Changelog

Changes in BMS v10

In this release we focused our efforts on consolidating the Nursery and Trial managers into a single multipurpose Study Manager. We’ve also implemented derived traits which enable BMS users to create arithmetic formulas and logical operation statements, in order to derive trait values and indexes from captured data. In addition to a simpler and more consistent interface, the new Study Manager provides new abilities to:

• Record opportunistic crosses in trials
  • Take samples from nurseries
  • Randomize nurseries
  • Use new study types
  • Ability to store the plate, and position within the plate, of a genotyping sample
• The location of a study instance has been made mandatory to facilitate reporting and geolocation of studies
• BrAPI: New call of calls implemented
• Calculated traits provides new abilities to:
  • Create a calculated trait via the ontology manager
  • Execute the desired calculations from within the studies taking other measurements as inputs.
  • Get visual indicators when a calculation is out-of-sync, out-of-bound, etc.
• Access to sidebar menu can be customized by role (trough backend – Data Manager assistance is required)

Please consult our Support Knowledge Base for troubleshooting articles on any known issue.

Important Note for Users deploying the BMS on a Desktop computer 
The BMS is optimized for higher spec computers; requiring more computing resources. This installer does not support data migration from earlier versions. Please backup your data and follow the instructions on this page before any installation. Users of version 3 (3.0.8 and 3.0.9) and older should contact us (under 'Users of earlier versions migrating to v8+') before attempting to run the installer

Changes in v9 DESKTOP & SERVER editions

This is the current version. The DESKTOP Edition is available for download here.
View this Fact Sheet for other product modalities.

BMS v9 presents the following improvements and new features:

• Coding and Fixing:
  • Automatic name generation for coded lines
  • Improved manual name customization for coded lines
  • Lines can be Ungrouped
  • Users can add new columns (including attributes and source) to their lists
  • Users can add new columns to their germplasm search results
• Admin: The  “Add programs” visibility is now customizable through  properties files
• Naming: Attributes of the female/male parent can be used in the naming; and attributes of the source of a germplasm can be used in the naming
• Sharing: Location can be edited and shared across programs; and lists can be shared across  programs

Please consult our Support Knowledge Base for troubleshooting articles on any known issue.

Important Note for Users of the Desktop Edition

BMS Desktop is optimized for higher spec computers; requiring more computing resources. This installer does not support data migration from earlier versions. Please backup your data and follow the instructions on this page before any installation. 

Users of version 3 (3.0.8 and 3.0.9 - DESKTOP) and older should contact us (under 'Users of earlier versions migrating to v8+') before attempting to run the installer

Changes in v8

This is the current version. DESKTOP Edition available for download here.

View the BMS Server PRO Technical Fact Sheet here (Multi-user server version).

BMS v8 presents the following improvements and new features:

• GDMS has been revamped to support Samples.

• Sample lists can be exported into CSV

• Users can query and download genotyping dataset directly from Germplasm Details and Studies

• Users can now share Locations across different Programs. Province is now being shown in the Location report.

• Users are able to import design with custom plot numbers

• V8 Desktop is now able to work in completely offline mode, from installation to execution, including Breeding View.

• Crossing performance has been improved to run efficiently through vast historical data.

• Users can now hide/show columns in the Germplasm Search results.

• Germplasm management UI improvements

Please consult our Support Knowledge Base for troubleshooting articles on any known issue.

Important Note for Users of Previous Versions

BMS Desktop v8 is optimized for newer/higher spec computers and requires more computing resources. This installer does not support data migration. Please follow the instructions on this page before any installation. 

If you have installed version 4, 5, 6 or 7 (SERVER) of the BMS, please contact us before attempting to run the installer. Users of version 3 (3.0.8 and 3.0.9 - DESKTOP): you can install v8 on the same computer, but must backup your data and make sure v3 is not running while installing the new version. We urge users of older versions to contact us for assistance.

