SM 2024

The user interface is upgraded.

Users of SM tools can now expect a better user interface in terms of overall style and responsiveness.

Bug fix

The sorting functionality on SM tool data browsers now work accordingly.

Messaging feature is enabled.

Request transactions now have a messaging feature () that logs the exchanges among users involved in the request. This can be accessed on the data browser, just beside the status column.

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New messaging feature

Processes surrounding request creation is improved.

The following improvements are implemented:

1. View selected marker groups. The data browser now shows the selected marker group/s for a request, instead of showing “(Not Set)”.

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   View selected marker groups

2. Updated status. A request’s status is reverted to APPROVED when the batch it previously belonged to gets deleted. Previously, the request retained the DESIGN GENERATED status even after the batch is deleted. When viewing () the details of the request, “Not Applicable” is reflected for the name and status of the batch it is linked to.

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   Updated status

3. View traits in ascending order. For ease of use, the available traits per trait category are now listed in ascending order as you complete the Service details of your request.

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   View traits in ascending order

Bug fixes

The following actions and processes can now proceed accordingly:

1. receive timely and relevant notifications, and

2. view marker groups by crop.

Changes to request details are reflected after batch deletion.

A request’s status is reverted to APPROVED when the batch it previously belonged to gets deleted. Previously, the request retained the DESIGN GENERATED status even after the batch is deleted. When viewing () the details of the request, “Not Applicable” is reflected for the name and status of the batch it is linked to.

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Updated request status

Selection of marker and assays is enhanced.

An improved user experience can be expected in the Service & Technology tab. Specifically, you can now:

1. View default marker and assay for fixed marker groups. For 1KRiCA, the marker and its assays are all selected by default. As such, these checkboxes will be grayed out and disabled.

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   Marker and assays for fixed marker groups are selected by default

2. Access pagination for markers and assays. The first 10 markers and assays are shown, while the rest can be accessed using the pagination feature.

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   Pagination for markers and assays

Bug fixes

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

1. View the correct set of action buttons beside a request, such that the accept and reject icons are not incorrectly shown, and

2. proceed to create a batch.

Management of a batch and its request/s is upgraded.

Lab managers can now expect a better user interface. The following improvements are implemented:

1. Selected marker panel is reflected. When viewing or updating the request/s in a batch, the selected marker panel/s are now shown as part of the requests' basic information found on the data browser, instead of showing “(Not Set)”. Additionally, this is also reflected on the summary section, whose background is colored in gray.

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   Selected marker panel is reflected

2. Service Provider and Technology selection is disabled. Once the batch is created, the lab manager is now restricted from changing the selected service provider and technology.

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   Service Provider and Technology selection is disabled

3. Vendor Controls. In the plate layout, the vendor controls are now correctly colored in gray.

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   Vendor controls

4. Intertek Vendor form. The SNP IDs are now reflected in the downloaded Intertek Vendor forms. The SNP IDs are based on the selected marker assays during batch creation.

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   Intertek Vendor form

5. Batch, plate, and sample codes. These codes act as identifiers for a batch, plate, and sample. The codes take into account the number of requests in the batch, the program type, year, and purpose, such that a batch whose request/s use the same program, year, and purpose will use those elements' initials. In contrast, when a batch contains requests with different programs and different purposes, the former uses the initials of the laboratory receiving the request, while the latter uses the “YY” code to denote different purposes. The batch, plate, and sample codes are also followed by the batch count, plate count, and first request ID.

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   Batch names

Data browser is improved.

The following improvements are featured in the tool’s data browser:

1. Status. To provide more information about a batch, a new column for status is now shown. This allows a more standardized workflow and look for the data browsers found across Service Management tools.

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   New status column

2. Delete icon. This action is now only allowed for batches with the DESIGN CREATED status.

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   Delete icon

Bug fixes

You can now proceed to encounter no errors when:

1. viewing and editing a batch, and

2. downloading the correct vendor form.

Management of marker information is enhanced.

The following features are improved:

1. User interface. On the Marker Groups tab, the columns for Trait Category, Trait, and Marker Group Name are now sorted in ascending order by default, while the view (), edit (), and delete () action icons are enabled alongside each marker as you edit a marker group.

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   User interface

2. Download markers. You can now expect to download () an accurate offline copy of the markers belonging to a marker group, including its associated data.

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   Download markers

3. Error notification. A more informative error notification is now reflected when creating a marker group name that duplicates an already existing one. Previously, users are only notified that the new marker group has not been created, instead of showing why there was an error.

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   Error notification

4. Marker FNR and FPR. The system now allows values between 0 to 1 for the FNR and FPR data fields when creating or editing a marker’s information.

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   Marker FNR and FPR

Bug fix

The column name for Chromosome is now spelled out for easier reference.

Service tab is improved.

When creating your genotyping request, the Services tab now displays additional data fields based on the purpose you select. There are three supported cases for this improvement:

1. Select marker group. For purposes such as genomic selection, additional fields will be loaded to allow you to select one or more marker groups. Simply tick the checkbox beside your preferred marker group/s.

2. Select trait/s. For purposes such as trait genotyping, additional fields will be loaded to allow you to select the trait category, trait, and marker group.

3. No additional fields to populate. For purposes such as sequencing, there is no required marker group or trait data to be selected. Simply click Next to move to the Review tab where you can finalize your request.

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Improvements in the service tab

Combine requests with different purposes into one batch.

