PerkinElmer Signals™ Notebook - What’s New

What’s New
This version 23.1 release of Signals Notebook brings improvements to bookmarks and the ability to get data into admin defined tables. Admins can now change the understanding and display of aromatic compounds on import. We have continued to make improvements to our ongoing Worksheets beta and have added new beta features for Inventory around deprecating amounts and calculating total amounts in Containers. Some of the existing beta capabilities for Materials are also now on general release and available to all administrators. Finally, we have also fixed a number of small bugs.


The following improvements are only available for users of Signals Notebook Individual Edition, Signals Notebook Standard and Signals Notebook Private Cloud

• Usability
• • –  Share bookmarks

The following improvements are only available for users of Signals Notebook Standard and Signals Notebook Private Cloud

• Chemistry
• • –  Convert mol or SMILES to aromatic or alternating single & double bonds
• Admin Defined Tables
• • –  Match columns on importing csv files
• Inventory
• • –  Scan Location Barcodes
  • –  Decrement Inventory containers from stoichiometry table (beta)
  • –  Total Amount in containers displayed in Materials (beta)
• Materials
• • –  Creation of lots/batches with the Material Table (beta)
  • –  Bulk export enhancements (available to all administrators)
  • –  Export of materials by ID (available to all administrators)
  • –  Bulk update of Materials (available to all administrators)
• Integrations & APIs
• • –  Convert export of mol files to aromatic or alternating single & double bond format
  • –  GET/Materials includes sequence field values for Primers
  • –  Endpoints for Worksheets
• Worksheets (beta)
• • –  Search of Worksheet properties
  • –  Number with unit fields

We also fixed several small bugs in this release. Details of the enhancements are described below.

The following OnDemand videos for Signals Notebook End Users are now available

• Adding to the Reagents Materials Library

Administrators should note we have updated our adherence to the SCIM standards. The field “displayName” for the ResourceType Group is now be required. Additionally the field “value” in the “members” multivalue attribute is also required. Any calls to SCIM endpoints in our public APIs will now require these values and will fail if the values are absent. Administrators should change their API calls to incorporate these values if these values are not already included.

Administrators should note that as part of the new bulk export enhancements we added a new Export Materials privilege. This privilege is enabled for the Standard User and System Administrator roles only. System Administrators can optionally add or remove this privilege from any role except the System Administrators role. New tenants will not have this privilege enabled for the Standard User role by default. This privilege was enabled in 22.10 but erroneously left out of the What’s New for that version.

Administrators are recommended to subscribe to the channels within our support news site found at https://informatics-support.perkinelmer.com/hc/en-us/categories/360004446171-Support-News which contains more information about releases and other pertinent product information.

This content is anticipated for release on our Production E3 environments, and for Private Cloud customers on our deferred release schedule, in July 2023.

Further Details

Usability

Users are now able to share bookmarked search queries with other users and groups of users in their tenant. If a user has a query/bookmark they want to share with other users or groups, they can select the “Share Search Query” option now available on their bookmarks under the “Manage Bookmarks” page.

The user can then select the groups and users they wish to send the search query.

The receiving user gets a notification with a link to the search query in their In-App notifications.

These notifications are currently In-App only and are not sent via email. They can be activated or deactivated by selecting the “In-App” option for “When someone shares an item with me” under the notification settings.

The receiving user can add the shared query to their own bookmarks by selecting the link in the notification to bring up the shared search query and bookmarking the search themselves.

The following improvements are only available to users and administrators of Signals Notebook Standard and Private Cloud and are unavailable as part of Signals Notebook Individual Edition.

Chemistry

Administrators can now define that chemical structures containing delocalized rings, imported from mol or SMILES formats, can be converted from aromatic to alternating single and double bond representation, or visa-versa. This setting will be applied to structures pasted into a ChemDraw document that are in SMILES or mol format, or when structures are imported via SDFile. The setting will not apply to imported cdx or cdxml files.

For example if the setting is changed to “Alternating Double/Single Bonds”, pasted or imported SMILES strings or mol files that have an aromatic representation will be converted to display in alternating single and double bonds.

Admin Defined Tables

Upload csv to ADTs has been improved to accept data in hidden ADT columns and allow for mapping of columns if columns in the csv cannot be automatically mapped to columns in the ADT.

Csv columns are mapped automatically based on column name, order and data type. If the csv has columns that cannot be automatically, a modal pops up allowing the user to manually map the unmapped columns.

If the user does not map all of the columns and opts to import the csv without all columns mapped, only mapped columns will import.

Inventory

Users can now scan the barcode of a location in addition to the name type ahead. User can toggle between the barcode scan icon and the location icon to choose which to select the location:

The scan of the location barcode is in all the workflows where the location is required.

Materials

Enhanced bulk export capabilities are now available to all systems without request. This enables export of up to 5000 items from the Materials Smart folder. There is now the ability to export by Asset or Batch. Previously users were restricted to export of 50 items at the Asset level and the export included all batches.

There is also a new option to export a CSV of Compounds or Reagents (SNB). This export will include IDs and properties but will not include any chemistry data.

