Revvity Signals Research Suite - 2024 Updates
The Signals Research Suite is a complete, integrated data capture, processing & analysis SaaS software for scientific research. Capture, manage, and share experiment data, notes and research findings in a secure and accessible environment built on the foundation of Signals Research Platform.
Releases By Year
What's New
This version 24.4 release of Signals brings new ways to find content, including new smart folder views to enable organization and recovery, and a new search facet to retrieve content by the system template used in creation. We have improved chemistry handling in ChemDraw documents especially around biomolecules drawn using the HELM notation standard. Administrators can now add a new “Sign and Keep Open” option that requests reviewers, and define External Actions on Plate Containers. Our previously beta capabilities around plate templates, container search tables and child materials are now available to all systems. We have added new beta capabilities for around Normalized Compounds, Internal requests and web based Spotfire access, the latter is only available under licenses of Signals Research Suite. Finally, we have also fixed a number of small bugs.
The following improvements are available for users of Signals Notebook Individual Edition, Signals Notebook Standard, Signals Notebook Private Cloud, Signals Research Suite Standard and Signals Research Suite Private Cloud. Certain features may only be available with appropriate licensing and/or with enablement by an administrator.
• Fundamentals
– Now” option added to calendar picker for Date/time properties and search
– Option to edit and view Spotfire Files and Inventa Analysis Objects in your web browser (beta)
– Adding a Spotfire File creates a blank Analysis file (beta)
– Smartfolder Table View
• VitroVivo
– Revised Cohort Definition Step in Study Designer
• Chemistry
– Labels are now hidden when monomers are expanded
– A cursor displays where a new structure will be drawn when in HELM editing mode
– Improved click selection behaviors for expanded monomer structures
– Definition line of a FASTA DNA/RNA sequence added as an annotation when pasted into a Chemical Drawing
– Flip structure
• Variation Tables
– Improved data entry in Horizontal and vertical summary views
• Plates
– Plate Templates available to all systems
• Inventory
– Container Search Table available to all systems
– Container Search Table export and update to column widths
– Internal Request of Materials with Aliquot (beta)
– Bulk Print Container Barcode
• Materials
– Creation of Child Replicate Materials available to all systems
– Creation of Child Materials from Materials Smart Folder available to all systems
– Calculated properties for Protein Materials
– Normalized Compounds (Beta)
• Search
– Search for objects by System Template used
• Administration
– “Sign and Keep Open” option for Reviewers
• Integrations & APIs
– POST /entities/{eid}/children/{filename} now allows you to specify a layout page to attach to
– GET /plates/{plateContainerId}/plates/{id} now contains the PlateID as an attribute
– PATCH /plates/{plateContainerId}/plates/{id} allows for updating of PlateID attribute
– A new endpoint has been added to update the status of a Container
– External Actions can now be created for Plate Containers
We also fixed several small bugs in this release. Details of the enhancements are described below.
The following OnDemand videos for Signals Notebook Administrators are now available:
• Variation Tables – Building initial formulation or mixture template
Developers in Signals Research Suite should note that a pagination limit has been added to the Signals Data Factory public and primary APIs.
Developers in Signals Research Suite should note that the Data Factory endpoints GET /maps and POST maps/search have changed the “created” and “updated” metadata fields to “createdBy” and “updatedBy”, respectively. Two new metadata fields, “createdAt” and “updatedAt” have also been added.
Administrators should note that we have changed the requirements around the unique naming of notebooks in a future release. Notebook name uniqueness is now case sensitive, and hence names differing only in case will be allowed. This behavior only applies for when Global Numbering is not enabled for notebooks.
Developers in Signals Notebook and Signals Research Suite should note that the endpoints GET /attributes/{eid} and PATCH /attributes/{eid} will now only return the "counts" object in the "attributes" object if a new query parameter is specified.
Developers in Signals Notebook and Signals Research Suite should note that Inventory will be updated to give more meaningful error codes, the error codes provided via the External API will now better align the API with the user interface, specifically regarding 4xx (400, 409 and 412) error codes. This change will be made in a future release. The following codes will now be returned: 456 (BARCODE_IN_USE), 457 (INVALID_COORDINATES), 458 (NAME_IN_USE), 459 (TYPE_NOT_EDITABLE), 460 (ANCESTOR_NOT_EDITABLE), 461 (PROPERTY_OR_FIELD_NOT_EDITABLE), 462 (ENTITY_IN_USE), 463 (NOT_A_GRID),464 (INVALID_TYPE), 465 (CONTAINER_NOT_DISPOSED), 466 (CONTAINER_DISPOSED_OR_FINAL_DISPOSED), 467 (TYPE_NOT_SUPPORTED), and 468 (VALUE_OUT_OF_BOUND).
Administrators are recommended to subscribe to the channels within our support news site found at https://support.revvitysignals.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 November 2024.
Further Details
The following improvements are available for users of Signals Notebook Individual Edition, Signals Notebook Standard, Signals Notebook Private Cloud, Signals Research Suite Standard and Signals Research Suite Private Cloud. Certain features may only be available with appropriate licensing and/or with enablement by an administrator.
Fundamentals
The calendar picker used for Date/Time properties now contains a “Now” option to facilitate the entry of the current time/date into the field. This option is also available in the calendar entry screen for search queries on time/date based properties.
The new Grid view option from Inventory Containers is being expanded to the Smartfolders in Signals Notebook. To utilize the new grid view users can select the new view icon. Users can select which properties are shown using the “Show/Hide” property picker.
