CB Milestone 8

Management of occurrences using sparse testing is improved.

The system now prevents you to:

1. Regenerate the design. From the EM data browser, select an occurrence that used sparse testing. Click the icon from the toolbar and choose Regenerate Design. An error message pops up to inform you that this feature is not supported for occurrences that used sparse testing.

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   Prevent regeneration of design

2. Add more occurrences. Edit () the details of an occurrence that used sparse testing. Unlike other occurrences, the Add Occurrence button is not enabled in the Occurrence tab for occurrences that used sparse testing.

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   Prevent adding more occurrences

Bug fixes

You can now expect to encounter no errors when:

1. generating a field layout for Breeding Trial experiments using the Partially Replicated (P-rep) design with diagonal checks, and

2. downloading plot design files.

Bug fix

You can expect to encounter no error when uploading occurrence data collection files.

Calculated traits with parameters that are also calculated is now supported.

In the latest version, the tool can now auto-compute other traits from derived parameters. As such, you can now get the value of E, where:

E = D+C

C = B+A

For rice, the following traits are now auto-computed from derived parameters:

1. Missing hill (MISS HILL),

2. Moisture factor (MF),

3. Percentage of hills harvested (HVHILL_PCT),

4. Corrected plot yield in kilograms adjusted to 14% moisture content (Corrected PlotYield(KG)_MC), and

5. Plot yield in kilograms adjusted to 14% moisture content (AYLD_KG_MC).

In the DC data browser, Upload a trait data collection file containing the required trait data to generate the auto-computed traits (see formula). Once uploaded, click the Quality Control icon () to open your transaction. In the Summary subtab, you can find the new auto-computed trait, which are indicated by the computed tag. In this initial version, previously committed traits are not yet included in the calculations.

Bug fix

Failed upload transactions are now correctly shown in the DC data browser.

Bug fix

In the Harvest Data tab, you can now properly filter records with an invalid state status.

Display of germplasm is improved.

When you replace some germplasm in a Cross Parent Nursery (CPN) experiment using the Planting Instructions Manager (PIM) tool, CM data browsers now correctly reflect the new germplasm.

From the EM data browser, select a created CPN experiment’s occurrence. Click the icon from the toolbar and go to PIM. This creates a packing job for the occurrence. In the Entry Management tab, Replace some entries. Move to the next tab to Submit the packing job. In the EM data browser, proceed to have your occurrence planted. When you create a cross list for the occurrence, you can now expect to see the new germplasm names reflected in the CM data browsers.

View additional data in trait data collection files.

Female and male entry codes are now featured in downloaded trait data collection files. From the CM data browser, select a cross list whose status is either Finalized or cross list specified. Click the download () icon from the toolbar and select Trait Data Collection. This opens a page where you can select the traits that you want to collect. Export the cross list for Field Book () and select With Trait Abbreviations to download the .csv file.

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Female and male entry codes

Sparse testing is now enabled for Breeding Trial experiments.

Implemented by both the Core Breeding and Breeding Analytics domains, sparse testing can now be used for Breeding Trial experiments in EBS. In this initial version, the partially-replicated (P-Rep) design can be selected for sparse testing. From the Design tab, you can access the following features:

1. Across Environment Design. This drop-down menu allows you to select random for sparse testing, which then loads the new interface where you can define your parameters.

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Across environment design

2. Experiment Settings. This section in the new interface lets you set the a) Number of Experiment Occurrences* and b) the Number of Iterations you require. Click Assign to begin assigning the replicates per entry.

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   Experiment settings

3. Total Number of Replicates per Entry for the Experiment. This is a new page where you can assign the total number of replicates (NReps) per entry or to selected entries in bulk. All the changes made here are automatically saved. Then, click the back icon () to continue working on your parameters.

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   Total NReps

4. Occurrence Design. This section lets you define your a) Occurrence Design, b) Experimental Design Parameters, and c) Field Layout. For Occurrence Design, only the P-Rep design is supported as of this version. In the Design drop-down menu, choose the Partially Replicated design to load the rest of the data fields.

