CB Milestone 9

Crop and taxonomy information is now displayed.

In the Search tab, a new data field for Crop is now enabled. By default, the crop used by your current program is pre-selected. Additionally, the results data browser now feature columns for Crop and Taxonomy data. These can be added to the data browser using the icon in the toolbar. Simply drag and drop these columns under the Visible Columns.

Lastly, the Taxonomy for each germplasm is also available when viewing () its basic information. You can view this in the modal window’s Basic tab after clicking the germplasm name across Core Breeding tools.

Bug fix

You can now proceed to download a germplasm Template from List in the Update tab.

Bug fix

You can expect to encounter no errors when adding items to the Working List.

Management of occurrences is enhanced.

This version implements the following improvements:

1. Occurrence page summary. When you update () the details of an occurrence, the option to Add Occurrences to Breeding Trial or Observation experiments is also available. After you are redirected to the Add Occurrence page, you can now expect to see a page summary just beside the toolbar. This details the number of total items in the current page.

   

2. Harvest status. View () your occurrence and go to the Crosses tab. Here, the Harvest Status column is now enabled. You can also filter this column, as well as include it in your exported () file.

   

3. Improved validation of uploaded occurrence data collection files. The validation process now skips blank columns. With this, you can now successfully Upload your occurrence data collection files even with blank columns present. Previously, the validation stops at the first invalid field it detects, such as blank columns.

   

Bug fixes

You can expect to encounter no errors when:

1. downloading a planting instructions file, such that all columns are properly labeled, and

2. uploading and validating an occurrence data collection file.

The Compute tab is improved.

The initial implementation of the Compute tab is now enhanced with the following features. Specifically, you can now:

1. Filter, Sort, and Select all formulas. You can now filter the formula data browser using the blank field just below the column names, while clicking the column labels allow you to sort contents in an ascending or descending order. The Select All checkbox is also enabled for bulk selection of formulas.

   

2. View and use formulas with parameters derived from other formulas. You can now compute for trait values whose formulas contain inputs that are the results of other formulas. For example, you want to calculate for traits A, B, and D, where:

   • A is an uploaded trait value,

   • B = A + C, and

   • D = B + E.

     

Bug fixes

You can expect to encounter no errors when:

1. completing the transaction for more than 500 plot trait data values,

2. calculating traits, and

3. filtering the data browser to view transactions with FAILED, IN QUEUE, and IN PROGRESS statuses.

More harvest use cases are enabled for Cowpea crop.

As EBS prepares to support the Cowpea (CWP) program, two additional harvest use cases are now supported to advance nurseries. Specifically, you can now;

1. Harvest F1 and F4 generations using Bulk method. F1 and F4 germplasm belonging to any type and whose state is NOT_FIXED can now be harvested using the Bulk method. In the Harvest Data tab, provide the harvest date and select Bulk as the harvest method. Commit and Create the harvest to generate records whose generations are F2 and F5 with germplasm state of NOT_FIXED and FIXED, respectively.

2. Harvest F2 and F3 generations using Single Plant Selection (SPS) method. F2 and F3 germplasm belonging to any type and whose state is NOT_FIXED can now be harvested using the SPS method. In the Harvest Data tab, provide the harvest date and number of plants. Commit and Create the harvest to generate records whose generations are F3 and F4, respectively, with germplasm state of NOT_FIXED.

Harvesting restorer (R) lines for rice is now supported.

A Test Cross Verification (TCV) experiment aims to identify maintainers and restorers from a test cross nursery. In Generation Nursery (GN) experiments using the TCV stage, you can now harvest FIXED germplasm using the R-line harvest method.

Using a PLANTED GN experiment with the TCV stage, download a trait data collection (DC) file with the trait Hybrid Material Type. During data collection, you can use “R” and “M” to indicate which ones are the restorer line/s and the maintainer line/s, respectively. Upload the DC file to your occurrence and proceed to HM. In the Harvest Data tab, display the Hybrid Material Type column using the icon. For those designated with “R”, select R-line Harvest as method and specify the harvest date and number of bags. Commit and Create the harvest records in the Creation tab. New germplasm are created, with their names appended with “R”. Lastly, FAILED harvests for this use case can be checked in the Harvest Data tab, where a icon can be clicked to show the details of the error.