Filters can be added to the side bar as normal or columns can be filtered by selecting the column and entering the filter value. Once added the filter will also appear on the side “Filter” bar.
Columns can be reordered by drag and drop. As with the card view the first 20 items are loaded with the option to “Show More” available at the bottom.
The grid view will now be available for Materials, Samples, Experiments, and Parallel Experiment Smartfolders.
VitroVivo
Strain and Gender information for animals must now be entered in the Cohort Definition step within the Study Designer. Regarding Strain, users can either select a value from a drop-down list or input a new value directly into the field. Gender can be selected from pre-configured options available in a drop-down menu. These updates eliminate the need to predefine Gender and Strain values in study templates.
Chemistry
Several usability enhancements are available for working with HELM structures. When monomers are expanded, the expanded monomer labels will now be hidden. In addition, when monomers are expanded there is improved click selection behavior. Double clicking on a bond or atom in a monomer will select that monomer. An additional double click will select the entire sequence.
When using the HELM editing tools, a cursor now indicates where a structure will be drawn prior to adding any monomers.
When pasting a DNA or RNA FASTA sequence with header into a Chemical Drawing, either directly or via the Text tool of the HELM Editor, the FASTA header will appear as an annotation.
There are two new tools available that allow users to flip structures horizontally or vertically.
Variation Tables
“Tab” can now be used to navigate around the Horizontal and Vertical Summary views to aid in systematic data entry. “Tab” will move to the equivalent field for the next Variant, or if the final Variant, to the next row in the first Variant. Shift-Tab will reverse the behavior.
Plates
Plate Templates is now available to all systems.
Inventory
The Container Search Table is now available to all systems.
Container Search Table update to column widths, users can hover over the line between the column headers to adjust the size of the column to fit the data:
The Container Search Table also now supports export. For users to export containers, they need to have a User Role that allows for the Export Containers privilege.
When exporting, if only a subset of containers are selected, only those rows will be exported. The export will only include the columns selected to be shown in the table.
If no rows are selected, the export will include all containers up to 600K, and only the selected/shown columns:
When the export is done, a notification will appear at the bottom of the screen and in the bell near the user name:
If the report is needed later, it can be found under the user name/Inventory Bulk Results/ Bulk Container Export. Files are saved for 30 days and then removed from the list.
Bulk Print container barcodes option is available on the bulk action Inventory page:
Materials
Admins may now configure calculated property fields for protein type Materials. The values will appear on the Material focus pages and can be added to Materials tables once configured. The values will be associated with the Asset level of the Material and calculated from the Materials amino acids.
Values are calculated when a Protein Material is registered or edited.
The creation of child replicate materials, previously available in beta, is now available to all systems.
The creation of child materials from the focus page of a parent material, previously available in beta, is now available to all systems.
Search
Objects can now be found by specifying the System Template used to create them. An “Origin Template” facet has been added to search. This will allow the user to search for an object by the name of the system template used to create it.
Administration
A new workflow option call “Allow add Reviewers and Keep Open” is now available. This option allows for a user to add reviewers without changing the state of the experiment type object (experiment, parallel experiment, or ADO).
The option can be enabled by selecting the new checkbox under Signing Settings and enabling the associated privilege.
Once enabled a user will be able select “Add Reviewers and Keep Open” under the Signing page. Users can add reviewers and continue working.
Integrations & APIs
The POST /entities/{eid}/children/{filename} endpoint has been enhanced to allow posting an attachment to a specific layout page.
Entity pages pageId’s are accessible through the following endpoint: GET /entities/{eid}/layout/pages
Endpoints for Plates have been enhanced to provide programmatic access to each plates “Plate ID” field.
The GET /plates/{plateContainerId}/plates/{id} and /plates/{plateContainerId}/plates now contain the “plateId” as an attribute of an individual Plate in the API response.
The PATCH /plates/{plateContainerId}/plates/{id} has been enhanced to allow updating of the “plateId” attribute as part of the request body. Example body below:
A new endpoint, POST /inventory/containers/{containerId}/status/{action} has been added to change the status of a Container. The accepted actions are dispose, finalDispose, restore, checkout and checkin.
External Actions can now be created for Plate Containers. For GET submit methods the URL parameter will contain the PlateContainers entity ID. For a POST the body will include basic details of the Plate Container.
The following capabilities are in beta and are only available to users and administrators of Signals Notebook Standard, Signals Notebook Private Cloud, Signals Research Suite Standard and Signals Research Suite 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.
Fundamentals
Users now have the option to edit and view Spotfire Files and Inventa Analysis Objects within their web browser. Spotfire Online requires no installation, is Mac compatible, and opens in a new browser tab.
Adding a Spotfire File creates a blank Analysis file (previously loaded a local file). Inventa Analysis Object now allows the option of choosing the opening method on creation (previously opened automatically in the locally installed Analyst).
The locally installed Spotfire for Signals Analyst is still available and is the suggested option for designing & creating advanced dashboards & workflows from scratch.
Inventory
Users with View access to Materials can make Internal Requests for a Material or a Material with the Batch/Lot specified.
Once the form has been filled out, the user will get a confirmation with a link. Users that create the Internal Request can edit them. Admins can edit if the Security Policy is set appropriately.
Users can also similarly request containers or Samples.
For Containers the form will be populated with both Material and Container information. For Samples the Sample information will be filled.