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   Occurrence design

   1. Experimental Design. Here, you can set the Number of Occurrences* to be created for the current parameter set. Then, supply the Number of Test and Check Entries and their respective replications. The Method of Replicating the Check Entries can also be set randomly or manually via the toggle () button. The latter option enables an icon () to let you select the checks you want to include in your parameter set. Simply Save and go back () to the main page to continue.

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      Experimental design

   2. Field Layout. A toggle () button is provided if you want to define the shape/dimension of the field layout. If the toggle is off, you only have to specify the Maximum Number of Plots. Otherwise, the Number of Rows and Field Order also needs to be defined. Once done, Save the parameter set.

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      Field layout

5. List of Parameter Sets. This section shows the list of the saved parameter sets. This expands once the parameters for all the occurrences have been defined. The options to delete () and edit () the parameter sets are available beside the status. If no other changes are required, you can Submit the design for randomization. A notification message informs you that the request was successfully sent, with the status changing from draft to RANDOMIZATION IN PROGRESS. Once done, the status is set to RANDOMIZED. Click the view () icon beside each parameter set to see the field design. In case you need to revise a parameter set, you can still do so by deleting () the generated plot records. This re-enables the options to delete () and edit () the parameter sets.

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   Parameter sets

Bug fixes

You can expect to encounter no errors when:

1. Auto-selecting the package records for entries with only one package record in the system,

2. Downloading a successfully randomized field layout using entry numbers,

3. Adding entries using the Advanced Nursery option following the order seen during preview,

4. Proceeding to the Review tab after successfully generating plots and/or planting instruction records,

5. Deleting entries and its associated planting arrangement records, and

6. Randomizing P-Rep designs with >4,000 entries.

Exporting custom files is improved.

From its initial implementation in 23.10, this version enhances user experience in exporting Metadata and Plot Data or Occurrence Data Collection files. Specifically, you can now:

1. Open the new export page. From the EM data browser, select one or more occurrences. Click the download button () from the toolbar. For this example, select Metadata and Plot Data from the drop-down menu. This opens a separate page that houses all sections mentioned in the 23.10 user release note. Previously, this feature is contained in a modal window.

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   Open the new export page

2. Expand data categories. Here, each data category is paired with a > icon to let users know these can be expanded.

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Expand data categories

3. View all related data. Beside each data category, all related data are now listed and immediately viewable. You can still remove some of the related data by clicking 'X' beside the data label.

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View all related data

4. Hide and display related data. When you expand a data category, a table for displayed and hidden columns is provided. By default, all related data are displayed and will be included in your downloaded file. To exclude other data labels, simply drag and drop down under the Hidden column.

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Hide and display related data

5. Download your CSV file. Click Export to begin the background process. This also redirects you to the EM data browser, where a notification () will be provided once the file is ready to be downloaded. Click the notification message to download the file on your device.

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Download your CSV file

Uploading of occurrence data collection files is enabled.

You can now upload occurrence data collection files for single or multiple occurrences. This allows you to update occurrence and management variables, such as Ecosystem and Fertilizer Brand Applications.

From the EM data browser, click the Upload button on the toolbar and choose Occurrence data collection. This opens a modal window where you can browse or drop your file and Validate it afterwards. A summary of the updates can also be reviewed before you Confirm these. Wait for the notification () informing that your occurrence and/or management data was successfully updated. You may then view the data via the Update Experiment and Occurrence () icon in the Occurrence and Management tabs. Take note that unlike plot data, uploaded occurrence data do not undergo quality control.

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Upload occurrence data collection files

Code generation is enhanced.

When customizing your entry code or plot code, only the exact suffixes you specify will be reflected by the system. These codes are used when generating your field tags and labels. Previously, the system automatically added a dash (-) before the actual suffix. You can access this improvement via the Update Experiment and Occurrence () icon and under the Code Generation tab. Here, you can specify the suffix you want to appear on your entry code or plot code.

