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.

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Get help with EBS features

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,

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   New creator and modifier columns

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

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   Improved page navigation

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.

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Displayed info panel when opening an occurrence with no collected data

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.

Viewing analysis requests is improved.

To improve user experience, the following features are now implemented:

1. Filter by occurrence and trait. In the ARM data browser, you can now use the filter feature under the Occurrence and Trait columns. Simply supply keywords in the data fields under each column header and wait for the data browser to reload with the filtered results. The filters can also be used at the same time, allowing for more narrowed results. Lastly, click on the icon to remove the filters.

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2. Scroll and navigate pages. When viewing () the results of your analysis requests, both the List of Jobs and Job Outputs panels now feature scrollbars and page navigation so you can easily move across results. This locks the position of both panels to view them at the same time. This feature is especially helpful for requests with more than 10 jobs.

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Creating multi-occurrence analysis (MOA) requests is improved.

The following features can now be accessed as you create your MOA requests. Specifically, you can now:

1. Select latest finalized jobs. In the Experiments tab, you can now tick the checkbox beside the occurrence name to select all the recently finalized job IDs. You can still also select other job IDs for specific traits. Additionally, unselecting one job ID also unselects the checkbox beside the occurrence name.

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2. Download BLUPs. In the Options tab, you can now add BLUPs to the list of data you can extract from the single occurrence analyses (SOA). The resulting zipped file thus contains the soa_result_predictions_BLUPs.csv file. Previously, the option to include BLUPs is disabled.

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3. View improved file names. After downloading the result files from SOA and MOA requests, file names now contain a unique hash at the end, while downloaded MOA input files are also renamed. This allows for more descriptive file names that can be easily identified by users.

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MOA reports are enhanced.

The following files from the downloaded () multi-occurrence analysis (MOA) results are now improved:

1. MOA report. This main CSV file’s worksheets now have improved relevance in terms of the datasets available.

   1. Request Info worksheet. The plot count column is now removed. It was decided that this data column does not contribute relevant information in the 2nd step-MOA.

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   2. 2nd Step - BLUPs worksheet. The numbering in column A is now in ascending order.

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2. Analysis input files. These files are now included in the folders created for each job in the request.

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Bug fixes

You can expect to encounter no errors when:

1. downloading SOA reports through MOA, such that correct entry rows are reflected with no duplicates,

2. viewing requests with a void status where all buttons and checkboxes are disabled, and

3. viewing each job in a request, such that the occurrence name is accurately displayed.

Visualize data for traits with at least one good or questionable data point.

In the Box Plot, Histogram, Scatter Plot, and Heatmap tabs, the trait list box now only contains those traits with at least one plot trait data whose quality control (QC) code is good or questionable. Otherwise, the trait list box will be empty. This feature allows users to generate valid visualizations from their plot trait datasets. Previously, all traits are enabled for visualization by default.

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Visualize data for traits with at least one good or questionable data point

Suppression of values in the Box Plot tab is enhanced.

The following improvements are featured:

1. Suppress values for traits with generated box plots. After generating the box plot graphs for some or all of the traits in your occurrence, the Suppress Values feature is enabled. Here, you can now select the trait whose data you want to suppress. Simply click the Trait drop-down menu to view the traits available for selection. Take note that only those traits with generated box plots can be seen in this list. Then, define the a) upper bound and/or b) lower bound trait values you want to suppress. Click Suppress to apply the changes to the box plot graph. These changes are also reflected in the Stats and Trait Table.

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   Suppress values for traits with generated box plots

2. Suppress good and questionable data. Aside from outliers, you can now also suppress non-outliers, such as good (G) and questionable (Q) trait data. After clicking Apply, the box plot graph/s are also updated. This feature is also renamed to “Suppress Values”, to correctly indicate the full scope of its functionality.

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   Suppress good and questionable data

Management of plot trait data is improved.

To improve user experience, the following improvements are featured:

1. View enhanced graph colors. A darker green shade now colors the graphs for all visualizations for better contrast. Previously, the graphs had a lighter green shade.