Inventory or System Administrators will be able to fulfill Internal Requests. Internal Requests can be fulfilled directly from the Internal Request object. All the required information will autofill and the administrator can Cancel or continue the Fulfill whereby the status will be updated to Fulfilled and the Location, Current User and Status will be updated.
If the Internal Request was for a Material or Material with Batch/Lot, the request will need to be updated to have a container associated. The administrator can select from a list of available containers.
If an Aliquot should be created, the Aliquot Container workflow can be initiated. A warning is provided if insufficient material exists to create the aliquot. Once the Aliquot(s) have been created, barcode(s) may be printed. The parent Container will also be updated.
The Internal Request will initially go to a Pending status to give the administrator time to determine when the request will be fulfilled/delivered to the requestor. The status can be further updated to Fulfilled. Internal Requests can be fulfilled in bulk in the Material Requests Table. Requests that have associated containers and do not require placement in a grid location will be fulfilled. Updating Status to Pending, Submitted or Canceled do not require containers and will work for grid locations. Requests in the Fulfilled status over 30 days old will be removed from the table.
Containers not associated with an Internal Request can also be Aliquoted. Navigate to the container to be aliquoted, define the amounts to be placed in each aliquot and print barcodes.
The child container(s) will have a new Container Property, Parent Container that is auto filled:
Materials
A new Material Library type called “Normalized Compound” is now available upon request. This new library type allows for a Salt Stripped or “Normalized” structure to be stored on the Asset level and the raw structure (or Salt form) to be stored on the Batch level.
In the administrator interface SN Config, an admin can create a “Normalized Compound”- type library by creating a new material type and selecting Normalized Compounds.
The Admin can define uniqueness rules for the structure that will apply for both the asset and batch level structures and select properties on the asset and batch level that can be used for uniqueness checking.
The structure option appears on both the Asset and Batch level record definition.
The Normalized Compound Material type comes with an out of the box Salt Stripper. To utilize this Salt Stripper during registration, the Admin must ensure that SMILES have been loaded in the Salt table on the SN Config.
If the Salt SMILES have been loaded, when the user goes to register a new material with a salt to the new Normalized Compounds library, the CDWS Salt Stripper will automatically recognize the presence of the salt. The stripped/normalized structure will be returned on the Asset level and the stripped salts will be added to the Salts table on the batch level.
On the registration modal the user will be able to review the normalized structure, the salt form at the batch level, and the stripped salts prior to registration. When they hit Register, the Normalized structure with undergo uniqueness checking against all other registered Asset level structures in the library, if a match is found, the user will be able to either use the match or treat as unique. If the user selects “Use Match”, the Batch level structure will undergo uniqueness checking against all other batches in the chosen asset.
If a match is found the user will be prompted to either use the match or treat as unique. If the user elects to “Use Match” the new batch will be registered under the same Batch Type as the selected match. If the user opts to treat the batch as unique, the batch will be registered with a new Batch type.
On the Material page users will have a preview of the Batch Structure visible.
What's New
This version 24.3 release of Signals brings a series of enhancements to the ChemCharts in Signals Inventa. We have also improved the Variation Table summary views and made this capability available to all systems. We have also made all of a series of improvements around Internal reference fields available to all systems. We have continued to work on our ongoing beta capabilities for the inventory container search table and new beta capabilities around creating Tasks and other Materials from Materials. Finally, we have also fixed a number of small bugs.
The following improvements are available for users of Signals Notebook Individual Edition, Signals Notebook Standard, Signals Notebook Private Cloud, Signals Research Suite Standard and Signals Research Suite Private Cloud. Certain features may only be available with appropriate licensing and/or with enablement by an administrator.
• Fundamentals
– Type or paste of internal references available to all systems
– Mapping CSVs with Internal references to tables available to all systems
• Inventa
– Redesigned Admin Configuration of Inventa Entities and Measurement Types
– Advanced HELM visualizations and analytics with ChemCharts
– ChemCharts Data Functions for Biological Sequence annotation
– New query and data summarization tool, the Integrated Summary App (beta)
• Variation Tables
– Horizontal and Vertical Summary views available to all systems
– Choose Component properties for display in Vertical Summary view
– Updated preview view
• Inventory
– Container Search Table (beta)
• Materials
– Bulk uploads of Materials with internal references available to all systems
– Bulk updates of Materials with internal references available to all systems
– Creation of Child Replicate Materials (beta)
– Creation of Child Materials from Materials Smart Folder (beta)
• Tasks and Requests
– Assign an Analyst during Task Creation and from the Task Container (beta)
– Create Tasks from Materials in Experiments (beta)
– Notification for Task creator regarding assigned analyst access (beta)
– Notification for Analysts when assigned a Task (beta)
– Create an Experiment from a Task Container (beta)
• Administration
– User Access events in Admin Audit trail will capture origin and proxy IP address
• Integrations & APIs
– Inventa/SDF Maps Public API
– POST /entities endpoint when creating Task now matches the UI behavior
– POST /entities endpoint when creating a Worksheet allows for a Name to be specified
– A new endpoint has been created to export all content of an Entity and its children
We also fixed several small bugs in this release. Details of the enhancements are described below.
The following OnDemand videos for Signals Notebook Administrators has been updated
• Attributes - How Best to Apply and Utilize
Developers should note that the primary APIs available for Signals Data Factory are being modified and ultimately deprecated in Signals Research Suite. Where relevant these primary API endpoints are being replaced as needed with public APIs available via the Data Factory Swagger page. If you currently use these primary APIs on Signals Research Suite, please contact our Support for further guidance.