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Generate entry code or plot code

Bug fixes

You can expect to encounter no error when:

1. mapping occurrences,

2. exporting metadata and plot data files,

3. saving package lists from the Entry tab,

4. saving plot lists in the Plot tab after viewing the location, and

5. saving occurrence data.

Management of collected trait data is improved.

This version provides the following enhancements in the management of collected trait data:

1. Use the location name as filter in the data browser. Click the quality control (QC) icon () beside an uploaded transaction. You may now click the location hyperlink placed at the upper right section of the QC page to go back to the DC data browser and automatically filter its contents using the location name.

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Hyperlinked location name

2. Color-coding of trait data is now consistent with Breeding Analytics' PDM and ARM tools. In the Plot and Cross subtabs, the color coding of trait data is now standardized with EM and Breeding Analytics' Phenotypic Data Manager (PDM) and Analysis Request Manager (ARM) tools. New data is in green, while invalid and missing ones are in red and blue, respectively. When you upload new values to update previously committed trait data, these values will be in yellow. Additionally, suppressed values are grayed out, while voided ones are in black. Committed trait data (also called Experiment value), possible outliers, and those with a QC code of good are plainly denoted by numerals or text.

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Color-coded trait data

3. Download dataset following the order of traits in the data browser. You can now expect that the order of traits shown in your downloaded CSV file follows the order you see on the Plot and Cross data browsers in the QC page. Open the QC page () and move to the Complete Transaction tab. Click Download Dataset to save the CSV file on your device.

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Download dataset following the order of traits in the data browser

Bug fixes

You can expect to encounter no errors when:

1. filtering the DC data browser using statuses, and

2. completing a transaction.

Harvest Manager

1. You can expect to encounter no error when downloading a list with more than 2,000 packages. Exporting this many records will be delegated to the background. A notification () will be provided once the file is ready to be downloaded. Click the notification message to download the file.

Inventory Search

1. The initial version of the Advanced Search feature is now enabled in the tool’s Search Results data browser. From the toolbar, simply turn the Advanced Search toggle on () to narrow down your search results according to the new filters that you set. In this initial version, sorting, filtering and moving to the last page of the results are not yet supported.

2. The correct number of records are now added to the Working List page.

3. Adding filtered search results to the Working List page can now also proceed as expected.

4. The bug causing unnecessary error messages to be displayed is fixed.

Germplasm

1. Uploading germplasm attribute files and downloading germplasm relation files now proceed accordingly.

Custom file exports are now enabled.

You can now define which occurrence-level and plot-level data to include in your exported CSV file. The feature supports the option to download Metadata and Plot Data or Occurrence Data Collection files. The latter can be accessed in the EM data browser or by viewing the details of an occurrence. From the Basic tab, click the download button () and choose Occurrence Data Collection. The modal window for both files have the same functionalities. Let’s download the former as an example.

From the EM data browser, select one or more occurrence. Click the download button () from the toolbar. Select Metadata and Plot Data from the drop-down menu.

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Generate metadata and plot data

In the modal window, you can:

1. View selected occurrence/s. All selected occurrences are displayed in the modal window for your reference. Occurrence names can be clicked if you want to view () more information about it.

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   View selected occurrence/s

2. Configure data format. In the Columns section, you can:

   1. Arrange data. Data categories are listed under Column Order. You can arrange these according to your preference, where the topmost data category becomes the leftmost data in the exported CSV file.

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      Arrange data categories

   2. Select data to download. Each data category has related data that you can choose to add to your CSV file. These are listed under Selected Columns. By default, all related data are included in the file. You can remove some of these in two ways: 1) click 'X' beside the data label, or 2) expand the data category to reveal a table where you can choose to show or hide related data by dragging and dropping them. You can also arrange the placement of related data to be displayed in the CSV file.

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      Select related data

   3. Add or remove values. A icon is featured beside each related data. When the icon is highlighted in green, it means that all the values of that data will be downloaded. Otherwise, the cells under the data will be left blank.

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      Add or remove values

3. Download your CSV file. Click Download to begin the background process. You may close the modal window and return to the EM data browser. A notification () will be provided once the file is ready to be downloaded. Click the notification message to download the file.

