: generative, derivative, and maintenance breeding methods
    • Create harvest labels
    • Add to seed inventory at harvest

    Manage Trials

    • Specify trial germplasm
    • Specify treatments, locations, and experimental design
    • Randomize layout of supported trial designs with the BMS design engine
    • Create field maps and planting labels
    • Create a trial field book for data collection
    • Track genealogies if trial germplasm is advanced by: generative, derivative, and maintenance breeding methods
    • Create harvest labels
    • Add to seed inventory at harvest 

    Manage Trait Ontology

    • Add new ontology terms
    • Edit existing ontology
    • Define a preferred name for terms within a program -for example, to reflect local language preference.

    Manage Locations

    • Add new locations
    • Define location type, such as breeding or seed storage location
    • Define program favorites

    Manage Genotyping Data & DNA Samples

    • Select and sample plants for genotyping
    • Store and retrieve SNP markers, molecular maps, and low-density genotyping datasets (<400K matrices)

    Search, Filter and Query Studies

    • Search studies by partial name and other details, like year and season
    • Graphical filtering of studies to assist selection decisions
    • Head to head query to compare the performance of test germplasm to standard entries across studies

    Statistical Analysis

    • Use the BMS experimental design engine to randomize trial germplasm.
    • Import trial desgins generated by external design engines
    • Export trial data for statistical analysis. Generate preformatted files for the Breeding View (BV), the BMS statistical package or use generic export features to analyze with the package of your choice.

    System Administration

    The BMS has roles and permissions that support the needs of small a large breeding institutions. Administrators add and manage users and permissions. System permissions are can be customized to suit institutions with different user specializations.

    This manual is designed to be a user guide. Developers and system administrators can find technical details about the system at the following links:

    V9 Release Notes

    Features & Improvements

    • Sort germplasm lists and inventory views by any column.
    • Germplasm attributes are available from the list view and can be exported.
    • Germplasm directories for each crop database have "Crop" folder to share lists between programs.
    • Expanded documentation of experimental designs
    • DNA sampling (beta): sample information available from germplasm details, improvements ongoing
    • Genotype data repository (beta): low-density genotype datasets (<4000K matrices), improvements ongoing
    • Terminology refinement: "fixation" is more generally defined as "grouped" to make use of grouping for pedigree distinctions
    • Expanded coding functionality, including automatic naming based on code level
    • Graphic filtering of study data to assist selections
    • Ability to edit location details and restrict locations to individual programs within a crop database