Administrators should note that when using Import Maps in Signals Data Factory, attributes no longer use attributeName as the name, but instead simply use name.
Developers in Signals Notebook and Signals Research Suite should note that the endpoints GET /attributes/{eid} and PATCH /attributes/{eid} will soon only return the "counts" object in the "attributes" object if a new query parameter is specified. This change will be made in a future release.
Developers should note that the POST /entities endpoint has been updated for creating Tasks. This update aligned the API behavior to match that of the UI, specifically regarding the display of columns for Task properties when adding Tasks to the Task table. Task tables will now always unhide the columns for properties defined in the new Task's associated Task Template, all other property columns will remain in their current state.
Administrators should note that we are changing the requirements around the unique naming of notebooks in a future release. Once this change is delivered, notebook name uniqueness will be case sensitive, and hence names differing only in case will be allowed. This behavior only applies for when Global Numbering is not enabled for notebooks.
Developers in Signals Notebook and Signals Research Suite should note that Inventory will be updated to give more meaningful error codes, the error codes provided via the External API will now better align the API with the user interface, specifically regarding 4xx (400, 409 and 412) error codes. This change will be made in a future release. The following codes will now be returned: 456 (BARCODE_IN_USE), 457 (INVALID_COORDINATES), 458 (NAME_IN_USE), 459 (TYPE_NOT_EDITABLE), 460 (ANCESTOR_NOT_EDITABLE), 461 (PROPERTY_OR_FIELD_NOT_EDITABLE), 462 (ENTITY_IN_USE), 463 (NOT_A_GRID),464 (INVALID_TYPE), 465 (CONTAINER_NOT_DISPOSED), 466 (CONTAINER_DISPOSED_OR_FINAL_DISPOSED), 467 (TYPE_NOT_SUPPORTED), and 468 (VALUE_OUT_OF_BOUND).
Administrators are recommended to subscribe to the channels within our support news site found at https://support.revvitysignals.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 2024.
The following improvements are available for users of Signals Notebook Individual Edition, Signals Notebook Standard, Signals Notebook Private Cloud, Signals Research Suite Standard and Signals Research Suite Private Cloud. Certain features may only be available with appropriate licensing and/or with enablement by an administrator.
Fundamentals
The ability to type or paste internal reference values, previously released in beta, is now available to all systems.
The ability to map internal reference values during CSV import to tables, previously released in beta, is now available to all systems.
Inventa
Data Factory’s entity and measurement type setup has been redesigned to streamline configuration.
A dedicated All Measurement Types section provides a sortable list of measurement types that can be filtered by admin-defined tags
Endpoints, Experimental Factors, and Annotations can all be directly assigned from the Measurement Definition page
The Organizational Hierarchy and Endpoints now leverage a completely revamped and interactive Expression Canvas
The ChemCharts Data Functions have been enhanced for Biological Sequence annotation.
Four new data functions support the removal of sequence gaps and annotation of sequences based on custom motifs, defined regions, or antibody liability sites
Advanced HELM visualizations and analytics have been added to ChemCharts.
HELM sequences can now be rendered in ChemCharts Tables
HELM rendering can be converted to a sequence like representation that supports annotations
Monomers or annotations can be hovered over to display more information, with details extracted from the Signals Monomer Library
HELM-specific data functions have been introduced to support analysis of HELM sequences. Users can perform sequence alignment, sequence search, similarity search, translation, polymer extraction, and property calculations. An example of the advanced HELM sequence search panel is shown.
Variation Tables
All variants will also now be selected for the Summary Tables unless otherwise unselected and the settings saved.
The administrative Preview and Try It Out views for Variation Tables are now available via the Preview button. This experience, which matches the experience for Worksheets, allows greater availability of the screen for definition of the tables.
The Horizontal and Vertical Summary views are now available to all systems.
The Vertical Summary view now also allows inclusion of Component properties for display. These can be selected from the “Select Properties for Display” popup.
Materials
The ability map internal reference values during bulk import or bulk update of Materials, previously released in beta, is now available to all systems.
Administration
Access events in the Admin Audit trail will now record both the Originator and Immediate IP addresses when the user is accessing Signals Notebook indirectly, such as via a proxy server. This is common when a given organization uses a third party web gateway application, and that application does not remove the originator IP address. In such cases the audit trail will reflect that a given user accessed from the origin IP address via the proxy IP address. Any intermediate IP addresses are not shown.
Integrations & APIs
Data Factory public API endpoints for creating, retrieving, and deleting maps are now available
Task creation behavior when utilizing the API has been updated to match that of taking the same actions via the UI.
The POST /entity endpoint has been enhanced for Worksheets. Developers may now specify a name to give to the worksheet as part of the request body when creating the new worksheet via API. This will overwrite the “name” attribute which by default is from the entities template.
This release contains a new set of asynchronous API endpoints to facilitate the bulk export of all an entities content, including its children and their respective content.
The new endpoints function as follows:
POST /entities/export/bulk/: This endpoint initiates the bulk export process for a specified entity. There are query parameters to specify if you want only the entity, the entity and its child entities, or the entity, its child entities and all their child entities. There are additional parameters to specify data types for chemical/stoichiometry formats. The request returns a Job ID for checking the status.
GET /entities/export/bulk/{jobId}: This endpoint allows users to check the progress of the export process. It provides real-time updates on the status of the export request.
GET /entities/export/bulk/{jobId}/contents: Once the export process is complete, users can use this endpoint to download a boundary separated .dat file.