Bug fixes

You can expect to encounter no errors when harvesting crosses, such that:

1. harvests with complete harvest data does not fail, and

2. resulting germplasm names are accurately generated.

RBAC is now supported.

This tool now implements role-based access control (RBAC), where users can only use tools and features that they have permission to access. These permissions are based on the roles assigned to the profiles in the Core System domain. Kindly contact your EBS admin for any additional access you may need.

RBAC is now supported.

This tool now implements role-based access control (RBAC), where users can only use tools and features that they have permission to access. These permissions are based on the roles assigned to the profiles in the Core System domain. Kindly contact your EBS admin for any additional access you may need.

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. In this version, you can now upload sparse testing randomization files that were generated outside EBS, whose parameter sets use the Unspecified design and all other EBS-supported trial designs except IWIN and OFT, subject to validation rules.

Create a Breeding Trial experiment and add entries. In the Design tab, select Random in the Across Environment Design drop-down menu. After the page reloads, toggle () the Design Workflow switch to Upload. Click the Upload () button and browse for your randomization file. Pre-validate the file to show the summary information. In the same modal window, select any aforementioned design for the parameter set/s and then Validate.

Once successful, Confirm the upload of the randomization file. You are then redirected to the Design tab to wait for the upload to finish. The view icon () is enabled as soon as the file is successfully UPLOADED.

Management of entries is improved.

The following features in the Add Entries tab is enhanced for ease of use. Specifically, you can now:

1. Use package codes to add entries. When adding entries () in the Entry List tab using the Input List, the modal window now features the additional option to use package codes. Simply tick the radio button () beside your preferred option.

   

2. Locate the fixed positions of the Back and Add Entries buttons . When adding a lot of entries via the Input List, the Back and Add Entries buttons on the modal window now occupies a fixed position. This prevents the buttons to move as you scroll down a long list of entries.

   

Bug fixes

You can now expect to encounter no errors when:

1. uploading design files created outside EBS for Breeding Trial experiments,

2. generating planting instruction records in the Site tab, and

3. creating experiments, such that no unnecessary error messages are displayed.

Entries that were replaced are now correctly reflected in crosses.

When replacing the entries of a crossing experiment, the new germplasm is now correctly reflected in the relevant data columns for the cross. The changes made in EM are also applied to the Cross Manager (CM), Harvest Manager (HM), as well as in all downloadable files related to the crossing experiment.

View () your crossing experiment and go to the Entry tab. Select an entry and click the Edit button in the toolbar. Then, click Replace Occurrence Entry and choose the Replace with Germplasm option in the modal window. Here, you can search for the germplasm and select the new one you want to use in your experiment. The modal window also provides a summary of the changes to be made. Once satisfied, click Confirm to finalize the entry replacement.

The changes are observed in the data columns for cross name, as well as the female and male parent, parentage, and seed source in EM, CM, and HM. The update is also applied to any crosses that were already created prior to entry replacement.

Validation of uploaded occurrence data collection files is enabled.

Occurrence data collection files allow you to update occurrence and management variables, such as Ecosystem and Fertilizer Brand Applications. In this version, validation of the uploaded files are now enabled to ensure that only valid values for each variable are uploaded to EBS.

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 provide your file and Validate it. An error message is now shown if your file has invalid value/s. It also provides a guide on how to revise the data to the accepted values and format. Once the upload is successful, you can view () the data in the Basic tab.

Management of experiments is improved.

The following functionalities were enhanced. You can now:

1. View packages harvested. When viewing () an occurrence’s Basic tab, data on the Packages Harvested are now shown. This displays the total number of plots and crosses that can be harvested for an occurrence. This is also a clickable link that redirects you to the Harvest Manager tool, which readily displays the occurrence’s harvest information.

   

2. Export harvest and pollination instructions. Maize users can now include the harvest and pollination instructions, if available, when downloading Metadata and Plot Data files. Simply select an occurrence in the EM data browser and click the download () button from the toolbar. Choose Metadata and Plot Data to open the export page, where you can see the new data under the Occurrence data category.

   

3. Expect newly generated entry/plot codes to be reflected immediately. Changes to the entry and plot codes are now immediately applied to the Plot tab, without the need to refresh the tab. This improvement can be accessed a) via the Update Experiment and Occurrence () icon in the data browser or b) by selecting and occurrence and clicking the bulk update () button from the toolbar. Then, choose to either Generate Entry or Plot Code. This update also promises a faster performance when loading the Plot tab page.