Changes in v7 - SERVER Edition

BMS v7 presents the following improvements and new features:

• Creation and storage of samples

• The ability to display samples associated with a particular germplasm in the details pop-up mechanism that is provided for all germplasm records

• The user can display the number of samples associated with a plot in the measurements tab of studies

• From the measurements tab, the user can open a pop-up to show a list of the samples associated with a given plot

• A BrAPI call was implemented for retrieving sample details

Please consult our Support Knowledge Base for troubleshooting articles on any known issue.

"The BMS maintains the integrity of breeding germplasm by allowing breeders to track full breeding history and associate development to different cooperators and locations. When the time comes to obtain plant variety protection, all of the supporting data is at the breeder’s fingertips." — Shawn Yarnes, Regional Deployment Manager, North-America

Changes in v6 - SERVER Edition

BMS v6 presents the following improvements and new features:

• Head to Head queries has been improved and enabled

• List and Studies are now clickable from within the Germplasm Details so you can navigate the  system more easily.

• “Starting plot number” increased to 9 digits

• Genotyping Data Management Module for SNP markers enabled

• Ontology differentiation between Analysis and  Analysis Summary (Summary statistics) variable

Please consult our Support Knowledge Base for troubleshooting articles on any known issue.

"This release underlined the importance of being patient and organized in order to be effective in software development. We managed to revamp and bring back major functionalities into the BMS, with moderate        investment. Success is where preparation and opportunity meet" — Mariano Crimi, Product Manager

Changes in v5 - SERVER Edition

BMS v5 presents exciting improvements and new features, among which are:

• Add/Remove germplasm  descriptors
• Germplasm delete
• Manual crosses workflow improvements
• Select all germplasm matches
• Unique plot identification and barcode generation
• Seed Inventory improvements (transaction history details, close lot feature)
• Open Source compliance: libraries audit and MySQL package detachment
• BV design license expiration; communication with user
• DB password securitization
• Trial Measurements tab, server side pagination and inline editing
• Linux deployment steps
• Standalone profiling
• Bug fixes to tutorial Load and Save

Please consult our Support Knowledge Base for troubleshooting articles on any known issue.

Everybody in the team is excited about this release. Among other reasons, it includes features that had been repeatedly requested by breeders, and provides more flexibility thanks to new functionality for system administrators. I’m looking forward to see BMS users’ reactions! " — Julian Pietragalla, Regional Deployment Manager  for Latin America

Changes in v4 - SERVER Edition

BMS v4 presents exciting improvements and new features, among which are:

• Performance and memory usage improvements
• Seed inventory reservation and label printing
• User administration module
• Centralization of germplasm import
• Augmented design generation and integration with Breeding View (BV)
• Coding and grouping tools
• Login and homepage institutional logo customization

Please consult our Support Knowledge Base for troubleshooting articles on any known issue.

"This is an important turning point for the IBP team. Our development process has been streamlined, our deployment team consolidated and reinforced locally, and our strategy resolutely refocused towards serving institutes of Africa and Asia. With the BMS v4, we now have a solid network solution to offer our partners, which will help them concretely in strengthening their data management practices, in line with institutional policies for data conservation, security, sharing, quality and legacy. In my view, this timely delivery is proof that our team and our core product have reached a new level of maturity and readiness to address the needs of our stakeholders. —  Jean-Marcel Ribaut, IBP Director

Changes in Version 3.0.9

This update addresses a number of minor bugs as well as functional and UI improvements, including:

• Removed the license cutoff date BMS
• Removed license cutoff for BV
• Disclaimer text added to the BMS User Agreement
• Resolved duplicate randomization of trial instances
• Resolved issue of empty methods table when creating custom crop
• Resolved issue where same GID applied to different germplasm
• Resolved issue deleting entries from a list in groundnut in v3.0.8
• Repaired issues with 'Other' crop in v3.0.8
• Ask Support widget patch for BMS 3.0.8

Known Issues with ver 3.0.9

• Importing nursery observations sometimes results in an erroneous confirmation message. Select Skip to import observations.
  
• Ontology updates have been made that render the preformatted 3.0 tutorial files incompatible with the 3.0.9 patch. Updates to the tutorial files will be made early in the new year.