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   Download custom file export

Management of occurrences is improved.

The following enhanced features are implemented for this version:

1. Exporting >1000 plots is now delegated to the background. From the EM data browser, click the location of an occurrence and open the Plot tab. If you have >1,000 plots to export, the current version prepares the plot list in the background. Click the notification () to download the file on your device.

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   Export >1,000 plots

2. Updated experiment and occurrence statuses. When all occurrences have the status of PLANTED in the EM data browser, the same status is reflected for the experiment in the EC data browser. The PACKED status will also be hidden in the EM data browser after an occurrence’s plots are planted.

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Planted status

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Hidden packed status in EM data browser

Bug fixes

You can proceed to encounter no errors when:

1. selecting all occurrences left after sorting, and

2. selecting all plots left after filtering.

Download features are enhanced.

This version provides the following improvements surrounding the download feature:

1. New DC file exports for cross lists. In the Cross Manager (CM) tool, new DC files are now available for cross lists with the status cross list specified and FINALIZED. You can see three (3) file options when you click the download () icon on the CM data browser: Test Cross Interface 1, Test Cross Interface 2, and Test Cross Interface 3. These contain specific variables that depend on your profile’s EBS access: Global (Admin), Program-specific, or Role-specific (Collaborator).

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New DC file exports in CM tool

2. Preserved trait order. The order of selected traits is maintained when you download your trait data collection (.trt) files. This is applicable when downloading the file from Experiment Creation, Experiment Manager, and List Manager.

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   Preserve trait order in .trt files

3. Exporting >1000 plot dataset is now delegated to the background. When you click Download Dataset in the Complete Transaction tab of the Quality Control (QC) page, a transaction with <1,000 plot records is immediately downloaded on your device. On the other hand, downloading >1,000 plot records is handled in the background. A notification () will be provided once the file is ready to be downloaded. Click the notification message to download the file.

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   Export 1,000 plot records

Bug fixes

You can now expect to encounter no errors when:

1. viewing trait headers on all theme color settings, and

2. using the bulk update feature in the Plot subtab of the QC page.

Additional harvests are now supported.

You can now add harvest records onto previously harvested plots and crosses in EBS. This feature can be accessed in the Harvest Data tab. Select plots or crosses with a Harvest complete status and click the new Add Harvest () icon from the toolbar. A modal window appears to let you supply additional harvest data, which depend on the previous harvest method used:

1. Bulk harvest + numbered harvest. This scenario lets you create new harvest records using numbered harvest methods. Select previously harvested plots/crosses that used the bulk method and create additional harvest records via the icon. In the modal window, provide the harvest date, numbered harvest method, and numeric variables. Proceed to the Creation tab and then to the Management tab to view the additional germplasm, seed, and package records.

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   Bulk + numbered harvest

2. Numbered harvest + bulk harvest. This scenario lets you create new harvest records using the bulk harvest method. Select previously harvested plots/crosses that used numbered harvest methods and create additional harvest records via the icon. In the modal window, provide the harvest date and choose Bulk. Proceed to the Creation tab and then to the Management tab to view the additional seed and package records. An additional germplasm may also be created depending on the germplasm state.

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   Numbered harvest + bulk

3. Numbered harvest + numbered harvest. This scenario lets you create new harvest records using numbered harvest methods. Select previously harvested plots/crosses that used numbered harvest methods and create additional harvest records via the icon. In the modal window, provide the harvest date, numbered harvest method, and numeric variables. Proceed to the Creation tab and then to the Management tab to view the additional germplasm, seed, and package records.

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   Numbered harvest + numbered harvest

Unlike harvesting plots/crosses for the first time, there is no need to Commit and Create additional harvest records because these are created automatically. Additional harvests are also capped at a hundred records at each time. For your reference, a table is provided to show the supported numbered harvest methods in this version:

Management of harvest records was improved.