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   Improved graph colors

2. Optimized saving process. This enhancement is deployed to avoid timeout errors when saving multiple changes at once.

Bug fixes

Reported issues were resolved. You can now:

1. view the Trait Table’s plot data properly, such that the data remains visible even after filtering and navigating to other tabs,

2. view occurrences with the TRAIT DATA COLLECTED status in the PDM data browser based on the selected program data filter,

3. open an occurrence from the Experiment Manager and expect to see the same program data filter in PDM, and

4. generate heatmaps, such that:

   1. all suppressed, missing, and bad trait values are now gray in color, and

   2. occurrences with no block data will not have the block option in the drop-down menu.

Processes surrounding randomization and uploading of designs are improved.

Backend enhancements are now applied to Core Breeding’s Experiment Creation tool when generating randomizations for your Breeding Trial design. Specifically, you can now:

1. View error notification for uploaded RCBD design file with Rep and Block columns. In the upload modal window, an error message is now displayed when you upload RCBD design files containing both Rep and Block columns. This is because, for non-sparse and sparse testing, RCBD only requires either the Rep or Block values, but not both.

2. Use the updated P-Rep design. Changes to the design definition for the non-sparse Partially Replicated (P-Rep) design is now implemented in the Design tab of Core Breeding’s Experiment Creation tool, where the rep information is not required. This enhances both the front-facing interface and the backend validation.

Non-sparse designs are improved.

Updated definitions for the following non-sparse designs were enabled:

1. Alpha-Lattice,

2. Randomized Complete Block Design (RCBD),

3. Augmented RCBD, and

4. Partially Replicated (P-Rep).

This supports the new user interface implementation in Core Breeding’s Experiment Creation tool, specifically in the Design tab.

Bug fix

You can now encounter no errors when:

1. uploading randomization files even when the columns for field coordinates are empty, and

2. uploading and validating a P-Rep, Augmented, and Unspecified designs file with or without Reps.

Browse and view genotype requests and their data.

From the left navigation panel, select the MDA tool. This should open the newly-enabled data browser, which houses genotype requests and their basic information. The icon allows you to view the request’s data stored in the following tabs: Genotype Data, Excluded Germplasm, and Excluded Markers. An info panel also provides a summary of Germplasm and Markers, as well as the Call Rate Threshold. As of this version, the filter features in the tabs and buttons in the Call Rate Threshold are not yet working, while data on Excluded Markers is not yet available.

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Browse and view genotype requests and their data

Bug fix

You can expect to encounter no errors when navigating to the MDA data browser and viewing genotype requests.

Accessing tools and programs is improved.

This version improves on the following:

1. Programs. On the program data filter, a scrollable drop-down menu is now featured when the available programs for selection is more than 10. This allows for an efficient display, preventing the list to occupy the entire screen.

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   Program drop-down menu

2. Timeout. After an hour of inactivity, you will be logged out of BA. A notification will be displayed to inform you that you have been logged out due to inactivity. Simply log in again to resume your activities.

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   Log out notification

Bug fix

The program data filters are working as expected, such that the data from the selected program data filter is reflected.

Downloading analysis results for each job is now supported.

This feature lets you download the result file for each of the single-occurrence analysis job/s that you have finalized. In the ARM data browser, a download icon () is enabled beside each of these. Previously, the result file can only be downloaded for each request when its status is closed.

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Download results from each job

Download notifications are now consistent.

When downloading the results of your requests, the notifications displayed now have standard messaging where the request name or job name is shown.

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Improved download notifications

Bug fixes

The Table of Residuals now display the correct number of records for each analyzed trait within an occurrence, while MOA reports are now generated without duplicate rows.

Data type validation is now enabled before QC codes are changed.

When converting the quality control (QC) codes of bad and suppressed trait data to good, data type validation is now applied to check if such changes are allowable or not. The process ensures that only those trait data with valid formats can be converted to good.

In the Trait Table, right-click on a trait data with the QC code of either bad, suppressed, or questionable. The option to convert these to Good or Questionable will only be available if the current trait data format complies with the expected data format for that trait and its data type. Otherwise, these QC code options are disabled. A brief explanation is also provided for your reference. Lastly, this feature can also be applied when changing QC codes individually or in bulk.

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QC code data type validation

Processes surrounding the upload of randomization designs are improved.