Changes in Version 3.0.8

This update addresses a number of minor bugs as well as functional and UI improvements, including:

• Resolves issues found in the 3.0.7 update that causes errors in the Single ite Analysis pipeline
• Extends the free public license for the BMS and Breeding View to December 31, 2015
• Resolves an issue with updating the BMS when installed in a user-selected directory
• Resolves minor issues with how variables were saved to datasets for nurseries and trials
• Resolves a bug that caused Single Site Analysis in Breeding View to fail for certain trial design types
• Improves the creation and mapping of new variables in the data import process
• Improves how favorite breeding methods and locations are handled throughout the BMS and in backups
• Improves list selection trees to include additional list details
• Adds the ability to show the maximum number of generations in a pedigree tree
• Adds the ability to store latitude, longitude, and altitude for breeding locations
• Adds the ability to clear parent lists and individual crosses in the Crossing Manager
• Improves the screens for selecting datasets for Multi-Site Analysis

Known Issues in Version 3.0.8

This version has two minor known issues:

1. When creating a new program with the "other" crop option, the list of Breeding Methods for the program is not automatically populated. Users can work around this issue by manually adding the breeding methods needed for the program, or they can contact the IBP support team for assistance.
2. Germplasm pedigree trees are not displaying if more than 15 generations are present.

Important Note for Users of Previous Versions

If you are already running an earlier version of the BMS, you will need to update to v 3.0.8 to update your free license. Please download the installer and follow the directions on this page for updating an existing installation. Your existing program data will be preserved with the upgrade, but we recommend that you backup your data prior to running the update.

Important Note for Users of Previous Versions

If you are already running an earlier version of the BMS, you will need to update to v 3.0.8 to update your free license. Please download the installer and follow the directions on this page for updating an existing installation. Your existing program data will be preserved with the upgrade, but we recommend that you backup your data prior to running the update.

Installation

With version 3.0 of the BMS, we have streamlined the installation process by offering a single installer option. Users will now be able to download one installer file instead of separate installers for infrastructure, application, and crop data. After downloading, the user can select options to install, and then the installer downloads all needed components and executes the installation. 

The single installer can be used for both new installations of the BMS and for updating existing installations.

New Browser-Based Fieldbook Tools

In version 3.0 of the BMS, the Nursery Manager and Trial Manager components of the BMS have been redesigned as browser-based applications that are fully integrated with the other core BMS tools in the workbench. The redesigned tools offer the following key benefits:

• users can move seamlessly between fieldbook tools and others in the workbench environment without launching a standalone application.
• the user interface is consistent with other BMS tools.
• nursery and trial template management has been significantly improved:
  • any existing nursery or trial in the database can be used as the template for a new nursery or trial; users no longer need to customize and manage Excel-based template files that reside outside the BMS
  • basic nursery templates will be included in the database to help new users get started
• the trial manager now supports an expanded range of experimental design types:
  • randomized complete block designs
  • resolvable incomplete block (also referred to as alpha lattice) designs
  • incomplete block designs
  • resolvable row-and-column designs (arranged in replicates)
  • row-and-column designs (not arranged in replicates)
• enhanced options for exporting measurement sheets including 
  • choice of either plot or serpentine order
  • formats compatible with a range of handheld data collection apps

Seed Inventory Management

In version 3.0 of the BMS we have introduced several features allowing breeders to manage seed inventory:

• ability to add inventory for seed when a when a nursery is advanced
• ability to view available seed inventory when working with lists and making crosses, including:
  • display of inventory levels in the list view and the individual germplasm view
  • display of inventory locations in the list view and the individual germplasm view
• ability to reserve seed inventory when working with lists and making crosses

The BMS is compatible with legacy ICIS tools for seed storage management. Interested users should contact the IBP team for additional information and assistance.