This version enhances the management and use of resulting harvest records. Specifically, you can now:

1. Arrange plot numbers in ascending order. In the Management tab, you can sort the plot records in ascending order for easier reference. Simply click on the Plot No. column header name once to follow an ascending order. While this will also arrange other associated plot data such as package labels, take note that the sequence number at the end of package labels are generated per batch of harvest. Thus, package labels may not always be listed in ascending order even when the plot numbers are.

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Records in ascending order

2. View notifications when deleting packages already used as entries. Package records are used as seed sources for experiments. The system now guards against deleting packages that were already used as entries via a modal window and a notification message.

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   Deleting packages already used as entries

Bug fixes

You can expect to encounter no error when:

1. harvesting crosses using the hybrid formation method, and

2. viewing the number of ears as you harvest.

Experiment Creation

You can expect to encounter no error when:

1. copying a Generation Nursery experiment, and

2. reviewing the details of an Intentional Crossing Nursery experiment before finalizing.

Inventory Search

1. You can add the contents of your working list to a saved list which you have read and write access to.

Germplasm

You can expect to encounter no errors when:

1. merging germplasm records,

2. uploading files in the Create tab,

3. filtering germplasm results using the Germplasm Name column, and

4. search results correctly follow the input order when using the Input List.

List Manager

1. You can now create up to 21 copies of each list entry.

Core Breeding Dashboard

1. You can expect to encounter no errors when accessing other EBS domains via the Domain Shortcuts () icon. Otherwise, a warning () message is displayed. Consequently, an error () message is provided when you try to access a tool from other domains using a Core Breeding tool entry point (e.g., Experiment Manager to Phenotypic Data Manager).

EBS Login

1. A new login page is enabled that uses a new identity authenticator: Amazon Web Services (AWS) Cognito.

File upload error messages are improved.

In the Design tab of Breeding Trial experiments, you can now expect to see more informative error messages when you upload an invalid design files generated outside EBS. You can use these error descriptions to correct your design file accordingly.

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Sample error messages

Bug fixes

You can expect to encounter no errors when you generate another planting arrangement after reordering entries in the Entry tab of a Generation Nursery experiment. Also, the bugs causing unnecessary error messages to be displayed were fixed.

Updating experiments' basic information is improved.

From the EM data browser, click the Edit icon () beside any experiment to update its basic information. In the Experiment tab, you can now manually update the required fields of Experiment Name, Stage, Experiment Year, Evaluation Season, and Experiment Steward. Any changes made are automatically saved.

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Update experiment’s basic info

Filtered view of the EM data browser is enhanced.

After filtering the experiments displayed in the EM data browser based on your preferences, the filtered view is now retained even after switching to another tool and logging out of Core Breeding. To reset the data browser, just click the refresh icon () from the toolbar or remove the filter.

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Filtered EM data browser

Bug fixes

You can expect to encounter no errors when you:

1. add or delete occurrences in an Observation experiment,

2. delete the last occurrence of an experiment, which also correctly deletes the experiment, and

3. access Printout templates based on the current program and tool used.

Auto-generated cross list name is now supported.

As you Create your cross list and provide the details in the Basic tab, the option to auto-generate cross list names are now provided via a toggle (). The auto-generated name follows this pattern: SITE-SEASON-YEAR-UNIQUE ID. Once all required fields are filled-out, the Next button is enabled. Previously, users were required to manually provide the cross list name.

Related to this new feature are the following:

1. Edit an auto-generated cross list name. Before you Finalize your cross list, you can still make changes to the auto-generated name. From the data browser, click the edit icon (). Then, update the auto-generated cross list name in the Basic Info tab.

2. Intentional Crossing Nursery (ICN) cross list name. An ICN experiment created in the Experiment Creation (EC) tool is also displayed in the CM data browser. The ICN cross list name uses the experiment name, as saved in EC, which you can also update and edit.

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Auto-generated cross list name

Parent List data browser is improved.

In the Review tab, the Parent List browser is enhanced with the a) personalize grid settings button (), b) refresh button (), c) pagination, and d) column sorting after the column name is clicked.

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Parent List data browser

Features around cross list deletion is enhanced.

