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The EBS domain’s landing page displays the version of the software available to users. This is also visible in the left navigation menu. Each version may highlight new key features, improvements, bug fixes, or all three. You may refer to the log below for more information in each version.

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The EBS domain’s landing page displays the version of the software available to users. This is also visible in the left navigation menu. Each version may highlight new key features, improvements, bug fixes, or all three. You may refer to the log below for more information in each version.

...

(blue star) Version 23.12.13

Expand
titleAnalysis Request Manager (ARM)

Pending jobs for new requests.

In the Jobs column, newly created analysis requests are now noted with

Status
titlepending
to indicate that it does not have jobs yet. Previously, the default label in the Jobs column was either “Single” or Multiple” to give an idea about the number of jobs created for a request.

Image Added

Color-coding of trait data is now consistent with Core Breeding tools and PDM.

When viewing ((blue star)) the job outputs for a request, the color coding of data is now standardized with PDM and Core Breeding’s Experiment Manager and Data Collection tools. Possible outliers are highlighted in light orange, while suppressed ones are in gray.

Image Added
Expand
titlePhenotypic Data Manager (PDM)

Color-coding of trait data is now consistent with Core Breeding tools and ARM.

In the Trait table, the color coding of trait data is now standardized with ARM and Core Breeding’s Experiment Manager and Data Collection tools. Cells with possible outliers are highlighted in light orange, while suppressed and bad ones are in gray and red, respectively. Questionable and good data are both displayed without color, while missing ones are highlighted in blue and denoted with “NA”.

Image Added

Bug fix

  1. You can now properly see the BA homepage before logging in and when signed out, and

  2. When clicked, tool names are highlighted in gray in the left navigation menu.

Expand
titleBreeding Analytics Platform (BAP)

The left navigation menu is improved.

For your convenience, you can now choose to have the left navigation menu always open. To do this, simply expand the left navigation menu ((blue star)) and find the > button near the bottom. Otherwise, click < to hide the menu.

Image Added

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(blue star) Version 23.11.29

Expand
titleAnalysis Request Manager (ARM)

Selection of experiment occurrences for single-occurrence analysis (SOA) requests is improved.

This version improves on the experiments and occurrences listed in the Experiments tab. Specifically, you can now:

  1. Select occurrences using the unspecified design. You can now use occurrences from Breeding Trial experiments using the Unspecified design to create a SOA request. From the ARM data browser, request for a SOA. Select the occurrence from the Experiments tab and choose the traits you want to request analyses for. Once done, click Submit to send your request. Wait for the results by monitoring the job statuses in the ARM data browser.

Image Added
Info

View the full demo here.

  1. Add more occurrences to your SOA request. This feature lets you select occurrence/s in the same experiment and add them to your current SOA request. To do this, check the quality of your trait data in PDM. After you quality-check (QC) at least one (1) trait in PDM, you can now proceed to Analyze your occurrence in ARM. You will be redirected to ARM’s Experiments tab, where all your experiment’s occurrences are listed. Here, the current occurrence is already selected, but you can select more for inclusion in your current SOA request.

    Image Added
Info

View the full demo here.

Selection of jobs for multi-occurrence analysis requests (MOA) is enhanced.

In preparation to support MOA requests soon, a better display of all

Status
colourBlue
titlefinalized
jobs in the Experiments tab is now featured. From the ARM data browser, request for a MOA. The job IDs for each analyzed trait is now housed in a drop-down menu. Select the jobs analyzing the same trait from at least two (2) different occurrences. You can unselect a job for a trait by choosing the “---” option. Additionally, a tool tip is shown when you hover your cursor over each job. This shows the date and time the job was finalized.

Image Added
Info

View the full demo here.

Bug fixes

You can expect to encounter no errors when:

  1. filtering the SOA and MOA Experiments tab data browsers and expanding each experiment to show occurrence/s, and

  2. voiding the last job in a request, which will automatically redirect you to the ARM data browser.

Expand
titlePhenotypic Data Manager (PDM)

Management of occurrences is improved.

This version resolves the PDM data browser’s limitations cited in the 23.09 version. Specifically, you can now:

  1. Browse more occurrences. You can now browse all Breeding Trial (BT) experiment’s occurrences in the PDM data browser. You can also navigate the list easily using the pagination and filter feature. Previously, only a hundred records were available in the browser.