List Manager

In version 3.0 of the BMS we have made some improvements to the List Manager, including: 

• refinements to the user interface of the List Manager to improve usability and maximize the space available to work with new and existing lists.
• ability to overwrite an existing list with changes or updates, e.g. if a user has modified an existing list she can now save it with the same name as the original list.
• seed inventory features have been integrated into the List Manager to allow the user to see stock levels and reserve seed for a list (see above).

Crossing Manager

In version 3.0 of the BMS we have made a number of minor functional improvements to the Crossing Manager, including: 

• ability to select a complete existing list to use as either a male or female parent list
• ability to delete individual entries from the male and female parent lists, and save modified parent lists with the same name as the original list.
• the display of male and female parent lists now shows the total number of entries and the number of currently selected entries.
• seed inventory features have been integrated into the Crossing Manager to allow the user to see stock levels and reserve seed for parent lists while planning crosses.

Germplasm Import

In version 3.0 of the BMS we have made improvements to the Germplasm Import tool, including:

• streamlining the import process to two steps instead of three and updating the the screen design to match other BMS tools
• the ability to import attributes, addtitional names and stock/inventory levels
• the ability for users to select pedigree options when importing a list with an advanced import template (with GIDs included): 
  • add all entries with new records connecting to existing sources
  • select existing germplasm wherever found
•  the user is now offered new options If the system finds matches during the import:
  • the option to ignore the match and add a new record for the germplasm instead
  • the option to remember the selected match and apply it for additional instances of the same GID in the import list.
  • The user can also choose to have the system accept single matches automatically if they are found during the import.

Analytical Pipelines

The Breeding View analytical pipelines have been enhanced with the following in version 3.0:

• the Single Site Analysis now includes new functionality to assist users with identifying outliers and allowing these to be excluded from the analysis
• summary statistics from the Single Site Analysis are now saved together with means data in the BMS database
• output reports for the Single Site and Multi-site analysis pipelines now include summary statistics.
• the BMS now includes R-AP and REML scripts that can be used for Single Site and Multi-site Analysis. 

GDMS

In version 3.0, we have added the following new features to the GDMS tools:

• ability to handle duplicate germplasms while uploading and retrieving the genotyping data
• genotyping data upload can be done through a importing a germplasm list 
• ability to upload MTA
• ability to create  haplotypes and search for lines with particular haplotypes 
• ability to query for a region of interest e.g. all markers in the QTL region or a chromosome
• ability to query for a particular allele 
• improved validation and error reporting

MBDT

The MBDT application is now integrated with the BMS IBDBv2 database, so that users no longer need to work with flat files when using this tool.

Program Administration & General Updates

In version 3.0, we have made the following improvements in these areas:

• the height of the header bar has been reduced in order to maximize working space for the BMS tools
• users can now open nurseries and trials directly from the Home screen
• program folders inside the BMS installation folder are now named with the program name instead of a number, making it easier to find analysis reports and other output files
• the Add Program process has been expanded to allow users to optionally set up favorite methods and locations when creating a new program
• the Program Details, Members, Locations and Methods management screens have been consolidated into a single tabbed screen under the Manage Program Settings link
• backup files automatically stored in the Backup folder are no longer removed during the un-installation process

Data Import Tool

Version 3.0 of the BMS includes several improvements to the data import tool:

• nurseries and trials imported through the Data Loader tool can now be opened in the new Nursery and Trial Manager tools
• the Data Loader now automatically reads details about the nursery or trial from the cover sheet during import
• users can now import means datasets using the Data Import tool.

Important Note for Users of Previous Versions

If you are already running an earlier version of the BMS, you will need to update to v 3.0.8 to update your free license. Please download the installer and follow the directions on this page for updating an existing installation. Your existing program data will be preserved with the upgrade, but we recommend that you backup your data prior to running the update.

List Manager

The primary change in the List Manager is a new screen design that uses a side-by-side layout for working with existing lists and creating new lists.

Other changes include:

• The order of columns in the List Details view has been changed based on user input.
• Viewing and editing of list headers has been moved to a pop-up view to maximize the space available for working with list details.
• The design of the pop-up Germplasm Details display has been revised to allow users to view multiple sections concurrently.

