BA 2024

Get help with EBS features.

You can now use the icon found on the top menu bar to open the links for the EBS User Guides and the EBS Support Desk. The former contains step-by-step instructions on how to use tools and their features, while the latter lets you request for additional support when needed.

Data browser display and layout is enhanced.

The following improvements are featured when using BA tools:

1. Expect a more compact and even layout of the main data browser and analysis results page, and

2. Automatically adjust the layout based on the device’s screen size for a better display, where the following are enabled for smaller screens:

   1. buttons and color legends in the Trait Table, and

   2. pop-up notifications, loading, and warning messages.

   3. vertical and horizontal scroll bars,

   4. fixed column headers,

   5. fixed page navigation features when viewing job outputs, and

   6. compact view of job output data and graphs.

The ARM data browsers are improved.

A series of improvements on the way you view and navigate the ARM tool and its browsers are in place. Specifically, you can now:

1. View creator and modifier columns in the main data browser,

2. Use enhanced page navigation when viewing analysis requests, such that at most 10 page links are provided.

Bug fixes

You can expect to encounter no errors when:

1. displaying the ARM data browser, such that only 10 page links are reflected on the page navigation menu,

2. requesting for MOA, such that the Experiments data browser shows a note when there are no results found,

3. submitting an analysis request, such that the status does not get stuck at PENDING , and

4. viewing the results of your SOA request, such that the weight of the SOA result is ≥ 0.

Be notified when accessing occurrences with no collected data.

An info panel is now immediately displayed when you open an occurrence with no collected plot trait data. The message includes instructions on how to troubleshoot the issue.

PDM data browsers are improved.

A series of improvements on the way you view and navigate the PDM tool and its browsers are in place. Specifically, you can now:

1. Scroll through the Stats Table with the column headers intact,

2. Pin or Unpin header/s in the Trait Table to freeze specific column/s, and

3. Display multiple scatterplot graphs within the workspace.

Bug fix

Reported bugs are now fixed. You can now expect that traits with no collected data will not be displayed in the Stats Table, so that errors in statistical calculations are prevented.

Generate non-sparse design with parameter sets that specify varying numbers of local checks.

The feature to generate randomizations for non-sparse Alpha-Lattice, Row-Column, Randomized Complete Block Design (RCBD), Augmented RCBD, and Incomplete Block designs using multiple parameter sets with a) all local checks included, b) some local checks included, or c) all local checks excluded is now enabled in the backend by SDM. This improvement can be accessed in Core Breeding’s Experiment Creation tool, specifically in the Design tab.

Design definitions are updated.

The updated design definitions for the Alpha Lattice and Partially Replicated (P-Rep) designs are implemented. The former is supported for non-sparse, while the latter is enabled for the sparse use case. This supports the new user interface implementation in Core Breeding’s Experiment Creation tool, specifically in the Design tab.

Bug fix

You can now expect to encounter no errors when uploading sparse Alpha-Lattice and non-sparse Augmented RCBD designs in Core Breeding’s Experiment Creation tool for breeding trial experiments.

Viewing, cleaning, and downloading genotype data is now supported.

When viewing () the results of your genotype request, the browser is divided into two sections: the top panel, housing summary information, and the main browser, where data is shown.

Using the top panel, you can now define the germplasm call rate threshold and the marker call rate threshold to Filter the displayed data. A Reset button is also featured to quickly set the thresholds back to its default value of 95%. On the main browser, the Marker Call Rates for each marker is also shown at the last row of the Genotype Data tab. To view any excluded germplasm and markers based on the set thresholds, the Excluded Germplasm and Excluded Markers tabs are enabled as well. When no germplasm or marker satisfy the indicated threshold filter, a message is displayed.

To allows users to use the genotype data as input for other analyses, the options to download () the filtered or all of the genotype data in either a CSV or TXT file format are also enabled. Beside this is the filename text field, where you can supply your preferred filename or use the auto-generated one.

Request for parental purity analysis.

To ensure that cross combinations produce the expected genotype, parental purity analysis is done. As such, genotyping requests with this specific purpose can now be used to request for parental purity analysis via the MDA tool.

Simply open your genotyping results by viewing () its data and click the Request Analysis button at the top right area of the browser. This redirects you to a new page. In the Parental Purity tab, only the Purity testing by internal consensus is supported as of now. Simply click Next to view the Results tab. In the table, a result of either TRUE or FALSE will be shown, where:

• TRUE indicates that all markers matched the expected genotype, and

• FALSE indicates that at least one marker did not match the expected genotype.

Click Next to view the Statistics tab. Allele 1 and Allele 2 indicates the count of the most common and second common allele, respectively. Beside these columns, the count of calls that are heterozygous and missing are displayed. Data on the percentages of the aforementioned are also provided, bearing the respective counts divided by the total number of samples.

Finally, the feature to download the results and create the filename is also hosted just above the data browser. A zipped file is exported containing separate CSV files for the results and statistics.

Bug fix

You can now expect to reset both the germplasm and marker call rates when clicking on the Reset button.