   

Bug fixes

The bugs causing errors in the following features are resolved. You can now:

1. filter the experiments displayed using the Program dashboard data filter () in the menu bar,

2. download accurate metadata and plot data files, such that these are:

   1. not empty,

   2. do not have duplicated rows, and

   3. do not contain data of voided plots.

3. expect to download mapping files that contain updated germplasm records after entry replacement,

4. update management protocols,

5. delete an experiment and expect that all related data are also removed,

6. add occurrences by uploading designs in the Design tab, and

7. expect that the plot numbers of a newly added occurrence to a Breeding Trial experiment follows a sequential order.

Selection of formulas for trait calculation is enabled in the new Compute tab.

Trait data values are calculated based on the parameters defined in a formula. The new Compute tab lets you choose from an array of formulas applicable to your raw data. Take note that this tab is enabled only when there are trait values to be computed. To access this feature, upload your trait data collection file with numeric trait data.

The new UPLOADED: TO BE CALCULATED status is used for all new file uploads. Open the Quality Control (QC) page by clicking the icon. You are automatically redirected to the Compute tab, where the list of all applicable formulas are enumerated and selected by default. Simply uncheck those that you do not need for your occurrence. Then, click Calculate. You will be redirected to the DC data browser, where your transaction should move from CALCULATION IN PROGRESS to an UPLOADED status. Wait for the notification () informing that trait/s have been successfully calculated.

Open the QC page again () and move to the Review tab, where all traits, both computed and uploaded, are now visible in the Summary and Plot subtabs. You can then proceed to Complete the transaction, which commits the trait data to the occurrence.

RBAC is now supported.

This tool now implements role-based access control (RBAC), where users can only use tools and features that they have permission to access. These permissions are based on the roles assigned to the profiles in the Core System domain. Kindly contact your EBS admin for any additional access you may need.

Bug fixes

You can expect to encounter no errors when calculating the following traits:

1. grain yield in Wheat,

2. days to booting in Wheat, and

3. total plot gap area in Rice.

First harvest use case for Cowpea and Soybean is now supported.

As EBS prepares to support Cowpea (CWP) and Soybean (SYB) programs, the first harvest use case for both crops are enabled in HM. You can now harvest plots using the Bulk method and whose germplasm state is “fixed”.

Select an experiment occurrence to harvest from Experiment Manager or directly in HM. In the Plots subtab, provide the harvest date for a germplasm whose state is “fixed”. Then, select Bulk from the harvest method drop-down menu. Move to the Creation tab to Commit and Create the harvest records. Once harvest is successful, the resulting package records are displayed in the Management tab.

Germplasm attributes for non-selfing crosses are now generated after harvest.

For every non-selfing cross that is harvested, the following germplasm attributes are generated:

1. Germplasm Year. This pertains to the year in the crossing date.

2. MTA Status. This provides the conditions set for germplasm exchange to partners. Additionally, new harvests will have a default IP status of PUD2.

3. Origin. This refers to the country where a germplasm was developed and collected. The format is Institute/Center Acronym-Country. For example, IRRI-India.

After harvesting a non-selfing cross, you can view the germplasm attributes by clicking the hyperlinked germplasm name in HM’s Management tab. In the modal window, click the View More Information button and go to the Attributes tab. These new germplasm attributes are useful for shipment transactions and further analyses.

Existing cross combination for each program is now recognized.

Within a program, when harvesting a cross that used the same parentage with a previously harvested cross, no new germplasm is created. This only generates additional seed and package records, which are attached to the existing germplasm.

Bug fixes

1. You can expect to encounter no errors when searching for records.

2. The bug causing the year filter to be predefined is resolved.

Selfing generations are now included in the downloaded Germplasm Relations file.

When you download the Germplasm Relations file, you can now expect to see the records of germplasm that were advanced using selfing. The Germplasm Relations file can be used for your Coefficient of Parentage (CoP) analysis. In the Germplasm data browser, search for your germplasm records and select those you want to export. Click the download icon () from the Search Results toolbar and choose Relations. A notification () will be provided once the file is ready to be downloaded. Click the notification message to download the file on your device. Previously, the exported Germplasm Relations file only included data from crosses.