The first part of this .dat file is a JSON object representing the table of contents of an experiment. It includes information about the experiment and its children, such as their eid (Entity ID), name, content type and content part for easily finding the specific content in the file.
The subsequent parts contain the actual content referenced in the table of contents separated by a boundary marker.
The following capabilities are in beta and are only available to users and administrators of Signals Notebook Standard, Signals Notebook Private Cloud, Signals Research Suite Standard and Signals Research Suite 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.
Inventa
We have added a new query and data summarization tool, the Integrated Summary App. The Integrated Summary App (ISA) provides a new approach for querying and summarizing data compared to the Global Search and SAR Analysis apps. The ISA has a more intuitive search interface that is further simplified by administrator configuration.
Administrators can set summarization methods per attribute within Data Factory. They can also define which attributes should be displayed by default in the downstream user search interface.
Signals Research Suite users can launch the new app from the Inventa Dashboard
Users first specify a Data Factory Project to query and define any entity attribute criteria. To add a measurement type to the query, users browse a flat list of measurement types organized by admin-defined tags.
Once added to a query, users are shown a table of pre-selected attributes, where they can specify search criteria.
A summary of the query criteria is available for immediate review, along with an exact preview of the layout and columns that will be returned
Once downloaded, attribute data is summarized based on search criteria and organized by clear headers. Optionally, the individual measurement tables can also be downloaded and even automatically organized into a single, comprehensive data table.
Inventory
Container Search Table was updated to allow search by Chemical Structure to find containers:
Materials
We have extended the ability to create child materials with new options from Materials Tables and the focus page of materials. When a user creates a child material of the same type as its parent, they will have the option to copy certain parent fields to the child material and to target the child material to the same table as the parent material. Previously a user would have to target the child material to an existing or newly created table.
When the user selects “Copy parent data” the next screen will allow them to choose some or all the fields available for copying. Note that not all fields from the Materials Table are available for copying to the child material.
Once created, the user may add additional data and register the new child material.
Users may now also create a child material from the Materials Focus page, previously this option was only available from the Materials Tables.
For Materials with Asset/Lot hierarchy, users will be asked to choose a parent lot for creation of the child and for self-replicates they will choose if they would like to copy data.
The user is then directed to a modal to populate meta-data of the child material with the parent link automatically populated. Once the user registers the new child Material, they will either go through duplicate resolution or end on the focus page of the newly created child material.
Tasks and Requests
When creating a task, it is now possible to assign an analyst during the process. If the option to assign an Analyst during task creation is taken the created tasks will be automatically have a status of submitted.
Tasks may be created and assigned directly from a Materials Table in the same Experiment. The status of the created task is dependent assignment of an Analyst at the time of creation.
Tasks can also be assigned after their creation directly from the Task table. It is also possible for the assigned analyst to directly create an experiment from the Task table.
Analysts can now receive email and in-app notifications when they are assigned a Task. The notifications are set under the User Settings menu.
What's New
This version 24.2 release of Signals brings a redesigned Study Designer App to Signals VitroVivo, updates to Inventory including new label templates, and a URL redirect capability for text elements. We have continued to work on our ongoing beta capabilities for the Inventory Container search, and added a beta capability to Variation Tables to provide summary views of the data. Prior beta capabilities for Variation Tables and Plate Autolayout are now available to all systems. Finally, we have also fixed a number of small bugs.
The following improvements are available for users of Signals Notebook Individual Edition, Signals Notebook Standard, Signals Notebook Private Cloud, Signals Research Suite Standard and Signals Research Suite Private Cloud. Certain features may only be available with appropriate licensing and/or with enablement by an administrator.
• Fundamentals
– URL redirect in text elements
• VitroVivo
– Redesigned Study Designer App
– Updated end-to-end workflow to support Treatment Groups
• Chemistry
– Attach Data to annotate compounds and populate mol file SGROUP data
• Variation Tables
– Admin definition of Variations Tables available to all systems
– Admin definition of Auto Naming for Variants available to all systems
– End user addition of Variations Tables available to all systems
– Horizontal and Vertical Summary views (beta)
• Plates
– Additional Concentration units
– Plate Autolayout available to all systems
• Inventory
– New Label Templates for Containers
– Container Search Table (beta)
– Update to Advance Search Filters
• Integrations & APIs
– SDF Project Load Public API
– External APIs for Variations Tables
– POST Materials Table
We also fixed several small bugs in this release. Details of the enhancements are described below.
Administrators should note that we are changing the requirements around the unique naming of notebooks in a future release. Once this change is delivered, notebook name uniqueness will be case sensitive, and hence names differing only in case will be allowed. This behavior only applies for when Global Numbering is not enabled for notebooks.
Developers should note that the POST /entities endpoint is being updated for creating Tasks. This update is to align the API behavior to match that of the UI, specifically regarding the display of columns for Task properties when adding Tasks to the Task table. Task tables will now always unhide the columns for properties defined in the new Task's associated Task Template, all other property columns will remain in their current state. This change will be made in a future release.
Administrators and users are reminded that we are in the process of transitioning to new URLs for accessing the application. The new access URLs have been available since early December, we intend to remove the original URLs at the end of March. We encourage you to update relevant bookmarks and start transitioning to using the new URLs if you have not done so already. If you would like the original URLs to be removed prior to the end of March, please contact our Support team (https://support.revvitysignals.com/hc/en-us/requests/new). Further information on the ongoing changes to our URLs and the potential actions you may need to take can be found here: https://support.revvitysignals.com/hc/en-us/articles/20264670846740-Signals-Notebook-Upcoming-domain-changes.