Image Added

  1. Immediately reflect QCed traits. In the Traits Table, you can now expect that quality-checked (QCed) trait columns are readily highlighted in green. Click the save ((blue star)) icon from the toolbar and mark the trait/s as QCed. Finally, Save the transaction.

    Image Added

  1. Select occurrences using the unspecified design. BT experiments using the Unspecified design are now included in the occurrences available for selection in the PDM data browser. From the PDM data browser, Explore the trait data quality of occurrences using the Unspecified design.

Image Added

Bug fixes

Reported issues have been fixed. The following are now working as expected:

  1. A heatmap graph is plotted using the planting arrangement X and Y (PA X, PA Y) values.

  2. Reflect new trait data in the Trait Table and Trait List boxes after you update your trait data to the latest available version from Core Breeding.

Expand
titleMolecular Data Analysis (MDA)

View the results of genotyping requests.

The Molecular Data Analysis (MDA) tool implements key analytical pipelines for molecular analyses supported within EBS. In this version, the MDA data browser lists all genotyping requests whose results are ready to be viewed ((blue star)) and downloaded ((blue star)). The data browser gets all genotyping requests with the status

Status
colourGreen
titleresults ready
from the Service Management domain’s Request Manager tool.

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Expand
titleStatistical Design Models (SDM)

Sparse testing is now supported.

Sparse testing allows test entries to be randomly distributed to different occurrences. As of this version, you can now use sparse testing for the Partially Replicated (P-Rep) trial design in Core Breeding’s Experiment Creation tool for Breeding Trial experiments.

Expand
titleBreeding Analytics Platform (BAP)

A new login page is enabled.

You can now log in to the Breeding Analytics (BA) domain using the new login page. Simply access the BA domain via the Domain Shortcuts ((blue star)) icon or using a link. A welcome message, a brief description of the domain, and its current version is featured in the login page.

Image Added

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(blue star) Version 23.10.25

Expand
titleAnalysis Request Manager (ARM)

Multi-occurrence analysis (MOA) requests are now supported.

The Request Analysis drop-down menu includes the option to request MOA. The following are featured:

  1. Experiments tab. This lists all closed single-occurrence analysis (SOA) requests that you can select. The data browser also shows the job IDs for each analyzed trait. To proceed with the MOA request, you need to choose the same trait from at least two (2) different occurrences for analysis. Doing so enables the Next button.

  2. Options tab. This allows you to extract the BLUEs and Analysis Metrics in a CSV format. In this version, downloading BLUPs is disabled. Click Submit to begin downloading the zip file containing the metrics and predictions files on your device.

23.10 ARM2.mp4

Management of single-occurrence analysis (SOA) requests is improved.

This version improves user experience in terms of managing jobs in SOA requests. The following enhancements are discussed below.

  1. View job IDs. From the ARM data browser, open a SOA request by clicking the view ((blue star)) icon. On the List of Jobs table, job IDs are now assigned for each analysis job for easier identification. The job ID is a system-generated code consisting of the prefix 'J', followed by a sequence number.

  1. Restricted access to

    Status
    colourYellow
    titlevoided
    and
    Status
    colourBlue
    titlefinalized
    jobs. When you choose to Void a job in a SOA request, the system will now disable access to it. Also, the system disables all buttons for Finalized jobs, except for the filter button ((blue star)). These prevent further changes to data.

23.10 ARM1.mp4

Bug fixes

Reported issues have been fixed. The following are now working as expected:

  1. In the Experiment tab, the Select All button is automatically unchecked when you unselect at least one (1) occurrence,

  2. Requests with >15 jobs are now processed successfully, and

  3. The

    Status
    titlecanceled
    request status is correctly displayed when all the jobs have a status of either
    Status
    colourYellow
    titlevoid
    or
    Status
    colourRed
    titleerror
    .

Expand
titlePhenotypic Data Manager (PDM)

Updated trait data can now be loaded.

A new Check for Updates button is featured in the Trait Table. This allows you to work on the latest version of your trait data, which the system gets from the Core Breeding domain. After clicking the button, you will be informed if the trait data you are working on is still Up To Date. Otherwise, the button will prompt you to Update Transaction. The consistency of trait data in the Stats and Trait Tables will be further improved in the coming versions.

23.10 PDM3.mp4

Management of trait data was improved.