The following can now be observed in the Design tab of Core Breeding’s Experiment Creation tool for Breeding Trial experiments:

1. Canceled design request status and error message. When the system encounters an error in the processing of your uploaded randomization file, the design request status of canceled is displayed along with a brief note on why the processing failed. The errors may be due to 1) an invalid file, 2) missing required columns, or 3) a mismatch in the number of occurrences in EBS and the number of occurrences in the uploaded file.

2. Some validation rules for uploaded unspecified design files were removed. All entries in the experiment are no longer required to be present per occurrence for both non-sparse and sparse testing. Additionally, all occurrences are no longer required to have overlapping entries with other occurrences across all parameter sets for sparse testing.

Bug fixes

You can now expect to encounter no errors when:

1. saving block values from an uploaded unspecified design for sparse testing,

2. generating plots using sparse testing, such that the Plot Count does not exceed the Max No. of Plots indicated, and

3. validating an uploaded randomization file containing extra columns.

Accessing tools and programs is improved.

This version improves on the following:

1. Programs. Users with admin roles can now view all and select any of the programs available in EBS. This lets you load the ARM and PDM tools with the program’s data. Simply click the Program Name located at the menu bar to change the current program data filter selected.

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   Programs for admin users

2. BA Tools. With the implementation of Role-Based Access Control (RBAC), access to BA tools now depend on the permissions granted to your user profile. In cases where you know how to access a tool via the URL but do not have permission to do so, an error message will be displayed informing you of this limitation. Otherwise, you should have no trouble using BA tools with which you have permission to use.

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   Warning message

View plot numbers, entry numbers, entry names, and germplasm codes in SOA job outputs and result files.

When viewing () job outputs of single occurrence analysis (SOA) requests, the Table of Residuals now show new columns for plot numbers, entry numbers, entry names, and germplasm codes. The Predictions tab also display the last three. These are also featured in downloaded () analysis result files. These improvements allow for easier identification and data analysis.

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New data columns for analysis results

Downloading SOA analysis result files are improved.

In the ARM data browser, a SOA request’s status will not be set to closed until the analysis result files are ready to be downloaded. Once you click on the download icon (), the zipped file should be available on your device.

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

In the ARM data browser, the Request Analysis drop-down menu now includes the option to request MOA. The following are featured:

1. Experiments tab. This lists all closed SOA job inputs that you can select. Expand (>) each row to show all job IDs for each analyzed trait. The minimum requirement to proceed with the MOA request is to select at least two (2) job inputs under the same trait from different occurrences. Doing so enables the Next button. However, you can still add single job inputs from different traits to be included in the MOA request. This will be permitted by the system, but a notification will be provided once you click Next.

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   MOA experiments tab

2. Options tab. This houses the options available for you. Specifically, you can:

   1. Download SOA result files only. This option lets you extract BLUEs and Analysis Metrics in a CSV format. Selecting either or both result files enables the Submit button, which you can click to confirm your download and redirect you to the ARM browser. As of now, BLUPs is not yet supported.

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      Download SOA result files only.

   2. Request for MOA [2nd step] only. This option lets you create one (1) MOA request. You can define the H2 threshold parameters before clicking Submit, which then redirects you to the ARM browser. Once ready, job results can be viewed () for each analyzed trait.

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      Request for MOA [2nd step] only

   3. Download SOA results and request for MOA [2nd step]. This lets you proceed with both options above. Simply Submit your request to be redirected to the ARM browser and wait for the analyses to finish.

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      Download SOA results and request for MOA

3. Job outputs. On the ARM data browser, the action buttons are enabled once the job outputs for your MOA request is ready. You can view () the results page, where a list of jobs is shown at the leftmost section, while job outputs are at the right. In this version, the job outputs supported are the Analysis Metrics and Predictions. You can also download () these on your device.

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   MOA job outputs

Bug fixes

The following reported issues are resolved. You can now:

1. create an analysis request without encountering errors,

2. download SOA analysis reports (.xlsx) and MOA predictions_BLUEs results, and

3. correctly exclude occurrences with no quality-checked (QC) traits and whose trait data have a QC code of bad (B) in the SOA Experiments tab.

Viewing data in PDM is improved.