Administrators are recommended to subscribe to the channels within our support news site found at https://support.revvitysignals.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 2024.
The following improvements are available for users of Signals Notebook Individual Edition, Signals Notebook Standard, Signals Notebook Private Cloud, Signals Research Suite Standard and Signals Research Suite Private Cloud. Certain features may only be available with appropriate licensing and/or with enablement by an administrator.
Fundamentals
If a user has inserted a direct hyperlink that uses the previous tenant URLs (using a Revvity Signals based string) into a text element and a user clicks on that link, a popup will prompt the user to continue to the new Revvity URL. This redirect applies if the local environment is in a revvity domain, the two environments correspond (example: revvity prod to Revvity signals prod), the tenant name is the same, and the URLs are true URLs (http(s)://….).
VitroVivo
Users can now use the redesigned Study Designer App to define animal cohorts (e.g., Male or Female cohorts, Wild Type or Transgenic cohorts), specify treatments and create treatment groups by associating cohorts with treatments.
In vivo applications, including Dose Preparation, Baseline Capture, Sequence of Events, Sequence File Generator, Mass Spec, Dose Verification and PK Parameters Apps, have been revised to support Cohorts and Treatment Groups. Updated In Vivo Apps will now include representations of cohorts and their associated treatment groups in data visualizations.
Chemistry
Chemists can now annotate part of their molecule using the “Attach Data” capability. This will allow annotation of a label to a specific part of a drawn molecule. If the structure is subsequently exported to a mol file, the annotation will be included in the SGROUP portion of the file.
Variation Tables
The definition of Variation Tables and their use by end users, previously released in beta, is now available to all systems.
Plates
Users can now select density units (e.g., ng/mL, mg/mL etc) from the list of Units available within the Concentration annotation layer.
Inventory
There are two additional label templates for containers to choose from: 60 x 40 mm and 150 x 65 mm with QR code and space for larger GHS Hazard pictograms:
Update to Advance Search Filters: Users can change the Parent, Child or Self options on a per row basis within an AND or OR query box:
Integrations & APIs
The new Data Factory API endpoint, POST projects/{projectId}/datasets/{projectId}/actions/load supports initiating a “loadAll” or “loadNew” job for a given project ID.
The POST /entities endpoint has been enhanced to allow the creation of Materials Tables for specific for specific Material Libraries.
Additionally, API endpoints for Variants Tables are now available. Existing Entities endpoints have been enhanced to include Variations tables as appropriate. Notably POST /entities has been enhanced to allow for creation of Variants Tables.
Along with the above enhancement there are a set of new endpoints specific to Variants Tables. There are three main groups of endpoints: Adding/Removing/Copying new variants to a Variants Table, Adding/Removing/Updating the content of the component table, and Updating the content of individual variant tables.
The following endpoints are used to fetch, replace, and update a Variant Table’s variants.
PATCH /variationsTables/{eid}: Used for adding, deleting, or replacing variants in the Variations Table.
PUT /variantsTables/{eid}: Used to replace the contents of both the component table and variant table(s) simultaneously. This is used only to replace the existing tables. This is not used to create new variants.
The following endpoints are for fetching, adding, and updating the rows in the component table of the Variations table:
PATCH /variationsTables/{eid}/components: Updates the entire component table, adding, deleting, or updating rows.
PATCH /variationsTables/{eid}/components/{rowId}: Updates the content of a specific row in the component table.
DELETE /variationsTables/{eid}/components/{rowId}: Will delete the row in the component table and all variation tables.
The following endpoints are for fetching and updating the rows in an individual variant table of the Variations table and deleting an entire variant table:
PATCH /variationsTables/{eid}/variants/{variantId}: Used to update multiple rows in the variants table simultaneously.
You can only update variant specific columns, not those take from the component table itself. Updating the component table row columns will update all the corresponding variant table columns.
DELETE /variationsTables/{eid}/variants/{variantId}: Will delete the whole variant table specified. You may not delete individual rows of a variants table as they are directly tied to the components table. Deleting a row in the component table will delete it for all variation tables.
The following capabilities are in beta and are only available to users and administrators of Signals Notebook Standard, Signals Notebook Private Cloud, Signals Research Suite Standard and Signals Research Suite 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.
Variation Tables
The end user can now view their Variants in a single Vertical or Horizontal summary view. Users select which Variants, Properties and Headers are displayed, the settings can be saved to be persisted. The Horizontal Summary must contain at least one of the Component properties. The user must select one of the Component properties to be displayed as the columns in the view.
Inventory
Container Search Table updates to the Location, Creator/User and Batch/Lot columns. The filter criteria selection box will remain available until users click out of the box.
Locations have been updated to be a type ahead that can have multiple options selected:
Creator/User columns have a type ahead instead of a long check box list:
Users are now able to search for a Material ID or specific Batch/Lot by using the Batch/Lot column:
Typing in the Material ID will return all the batches/lots with containers associated:
What's New
This version 24.1 release of Signals brings a new beta capability to describe Variations Tables. Designed primarily for enabling variations of mixtures for formulation science, these are two tier hierarchical tables that facilitate the description of variations between similar sets of tabular data. We have added the ability to filter Internal references in ADTs to limit to objects within the same experiment or parent, and enhanced Materials Tables to display the hazard pictograms from the Materials used. We have continued to work on our ongoing beta capabilities for Container search in Inventory and on the use of entity names to populate Internal References, the previously beta capabilities around HELM monomer management and curation are now available on all systems. Finally, we have also fixed a number of small bugs.