NRep data are excluded when copying the entries of an experiment.

Entries can be assigned their respective total number of replicates (NReps). When you add entries to your experiment using the Copy Entry List option, the entries' NRep data is duly excluded.

Bug fixes

You can expect to encounter no errors when:

1. adding entries using the Copy Entry List option,

2. displaying the correct number of selected entries in the Entry List tab and in the Design tab during bulk update of Total Reps,

3. managing crosses in the Cross tab, and

4. using CIMMYT RCBD and CIMMYT Alpha-Lattice designs.

Exporting the QC codes of plot trait data is enabled.

Quality control (QC) codes are assigned in the Data Collection tool or during quality checking in the Breeding Analytics domain’s Phenotypic Data Manager. In this version, QC codes are now included in the exported metadata and plot data files for rice programs. Specifically, you can now:

1. Export QC codes. The following QC codes can now be exported side-by-side with the plot trait data values: good (G), questionable (Q), bad (B), missing (M), and suppressed (S). From the EM data browser, select occurrence/s with the status TRAIT DATA COLLECTED and/or TRAIT DATA QUALITY CHECKED. Click the download button () from the toolbar. Select Metadata and Plot Data from the drop-down menu. In the Trait data category, choose the traits whose data you want to download and click Export. A notification () will be provided once the file is ready to be downloaded. Click the notification message to save the file on your device.

2. Set plot trait data values to NA. You can now use “NA” to denote plot trait data values with QC codes of M, B, and S. This feature can be accessed when exporting metadata and plot data files. In the Data section, click the gear icon (⚙️). Turn the toggle on to Replace Trait Data with NA and click Export to begin the download.

Management of occurrences is enhanced.

This version implements the following improvements:

1. Experiment and occurrence names can now be updated after changing Stage, Year, or Season. When editing () an experiment’s stage, year, or season, a modal window pops up to confirm if you want the experiment name and occurrence name/s to be updated according to the changes.

   

2. Improved labels and descriptions in the Metadata and Plot data page. The page features improved instructions and renamed sections. Here, the Columns, Column Order, and Selected Columns were replaced by the labels Data, Data Categories, and Related Data, respectively.

   

3. Export more data. You can now include Germplasm Attributes, such as MTA Status and Germplasm Release Year, as well as the Field data in the Metadata and Plot Data files that you can download. Germplasm attributes will be available under the Germplasm data category, while Field is under the Occurrence data category. Additionally, you can include the occurrence name, occurrence code, occurrence number in your exported Occurrence Data Collection files.

   

Bug fixes

The bugs causing errors in the following functionalities are fixed. You can now:

1. open the View Occurrence page by clicking the icon and opening the page in a new tab,

2. be informed that at least one occurrence should be selected before downloading Data Collection Summary, Metadata and Plot Data, and Occurrence Data Collection files.

3. download metadata and plot data files according to the program configuration,

4. access EBS menu bar options,

5. navigate the pages when managing experiments with >100 occurrences,

6. view uploaded management data from occurrence data collection files, and

7. expect the year column filter to be properly limited by the year data filter in the EBS menu bar ().

The Dataset tab is renamed to Review.

After uploading your trait data collection file, go to the Quality Control (QC) page using the icon. You will see the newly renamed tab, which still hosts the Summary and Plot/Cross subtabs. This tab is renamed to prepare for upcoming features.

Bug fix

The bug causing calculated traits to be null or voided after upload is fixed.

Bulk update of harvest data is enhanced.

Updating harvest data in bulk for more than 2,500 plots or crosses is now delegated to the background. In the Harvest Data tab, select more than 2,500 records and then click the bulk update button (). A modal window pops up to show the total number of plots or crosses selected and the data updates to be done. When some records already have harvest data prior to the bulk update, the option to overwrite existing data is also provided via a modal window.

Proceed to update the harvest data in bulk. The UPDATE IN PROGRESS status is reflected as the update is done in the background. Once done, a notification () will be provided.

Bug fix

You can expect to encounter no errors when:

1. printing harvest labels for materials without cross-parent information, and

2. harvesting wheat plots whose seed names follow the user’s customized entry code, if applicable. Otherwise, the seed names follow the system default entry codes.