Introduction

BMS 7.0-8.0 Manual

 

  • Breeding Management System Server v7.0

    Breeding Management System Server v7.0

    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 v7.0 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
    • 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

    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:

    V7 Release Notes

    New Features & Improvements

    • Improved constancy in Germplasm Manager tabular views
    • Germplasm details: related nurseries and trials are now clickable
    • Improved constancy between the menu options in Trial and Nursery Manager
    • Export trial and nursery book with variables defined by type: date (D), numeric (N), categorical (C), text (T)
    • Reduce the number of summary statistics saved to the BMS from Breeding View Analysis: MEAN, MeanSED, PVALUE, HERITABILITY, and CV
    • Improved filters on head to head query: Able to filter by All, Traits and Analysis (only variables from the ontology, not the summary statistics)
    • Improved the export formatting to support compatibility with Kansas State University Fieldbook application
    • Grouping Options: able to track and code fixed and hybrid lines
    • Genotype data management (BETA): Ongoing development to fix, simplify, and improve previous functionality
      • Create genotype sample entities associated with study plots
      • Limit marker-type to SNPs only
      • Remove options to launch Flapjack. Keep Flapjack formatted output file option.
      • Marker by germplasm matrix export: replace .txt option with .csv
      • Simplify the user interface: remove broken links, title options more intuively

    Bug Fixing & Performance

    • Super administrator can no longer deactivate self
    • Ontology reengineering
    • Removed export options to unsupported external data collection apps, DataKapture and Fieldlog.