The following improvements are available for users of Signals Notebook Individual Edition, Signals Notebook Standard, Signals Notebook Private Cloud, Signals Research Suite Standard and Signals Research Suite Private Cloud. Certain features may only be available with appropriate licensing and/or with enablement by an administrator.
• Fundamentals
– Mapping CSVs with Internal references to tables (beta)
• Chemistry
– HELM Monomer editor available to all systems
– HELM Monomer Curation Application available to all systems
• Admin Defined Tables
– Filter for “In this Experiment” for ADT internal reference searches
• Variations Tables (beta)
– Admin definition of Variations Tables
– Admin definition of Auto Naming for Variants
– End user addition of Variations Tables
• Materials Tables
– Hazard Pictograms in Material Tables
• Worksheets
– Before/after views for Recorded reasons for Change included in printed PDF
• Inventory
– New Label Templates for Containers
– Container Search Table (beta)
– Move Location Privilege
• Materials
– Bulk download of Chemistry based Materials with file attachments
– Bulk uploads of Materials with internal references (beta)
– Bulk updates of Materials with internal references (beta)
– Bulk import/export chemical materials as SMILES or InChI available to all systems
– Bulk update of chemical Materials with SMILES, InChI, or HELM available to all systems
– Bulk upload of HELM Materials available to all systems
• Tasks and Requests
– Task statuses display with new colors
• ELN Archive
– API key for ELN archive can be managed by System Administrators
• Administration
– Admin Audit Log shows users IP address for user login events
– Addition of SMILES data to the Salts list in SN Config
– Privileges to manage HELM Monomer Libraries available to all systems.
– Configuration Transfer of HELM Monomer library available to all systems.
• Integrations & APIs
– Public APIs for Inventa/SDF
– Enhanced SCIM endpoints to allow license assignment
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
• Getting Started with Signals
Developers should note that the GET /entities endpoint has been updated to exclude Trashed Items by default. The "includeOptions" will now default to "untrashed" when no explicit parameters are specified. To get the current pre-change behavior you can include "trashed,untrashed" as the "includeOptions". This will not impact users who are already using specific "includeOptions" as part of their usage of the endpoint.
Administrators and users are reminded that we are in the process of transitioning to new URLs for accessing the application. We added the new access URLs shortly after the prior release and intend to remove the original URLs at the end of March. We encourage you to update relevant bookmarks and start transitioning to using the new URLs if you have not done so already. If you would like the original URLs to be removed prior to the end of March, please contact our Support team (https://support.revvitysignals.com/hc/en-us/requests/new). Further information on the ongoing changes to our URLs and the potential actions you may need to take can be found here (https://support.revvitysignals.com/hc/en-us/articles/20264670846740-Signals-Notebook-Upcoming-domain-changes).
Administrators are recommended to subscribe to the channels within our support news site found at https://support.revvitysignals.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 2024.
The following improvements are available for users of Signals Notebook Individual Edition, Signals Notebook Standard, Signals Notebook Private Cloud, Signals Research Suite Standard and Signals Research Suite Private Cloud. Certain features may only be available with appropriate licensing and/or with enablement by an administrator.
Chemistry
The Hierarchical Editing Language for Macromolecules (HELM) Editor is available to all systems with this release. The tool allows users to represent biopolymers and other structures rapidly with monomer building blocks. The tool is available across Signals Notebook with any ChemDraw canvas. To use the tool a System Administrator must activate at least one HELM Monomer library and enable user access.
The HELM Monomer Curation app is now available to all systems. This enables management of custom monomers and custom monomer libraries.
Admin Defined Tables
There is a new option to limit the queries for internal references in ADTs to return objects/entities within the same parent as the ADT. For example, if the “Limit to entities in the same parent” is selected and the query is defined to return Samples, then the end user will only be able to see samples within their current experiment.
Materials Tables
Hazard Pictograms are now available in Material Tables:
Worksheets
Before/after views of the changes in Locked fields, resulting in a Recorded Reason for Change, are now optionally included in the exported PDF output. If the value in a Locked field is changed, and the user is forced to record a reason for the change, the before/after view is recorded in the History of the Experiment. Now, if the Experiment is exported to PDF and the History included, the event for the change will also print the before/after views.
Inventory
New Label Template for Containers 50 by 101 mm with QR code and space for hazard pictograms:
Label will be available for users after the Administrator has saved the template.
New User Role privilege has been added to allow Administrators to select User Roles to allow users to move the contents of a given location. This privilege previously was only available to Inventory Administrators:
Materials
There are now options to include file attachments when exporting chemical type Materials such as Compounds or Reagents (SNB). User may choose to download a zip archive with or without chemistry if they wish to obtain attachments with those downloads.
The previously released beta capabilities whereby users may bulk import, export, or update Materials with Chemical structures using SMILES, InChI, or HELM formats are now available to all systems. There are format requirement prompts on each relevant page and example download files for both bulk import and update pages.
Tasks and Requests
Task statuses have new colors to help users distinguish between them. The new status colors display on the Task table, Task-to-do table, Task Dashboard, and individual task screens.
ELN Archive
For customers who have the ELN Archive enabled, the API key for the archive can now be managed directly in SNConfig. System administrators can create new keys, delete keys and copy existing keys.