Lab managers can now select and combine genotyping requests made for the same service provider/laboratory into one batch, even when their purposes vary. Also, lab managers can view and select other marker groups aside from the ones already associated to the request.

From the GSM data browser, select requests with different purposes but with the same service laboratory and proceed to Create a Batch. Select additional marker group/s in the Service & Technology tab and then Save Selection.

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Combine requests with different purposes into one batch

Editing plot or package lists is now restricted.

When lab managers edit a submitted request, the radio buttons in the Entry List tab’s data browser is now disabled. This is to prevent lab managers from changing the requestor’s selected entry list. A note describing this limitation is also reflected on the data browser. Previously, radio buttons were available in this data browser.

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Editing plot or package lists is now restricted

Batch creation is improved.

The process of creating a batch is now more intuitive. This feature is also improved through integration with Marker DB. Specifically, lab managers can now:

1. View selected marker group/s. In the Service & Technology tab, the marker group/s selected during request creation are now checked () by default. Also, lab managers can still revise the marker group selection during this step, depending on the chosen purpose.

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   View selected marker group/s

2. Update the request’s marker group. As you create a batch, you can now manage its marker group selection in the Service & Technology tab. Here, you can select or unselect marker groups and proceed to finalize the batch.

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   Update selected marker group/s

3. Select relevant service providers. In the Service & Technology tab, the Service Provider drop-down list now provides you with a list of providers applicable to the request made. For example, if a request has a marker group, only providers associated to the marker group will be available for selection in the drop-down menu.

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   Select relevant service providers

4. Select relevant technologies. In the Service & Technology tab, the Technology drop-down menu list now provides you with a list of technologies applicable to the service provider selected.

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   Select relevant technologies

5. Select relevant assays. In the Service & Technology tab, assays can now be selected after defining the technology. You can then proceed to Save the Selection. The selection of assays depend on the marker group associated with the request, where fixed panel groups will have assays selected by default indicated by a grayed-out checkbox.

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   Select relevant assays

6. Plate Layout. When designing the plate layout, the Plate Fill Direction is now set to “columns” by default. You can still set this to “rows” by clicking the drop-down menu. Also, you can expect the plate color for Intertek’s internal controls (H11, H12) to be green.

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   Plate layout

Bug fix

You can expect to encounter no errors when viewing all selected marker groups.

View marker group and assay information.

In the data browser, you can now view () the marker group and assay/s selected for the requests in a batch. This allows lab managers to view the marker groups and assays in a batch before sending it to the service provider.

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View marker group and assay information

Bug fixes

The following features are now working as expected:

1. viewing a newly created batch, and

2. uploading result files.

View and edit marker groups.

A marker group’s basic information, such as trait and trait category, is now displayed when viewing () and editing () marker groups via the data browser action icons.

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View and edit marker groups

Bug fixes

You can now expect to encounter no errors when:

1. viewing and editing the details of a request, and

2. viewing the program in the data browser, such that it is correctly populated.

Bug fixes

You can now expect to encounter no errors when:

1. viewing submitted requests in the data browser,

2. generating plates,

3. viewing and editing the details of a request, and

4. viewing the program in the data browser, such that it is correctly populated.

Positive controls are now reflected in the downloaded vendor file.

When assigning positive controls to a batch, the same is now used to denote the sample name found in the downloaded vendor file. This rectifies the previous use of “blank” to indicate positive controls.

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Positive controls in downloaded vendor files

Full names are now displayed in the data browser.

To maintain consistency across EBS data browsers, the RM data browser also displays the full name (Surname, First Name) of transaction owners. This is applied to the Requester and Modifier data columns.

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Requester and Modifier name format

Selection of individual markers linked to the same trait is enhanced.

Some traits have several markers associated with it. In this version, you can expect a better display of the markers available for each trait, such that you can easily select those that you require for your genotyping request. This feature can be accessed in the Services tab as you create your request.

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Selection of individual markers linked to same trait

Bug fixes

You can expect to encounter no errors when:

1. filtering the data browser,

2. viewing plot and package lists in the Entry List tab, and

3. downloading vendor files from the data browser.

Full names are now displayed in the data browser.

To maintain consistency across EBS data browsers, the GSM data browser also displays the full name (Surname, First Name) of transaction owners. This is applied to the Requester and Modifier data columns.

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Requester and Modifier name format

Bug fixes

You can expect to encounter no errors when filtering the data browser.

AgriPlex vendor files are improved for IRRI GSL use.

Lab managers and lab team members from the International Rice Research Institute’s Genotyping Service Laboratory (IRRI GSL) can now expect to download () AgriPlex vendor forms, whose formats subscribe to their requirement. These specific formats are used for the following data fields:

1. Plate ID: “GSL_B_< batch sequence number>”

2. Sample Name: “<sample sequence number>”

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Full names are now displayed in the data browser.

To maintain consistency across EBS data browsers, the BM data browser also displays the full name (Surname, First Name) of transaction owners. This is applied to the Creator and Modifier data columns.

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Creator and Modifier name format

Bug fixes

You can expect to encounter no errors when:

1. filtering the data browser,

2. creating a batch, and

3. deleting a batch, such that the notification is accurate.

Bug fixes

You can expect to encounter no errors when:

1. viewing the date of creation and name of creator in the main data browser, and

2. creating markers, such that the interface requirements conform with database requirements.