EBS 8

Release date

EBS 8 release notes

EBS Milestone 8, which covers the development period from September to December 2023, highlights user-driven features and improvements. The Breeding Analytics domain enabled the download of single-occurrence analysis results for multi-occurrence analysis requests and developed the backend work to support sparse testing using the P-Rep design in Core Breeding. New custom file exports and additional harvests are now supported in Core Breeding’s Experiment Manager and Harvest Manager, respectively. Large file exports are also delegated to the background for efficiency. The Service Management domain improved Gigwa and its integration with other tools, while the Core System domain released development builds of the Place Manager, Workflow Management, and Organizational Units.
Domains

Breeding Analytics

Phenotypic Data Manager

User experience was improved to include a data browser that displays Breeding trial experiments with the status TRAIT DATA COLLECTED. Management of trait data was enhanced to include provisions for edit history, transaction update, changing quality control codes in bulk, and color-coding that is consistent across EBS tools that store trait data. Visualizations were improved for Heatmaps and Box Plot graphs, with the latter enabling suppression of possible outliers.

Analysis Request Manager

Managing and viewing the results of single-occurrence analysis requests was improved via the filter and edit features in the Table of Residuals, the restriction for FINALIZED and VOIDED jobs, as well as the consistency of color-coding for trait data across EBS tools. Unique job IDs are displayed, which aids the selection of traits whose result files can be used in multi-occurrence analysis requests. This is part of the initial implementation of Operational Analytics – Phase 2. Breeding Trials using the Unspecified design was also included in the experiments available for selection in the ARM data browser.

Statistical Design Models

To provide users more options in conducting breeding trial experiments, sparse testing was enabled in Milestone 8. The initial experiment design available is Partially replicated (P-Rep) design. This option is now available in the Core Breeding Experiment Creation tool.

Molecular Data Analysis

MDA implements key analytical pipelines for molecular analyses supported within EBS. The tool displays the results of genotyping requests as processed in the Service Management domain. Viewing results, as well as downloading current, cleaned, and all genotyping request data are supported.

Breeding Analytics Platform

The BAP launched its login page consistent with Core Breeding, where a welcome message, brief description, and its current version is featured. An improved left navigation menu is supported for a better user experience, while a more personalized use of BAP tools is now possible via the program filters.

Core Breeding

Experiment Creation

Implemented by both the Core Breeding and Breeding Analytics domains, sparse testing was launched in Milestone 8, with the Partially Replicated (P-Rep) as the first design to be supported. The Design tab was updated to host this feature’s capabilities, i.e., to customize the parameters for each occurrence based on the design. P-rep parameters include setting the test and check replications and the method to replicate checks, among others. EBS also prevents users to re-generate designs and add occurrences to experiments using sparse testing.

Experiment Manager

Customizable file exports are now supported in EM, specifically the Metadata and Plot Data and Occurrence Data Collection files. These are accessible from the EM toolbar in the main data browser. Users can choose to export data from single or multiple occurrences, as well as configure the data format and select data categories to include in the exported file. Occurrence Data Collection files can also be uploaded for single or multiple occurrences to update occurrence and management data. In Milestone 8, code generation, large plot file exports, data browser filters, and experiment statuses were also improved for a better user experience.

Cross Manager

Three new data collection files can now be downloaded for cross lists with the status CROSS LIST SPECIFIED and FINALIZED. These files are now similar to occurrences. EBS administrators can specify role-specific CSV file templates that users can export directly from CM for use in data collection. The file can then be uploaded back to EBS. The tool also enabled auto-generated cross list names and the addition of female and male entry codes in downloaded trait data collection files. Cross list deletion, germplasm names, and data browsers were all improved in Milestone 8.

Data Collection

A new UPLOADED status is available in the DC data browser to denote successfully uploaded trait data collection files. The tool also enhances the management of trait data in the Quality Control page using the sort, location name filter, and the bulk update feature for missing trait values, while color-coding of trait data is now consistent across all EBS tools. New auto-computed traits, such as Missing Hills and Moisture Factor, were enabled provided that the necessary trait data are present. The trait order is also preserved when downloading datasets and trait data collection files, while the download of large plot datasets is delegated to the background.

Harvest Manager

Additional features were made available for HM in Milestone 8. Selected bulk, individual spike, and single plant selection are new harvest methods supported for the wheat program, while additional harvest records can now be created onto previously harvested plots and crosses using a combination of bulk and numbered harvest methods. The tool guards against deleting packages that were already used as entries using warning notifications. Background processes are also enabled for large file exports.

Inventory Search (formerly Seed Search)

The Seed Search tool is renamed as Inventory Search. In Milestone 8, the initial version of the Advanced Search feature was enabled in the tool’s Search Results data browser. This allows users to further narrow down search results by specifying more parameters and conditions. In the Working List, package quantities are now displayed to provide more information.

List Manager

The column for Designation was renamed to Germplasm Name. This new column is featured in seed lists, inventory lists, and germplasm lists. The same is reflected in the downloaded files as well. The tool also supports creating up to 21 copies of each list item.

Service Management

Request Manager

Management of genotyping requests and the RM data browser have all been enhanced in Milestone 8. A new set of request statuses that provide more information on the progress of genotyping result files are featured in the RM data browser, while several columns were renamed to improve consistency across data browsers. Information on who and when a request was modified is also enabled. Seed and DNA were added as new tissue options for genotyping requests. Selected traits are now displayed in the Services tab, while trait, category, marker panel data are also included when viewing details of a request.

Genotyping Service Manager

Laboratory managers are now allowed to modify or complete the details of a submitted genotyping request, while the Service column is now labeled as Marker Group in the GSM data browser.

Batch Manager

Notifications were improved to better inform users after creating a batch with more than or less than 10,000 samples, while an enhanced file validation for uploaded genotyping request files is also supported. The BM data browser also features renamed columns to be consistent with Request Manager.

Core System

Printout

Data managers can now import and export report templates across different EBS instances using this tool. The Season Summary template and Standard Materials Transfer Agreement template were also created and placed under System Templates. With this, the former is now available for download by regular EBS users in Core Breeding.

User Management

In Milestone 8, EBS admins can now designate permissions specific to the Core Breeding (CB) domain when assigning roles to user profiles. Roles can also be updated to allow or restrict access to specific CB tools.

Place Manager

EBS admins can use PM to create and manage location data of experiments (places) and storage data for materials (facilities). In Milestone 8, features surrounding Facilities and Containers were enabled in the initial version.

Organizational Units

This tool allows EBS admins to create and manage organizations and their units, which come from the Contact Relationship Manager (CRM) tool. Basic data browser functionalities and management functionalities, such as adding, editing, and deleting units are supported in its initial version.

Login

In Milestone 8, EBS implemented a new identity authenticator using Amazon Web Services (AWS) Cognito. This can be observed as you log in to EBS and its domains.

 

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More information on the EBS Milestone 8 is available in the page.

For questions or concerns, please file a support ticket via the . We look forward to hearing from you.

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