Page Comparison

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.

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.

   24.04 PDM new version.mp4

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.

   

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.

   

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

   Status
   title 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.

Bug fix

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

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.

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

   Status
   colour Red title 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.

   

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.

   

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.

Downloading SOA analysis result files are improved.

In the ARM data browser, a SOA request’s status will not be set to

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

   Status
   colour Blue title 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.
   

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.

      

   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.

      

   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.

      

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.

   

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:

   Status
   colour Green title PLANTED

   ,

   Status
   title TRAIT DATA COLLECTED

   , and

   Status
   title trait data quality checked

   .
   

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.

   

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.

   

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.

   

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.

      

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.

      

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.

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 buttonto proceed to the ARM tool manually. Previously, users were automatically redirected to ARM once all traits have been QCed.

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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.