This version improves on the following features in the main data browser and the occurrence data browsers. Specifically, you can now:

1. View occurrence statuses. In addition to other basic information, the PDM data browser now also displays the occurrence status. This can be viewed after expanding (>) an experiment to see its occurrence/s. To recall, the PDM data browser only lists occurrences with the following statuses: PLANTED, TRAIT DATA COLLECTED, and trait data quality checked.

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   New occurrence status data column

2. View more experiments and occurrences. You can now view all experiment types in the PDM data browser. As such, trait data from all experiments and occurrences can now be inspected using PDM. Previously, only Breeding Trial (BT) experiments were available for trait data quality checking.

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   View all experiment types in PDM

3. Switch to view another occurrence from the same experiment. You can now easily jump from viewing the trait data of one occurrence to another from the same experiment. Simply select another occurrence to display using the new drop-down menu just above the subtabs and wait for the new trait data to be loaded. This feature is also applicable when generating the box plot, histogram, scatter plot, and heatmap graphs. Take note that the drop-down menu is disabled for experiments with only one occurrence.

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   View another occurrence in same experiment

Management of transactions are enhanced.

The following features surrounding the management and saving of transactions are upgraded:

1. Save only BT experiments, except those using OFT stage. Saving () and sending the transactions for analysis to ARM still only applies to BT experiments whose stage is not On-Farm Trial (OFT). This is related to the improvement on viewing all experiment types in the PDM data browser. A warning message is shown on the Save Transaction modal window to inform users of this limitation when trying to save the transaction of an unsupported experiment type and stage. Similarly, the Analyze button will remain disabled for these unsupported cases.

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   Save valid experiments only

2. Save transactions with or without selecting traits. In the Save Transaction modal window, a new description is provided to inform you that you can now Save your transaction with or without selecting trait/s. Both saved changes are reflected in Core Breeding’s Experiment Manager. Previously, you can only save a transaction after selecting trait/s. This improvement affects the quality control (QC) codes of the saved data (), specifically for questionable (Q) data. This means that in each saved transaction:

   1. questionable (Q) data is converted to good (G) for selected traits, while

   2. questionable (Q) data, and all other data QC codes, are retained for unselected traits.

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      Save transactions with or without selecting traits

3. Revised criteria are now applied when marking traits as QCed. Trait data columns with at least one (1) good data and no questionable data can now be marked as quality-checked (QCed), provided that the user explicitly does so using the Save Transaction modal window. Additionally, traits whose data are all or have a mix of questionable, suppressed, bad, and missing cannot be marked as QCed.

   Previously, trait columns can be QCed if:

   1. all of its data are not missing (NA),

   2. it has no questionable data, and

   3. has been explicitly marked as QCed.

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      Mark traits as QCed using new criteria

Uploading of sparse testing randomization files generated outside EBS is now supported.

In EBS, sparse testing is a way of randomly allocating test entries to different occurrences. Groups of occurrences with specific protocols are called parameter sets. These configurations include the trial designs applied to the parameter sets.

In this version, the backend features to support the upload of randomization files for sparse testing are now enabled in the Core Breeding domain’s Experiment Creation tool. This allows users to submit their own randomization files whose parameter sets use the Unspecified design and all other EBS-supported trial designs except IWIN and OFT, subject to validation rules.

Bug fix

You can expect to encounter no errors when:

1. validating a non-sparse testing file in Core Breeding’s Experiment Creation tool, and

2. generating the randomization for sparse testing, where the total number of plots created are now less than or equal to the specified NRep per entry.

RBAC is now supported.

The Breeding Analytics domain now implements role-based access control (RBAC), where users can only use tools that they have permission to access. These permissions are based on the roles assigned to their profiles in the Core System domain.

Bug fix

In the Table of Residuals, the bug causing the column filters to reset after selecting checkboxes is resolved.

Remain in PDM after all traits are QCed.

After saving () and marking all traits as quality-checked (QCed), you can now stay in PDM to further inspect your occurrence’s trait data. Once done, you can click the Analyze button to proceed to the ARM tool manually. Previously, users were automatically redirected to ARM once all traits have been QCed.

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Remain in PDM after all traits are QCed

Bug fix

You can expect to encounter no errors when:

1. viewing accurate X, Y, and Z values in the heatmap graph, and

2. processing all QCed traits that were saved.