Crossing Manager

The Crossing Manager in version 2.1 features a completely redesigned the interface that makes it easier to choose germplasm entries to use in parent lists. Users can now open one or more existing lists in the Make Crosses screen, then drag entries from these lists into the parent lists, whereas in previous versions, parent lists had to be created prior to entering the Crossing Manager.

In addition, we have made several functional changes:

• Users can now specify a group of crossing settings and save them for future use; this eliminates the need to rely on external Excel templates for defining crossing settings.
• Users can now specify their own separator character for parentage strings for crosses.
• Users can now specify a starting sequence number for new crosses.

Multisite (GxE) Analysis Output

Version 2.1 of the BMS includes the following improvements to the Multisite Analysis (GxE) report output generated by Breeding :

• Marginal means are now provided on each trait sheet, to the right of the locations
• The means of all the columns are provided at the bottom of the table.
• The rank order of the these means are provided down the right side of the table

This version also resolves intermittent problems launching Flapjack files after analysis.

GDMS

Version 2.1 of the BMS includes an updated version of GDMS with the following new functionality:

• MTA upload, retrieval and deletion
• Ability to create haplotypes
• Ability to search for lines with particular haplotypes
• Ability to query for a particular allele e.g.: all lines which contain the desired allele?
• Ability to query for a region of interest e.g.: all markers in the QTL region or a chromosome arm
• Ability to search a region between two flanking markers
• Assorted minor bug fixes

Data Loading Tool

Version 2.1 of the BMS includes a number of improvements to the “wizard” data loader to:

• Better guide the user through the data loading process
• Provide better information when errors are encountered to help the user correct the issue and proceed.

Usability Improvements

In version 2.1 of the BMS, we have made a number of improvements to make it easier to use the administrative screens, and have added some features to improve usability throughout the application.

Login Screen

The Login screen has been improved with the following changes:

• Layout of the screen has been adjusted to address user input from recent training sessions.
• The Login screen now includes a pop-up tip to explain to users that the login for the BMS is not the same as for the IBP portal, which is a common question that we receive from new users.

Managing Program Members

The screen to manage program members has improved with the following changes:

• The screen now supports drag-and-drop to move members into or out of a program.
• When managing members in the New Program flow, the user who is creating the new program now appears in the Selected Program Members screen by default. À

Managing Locations

The design of this screen has been changed to address usability issues in the previous version:

• Screen now supports drag-and-drop from the Available Locations to the Favorite Locations table.
• Controls to select entries have been changed to checkboxes and moved to the left column for consistency with other tools and so that they are available without horizontal scrolling.
• Users can now select multiple entries for more efficient manipulation of the Favorites list.
• Added the ability to specify a Province/County when adding new locations.

Managing Breeding Methods

We have made changes to the Method Manager tool that parallel items 1-3 described for the Location Manager above. We have also revised labels in this tool based on input from breeders.

New UI Controls

We have added a few new UI controls to make it easier for users to manage screen space in tools with complex interfaces, such as the List Manager.

Show/Hide Toggle for Main Menu

This is located in the breadcrumb bar, and shows or hides the main left menu with a single click.

Toggle controls in List Manager

In the List Manager, we have added toggle controls that users can click to show or hide the List selection tree and the Build New List panel. This allows users to quickly reallocate space for the task they are performing in the List Manager, for example:

• After selecting and opening the lists you want to work with, you can minimize the tree panel to give more space to the List Details and Build New List panel.
• You can also easily open or close the Build New List panel depending on whether you are actively building a new list or not.
• In addition to the show/hide controls, you can also click on the edges of the List Details and Build New List panels to adjust the size.

Additional Changes

We have also made the following additional changes in BMS version 2.1:

• In the Help screen, users now have the option to view an HTML version of the User Manual in a browser tab in addition to the PDF version. (Note: you must run the Documentation installer in order to make the HTML help files available in the system.)
• The Study Tree control used in the in the Home screen and the Study Browser now offers the same controls to add folders, and to rename folders and nurseries and trials that are available on the List Tree in the List Manager.