  1. Suppress values in the Box Plot tab. You can now define the values to suppress as trait data is visualized in a box plot graph. Select a trait and then Generate the box plot graph. The new Suppress Outliers section will be displayed, where you can define the a) upper bound and b) lower bound trait outlier values to suppress. The former suppresses all possible outliers for that trait that is greater than or equal to the identified value, while the latter suppresses all possible outliers for that trait that is less than or equal to the provided value. Click Suppress to apply the changes to the box plot graph and to the Trait Table.

23.10 PDM1.mp4

  1. Reflect quality-checked (QCed) columns. All QCed trait data columns are highlighted in green, which are correctly reflected every time you open a new transaction.

23.10 PDM2.mp4

Bug fixes

You can expect to encounter no errors when opening and creating a new transaction.

...

Expand
titleAnalysis Request Manager (ARM)

Management of single-occurrence analysis (SOA) requests is improved.

This version improves user experience in terms of managing SOA requests and results. Specifically, you can now:

  1. Display the results of the first job with a

    Status
    colourGreen
    titleready
    status. From the ARM data browser, click the view icon ((blue star)) beside the request name. This redirects you to the analysis results viewer page, where the results of the first
    Status
    colourGreen
    titleready
    job is immediately displayed. If there are none, then the next job with a
    Status
    colourBlue
    titlefinalized
    status is shown.

  2. Navigate back to the ARM browser. A new Backbutton is enabled in the analysis results viewer page, so you can be redirected to the ARM data browser.

  3. Finalize and continue to the next job. When you Finalize a job, the next

    Status
    colourGreen
    titleREADY
    job is automatically loaded. After finalizing all jobs in a request, you are prompted to stay in the analysis results viewer page or go back to the ARM data browser.

  4. Easily manage your results. In the Table of Residualstab, a new filter button ((blue star)) allows you to show a) possible outliers only, b) suppressed data only, or c) both. The new Edit button also lets you 1) suppress all possible outliers, or 2) suppress all selected data points.

23.09 ARM_with TOC.mp4

Bug fixes

You can expect to encounter no errors when voiding a job in an analysis request.

Expand
titlePhenotypic Data Manager (PDM)

Browse occurrences from the PDM data browser.

You can now access occurrences directly from the PDM data browser, so you can easily check the quality of your data. The occurrences listed in the browser is limited to Breeding Trial (BT) experiments with a status of

Status
titletrait data collected
, which are the same requirements when using the Experiment Manager as an entry point to PDM. In this version, only the first 100 records are shown in the browser. This version also excludes BT experiments using the On-Farm Trial stage and the Unspecified design.

Log in the Breeding Analytics domain using your institution credentials. Open the left navigation menu and choose PDM. From the browser, look for your experiment and click the expand icon (>). Then, select an occurrence and click Explore to begin assessing your trait data.

23.09 PDM1.mp4

View the audit trail for trait data.

An audit trail is a list of changes made to the quality control (QC) code of the data. This lets you view an edit history containing details on who made the changes and when, provided that these changes were saved. This feature is available in the Trait Table. Simply right-click on a cell and choose to show edit history. The small pop-up window displays the most recent change to the data. It also shows how many changes have been made altogether. You can display each change using the page navigation icons (< and >).

23.09 PDM3.mp4

Management and visualization of data is improved.

The following enhanced features are implemented for this version:

  1. Change QC code by trait. This option lets you update the QC codes of trait data in bulk. From the Edit button, choose to change QC code by trait. This opens the modal window, where you can choose the Trait and then the QC code you want to apply to the dataset. A notification then confirms the changes applied in the Trait Table. Click the refresh icons ((blue star)) in both the Stats and Trait Tables to update the values.

23.09 PDM.mp4

  1. Heatmaps now use planting arrangement (PA) X and Y values. When visualizing the magnitude of the occurrence’s plot and trait data in the Heatmaps tab, the PA X and PA Y values are now used in the graph. Previously, it used the Field X and Field Y values.

23.09 PDM2.mp4

Bug fixes

Reported issues have been fixed. The following are now working as expected:

  1. In the Trait Table, changes to QC codes are now immediately reflected onto the data and in terms of the cell background color.

  2. In the Stats Table, bad values are now properly excluded in the computation for the No. of Valid Values.

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Expand
titleBreeding Analytics Platform (BAP)

Page reloads automatically after selecting a new program.

A program filter is available in the domain’s menu bar. Selecting a program tells the domain that you want to view and access only the experiments, occurrences, and data under that program. When you want to switch to a different program, the page will now reload to refresh the browsers and display only the data under it. This feature is available for both the PDM and MDA tools.

23.09 PDM4.mp4

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