When you delete () a cross list, notifications () are now provided for your reference. Notifications are prompted if the deletion is in queue or in progress. Additionally, all associated pollination and trait protocols are also deleted when you delete a cross list that has not been finalized yet.

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Be notified about cross list deletion

[ADMIN] Configure downloadable germplasm attributes file.

From the Add Parents tab, Data managers (DM) can now build the germplasm attributes file that can be downloaded by users. DMs may configure the file for the KE (maize) and IRSEA (rice) programs and users with collaborator roles.

Bug fixes

You can expect to encounter no errors when adding parents to a cross list.

Mark trait values as missing in bulk.

When validating your occurrence’s trait data in the Plot tab of the Quality Control (QC) page, the feature to change uploaded trait values to missing (NA) is now enabled. Select the values you want to update by ticking () the checkbox on their respective rows. From the toolbar, click the Bulk Update icon () to open the modal window. Here, you can select the Trait from the drop-down menu and tick () the NA checkbox. You can then proceed to mark trait data as missing for 1) selected or 2) all values of the trait.

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Bulk update trait data to ‘NA’

Management of trait data is improved.

The following enhanced features are implemented for this version:

1. Download more informative trait data collection files. Users with Breeding Trial experiments using the Row-Column design can now download () trait data collection files that include columns for a) row block number and b) column block number.

2. Sort data per column. This feature is available in the Plot subtab of the QC page. You can now sort individual trait columns by clicking on the column header name. The first click sorts data from low to high or A to Z, while the next one sorts it the other way around. In this version, you can only sort one trait column at a time.

3. See the new UPLOADED transaction status. The new status is reflected on the DC data browser after successfully uploading a trait data collection file. Previously, a validated transaction status is shown for this process.

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Trait data management

Bug fixes

The bugs causing errors in the following processes were fixed:

1. applying multiple suppression rules to the same trait, and

2. downloading accurate records.

New harvest methods for fixed materials in wheat are supported.

Three (3) new harvest use cases were enabled for wheat plots that have a germplasm state of ‘fixed’ namely, a) selected bulk, b) individual spike, and c) single plant selection. The first creates one (1) seed and package record, while the rest creates multiple seed and package records, depending on the specified number of plants in the Numeric Variables column. Previously, these harvest methods were only applicable for non-fixed wheat materials.

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New harvest use cases for wheat

Bug fixes

1. To address errors encountered due to data whose quality control (QC) code is ‘bad’, the following fixes were applied:

   1. HM validation will prevent harvesting of plots if it detects a ‘bad’ QC code from the harvest data and not the phenotypic data, and

   2. The ‘bad’ QC code is also removed once the data is replaced with a valid one.

2. In the Management tab, an error message will pop-up if you attempt to download an empty browser.

Germplasm

1. In the data browsers, the columns for Designation, Germplasm, and Entry Name have all been replaced by the Germplasm Name column. The same will be reflected to downloaded files.

2. You can also expect to encounter no error when downloading multi-paged germplasm search results.

Inventory Search (formerly Seed Search)

1. The Seed Search tool is renamed as 'Inventory Search'.

2. In the data browsers, the columns for Designation, Germplasm, and Entry Name have all been replaced by the Germplasm Name column. The same will be reflected to downloaded files.

3. A new Package Quantity column is featured in the Working List page.

4. You can also expect to encounter no error when adding filtered results to the Working List page.

List Manager

1. In the data browsers, the columns for Designation, Germplasm, and Entry Name have all been replaced by the Germplasm Name column. The same will be reflected to downloaded files.

2. You can also expect to encounter no error when displaying the contents of your germplasm or seed lists.

Inventory Manager

1. In the data browsers, the columns for Designation, Germplasm, and Entry Name have all been replaced by the Germplasm Name column. The same will be reflected to downloaded files.

Core Breeding Dashboard

1. Trials and Nurseries widgets will now exclude experiments with a draft status on the lists.

2. The bugs in the tool widget selector were fixed, where the recently removed tool can now be selected to be added again in the Tools widget.