If the user leaves Signals Notebook during the export process they may retrieve downloads from the Bulk Export section of the Materials Bulk Results, accessed from the user menu. Note that a maximum of 50 results will be stored in the system and results will be stored for only 60 days before being purged from the system.

The Export by ID feature is now available to all systems without request. Users can submit a list of Material IDs for a given library to retrieve the download.

IDs must come from a single library but can include Asset or Batch ids for a given library. Compounds and Reagents (SNB) libraries can be downloaded as an SDF or CSV.

Bulk update of materials is now available to all systems without request. The update applies to a single type of Material per action and must include IDs that map to existing materials. The user selects fields to update after including an appropriately formatted CSV file. There is also an option to clear non-required fields during the update.

Bulk updates will include reports under the Materials Bulk Results. A file can be downloaded to understand why any updates were unsuccessful. Up to 50 results will be saved in the system and all results older than 60 days will be automatically purged.

Integrations & APIs

We have enhanced our API endpoints that allow export of structures in various chemical formats to allow conversion to either aromatic or alternating single and double bonds. The aromaticRepresentation parameter applies to endpoints such as GET/stoichiometry/}eid}/{rowid}/structure. The parameter applies only when exporting to mol or SMILES formats.

The GET/materials/{eid}/properties endpoint has been enhanced with a parameter to include sequence information in the response. This enrichSequence parameter will allow the sequence property type data to be included in the response from libraries that utilize this property. This does not apply to when the sequence is determined from adding a sequence based file.

We have also added a GET/worksheet and PATCH/worksheet endpoint. These endpoints will be visible regardless if you have activated the Worksheets beta but will not be usable without having done so.

The following capabilities are in beta and are only available to users and administrators of Signals Notebook Standard or Private Cloud upon request. Please contact your account representative or our support team if you would like access to the following features. They are unavailable as part of Signals Notebook Individual Edition.

Inventory

Users will now be able to decrement amounts from Signals Inventory containers from the stoichiometry table. Note: This functionality is not available in Parallel Experiments.

Administrators will notice that the Inventory Decrement column is available in the Chemistry Settings and hidden by default. The Clear value when element is copy-pasted is permanently defaulted to be checked. Administrators can make appropriate adjustments depending on if Signals Inventory is in use:

When users add Material or Sample containers to the Chemical Drawing, the Inventory Decrement cell will be available. When users type an amount into the Inventory Decrement cell, the amount will automatically be deducted from the container. Users will see a green checkmark in the bottom of the table. If the incorrect unit is used, the user will see a red x in the bottom of the table and will need to correct the action for the correct decrement to be completed.

Previous to typing an amount into the Inventory Decrement cell, the container had 0.5 g, the Current User was Unassigned and the Status was AVAILABLE:

After typing into the Inventory Decrements the container amount is updated, the Current User is changed to the signed in user and the Status changes to “IN USE”.

If the decrement typed is larger than what Inventory has recorded, the user will be able to complete the decrement, but the container will automatically have the Status set to EXHAUSTED:

If the user deletes the row or the drawing and has a value in the Inventory Decrement field, a warning will appear:

If the user closes the experiment but forgets to type a value into the Inventory Decrement, they will get a warning. Users can continue and close the experiment or cancel out and go back and update the amounts in the Inventory Decrements:

Users will also now see the Total Container Amount of a Material reported on the Material’s details page. The total amount is reported as a sum based on the unit type selected. For example, if the material has containers in both mass and volume, the amount total will add all the mass containers and report it in grams. The same is true of volume and the total will be reported in milliliters:

Count will be reported as a number with no units. The Total Amount per Lot or Batch is reported in the Container Amount column on the Batch/Lot page:

Containers that are in the Exhausted, Disposed or Final Disposed status will not be counted in the Amount Total. Containers in the Disposed or Final Disposed Status will no longer show by default in the expanded container view:

To view disposed containers or to hide empty columns use the filter icon in the top right corner of the table:

Materials

With the beta feature enabled it is possible to use Materials tables configured for registration to also create batches/lots of an existing material. This is possible for all Materials with Asset/Batch configuration, including Compounds and Reagents (SNB). Admins must first enable a given Material Table for registration or batch creation:

To create a new batch of any given material, users must first add a valid item to an existing Materials table. The user will then see a new option to create a batch/lot from the menu item next to the item ID.

A modal will then open and allow the user to enter metadata and specify the number of batches to create.

Once completed, the batches will appear in the Materials Table with IDs. Note, Compounds and Reagents (SNB) cannot be edited from the materials table. To update values after creation the user will have to navigate to the individual batch in the Materials Smart Folder.

Worksheets

We have enabled search on Worksheets. Worksheet elements can be retrieved via searching for Type=Worksheet. Additionally the properties filled in within worksheets can also be searched, each property is prefixed with “Worksheet”.

We have added a new property type for numbers with units. Administrators can now define united number fields in Worksheets, whereby they select the property type, select the measure type, such as mass, and can define a default unit, such as grams.