Administration
The Admin Audit Log will now record the IP address used when a User Access event is recorded.
There is now the option to load SMILES data into the Salt table under System Settings.
Admins can generate their own SMILES strings using chemdraw or bulk load the SMILES data for all system salts by exporting the System salts list to csv then uploading that csv to bulk update the salt list. The SMILES data be utilized in future capabilities being developed within the Materials Library.
Privileges to manage HELM Monomer Libraries available to all systems. System administrators can assign privileges to user groups for access and management of HELM Monomer libraries.
Configuration transfer for HELM Monomer libraries is available to all systems. The configuration of custom libraries as well as the HELM Monomer library search order can be included in a transfer between Signals tenants.
Integrations & APIs
The first set of Public APIs for Inventa/Signals Data Factory are now available. They can be accessed from the System Settings within SNConfig.
The GET/POST projects endpoints support retrieving a list of Inventa projects and creating a new project
The GET/DELETE projects/{projectId} endpoints support retrieving or deleting Inventa projects by their identifier
The GET/POST projects/{projectId}/datasets endpoints support retrieving a list of datasets for an Inventa project and creating a dataset within a project
The GET/DELETE projects/{projectId}/datasets/{datasetId} endpoints support retrieving and deleting specific dataset in a project based on the dataset ID
The GET/POST projects/{projectId}/datasets/{datasetID}/datasources endpoints support retrieving a list of datasources for a specific project dataset and creating a new datasource for a specific project dataset.
The GET/DELETE projects/{projectId}/datasets/{datasetId}/datasources/{datasourceId} endpoints support retrieving and deleting a specific datasource in a dataset
The POST projects/{projectId}/datasets/{datasetId}/datasources/{datasourceId}/actions/update-settings endpoint supports modifying the settings for a specific datasource
We will continue to expand the list of available Data Factory public APIs in future releases.
SCIM Endpoints have been updated to support management of user licenses. This allows API users to check, update, and delete licenses from a User individually or in bulk via enhanced SCIM endpoints.
The SCIM Schema endpoints have been updated to include licenses as part of the UserProperties:
The SCIM Schema endpoints have been updated to include licenses which includes three subAttributes – “id” representing the id of the license, “name” representing the name of the license, and “active” representing whether the license is active:
The GET SCIM User endpoints have been updated to include the user’s licenses:
All of a user’s licenses are returned in the “licenses” object in the UserProperties:
The PATCH and PUT SCIM User endpoints have been enhanced to activate and deactivate licenses for a user:
Example body of an activate request via the PATCH SCIM Users endpoint:
Example body of a deactivate request via the PATCH SCIM Users endpoint:
Example body for updating multiple licenses via the PUT SCIM Users endpoint:
The above operations are available in bulk via the SCIM Bulk endpoint:
The following capabilities are in beta and are only available to users and administrators of Signals Notebook Standard, Signals Notebook Private Cloud, Signals Research Suite Standard and Signals Research Suite 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.
Fundamentals
Users may now upload CSVs that include internal references to Tables and Materials Tables. Internal references must be valid and unique across the system to be accepted. Delimiters are required for multi-select internal references. For column headers that do not map to the tables, the user will be prompted to map the values. If there are any errors in the upload, the user will be notified, and no values will be added to the table.
Variations Tables
We have added a new content entity type called Variations Tables. These objects were designed primarily to satisfy the needs of varying compositions and conditions in materials sciences although they have broader applicability.
Users can select a Variations Table template to use. Once selected they can fill in a Components table to describe their high level composition. This components table allows data entry in our standard set of property types, data can be added via lookup to an Internal or External Data Source, manually entered or calculated via equations in appropriate columns. Data can also be uploaded via CSV or pasted into the relevant cells. Data can also be downloaded to csv, or copied to clipboard as tab delimited text.
Once the Components have been defined, the user can add a series of Variants. In these Variants tables, they can add data to additional columns appended to the list of components. Again, the Variants allow data entry in our standard set of property types, data can be manually entered or calculated via equations in numeric columns. Data can be copy/pasted, but cannot be uploaded from csv files. Users can create new Variants or can clone existing Variants. Data for individual, or for all Variants, can be downloaded to csv, or copied to clipboard as tab delimited text. Variants are named according to a naming sequence defined by the System Administrator.
Variation Table Templates are defined by an administrator in the Table Templates folder in SNConfig. Administrators can define Headers and Properties at both the Components and Variants level, from the standard library of property types. All Component Properties are also added into the Variants view but can be defined as hidden by default if not typically needed. The admin can select Internal/External Data sources for use in the Components view, and define equations on appropriate columns to calculate the values.
The names for the Variants are generated automatically. A System Administrator can define a string format for the naming in System Settings. This naming format then applies to all new Variations created using all Variation Table Templates.
Inventory
Additional updates have been made to the column headers in the Container Search Table results. For barcode/ids users can click on the header and sort or filter the results:
For all other headers besides Barcode, there is a Hide Column option.
For the Amount Available/ fields that are numbers with units the Filter will allow you to enter a value. For container properties, you can Sort as well:
The operator can be updated:
For Locations, a path can be selected to narrow the results:
For Date headers you can enter a date and change the “before” operator:
To reorder the columns, drag and drop the header where you would like it:
Before:
After:
Materials
Users may include internal references in bulk uploads to Materials Libraries. Users specify the column with the internal references and the delimiters in the CSV for upload. Users may specify new delimiters if desired. Values must be unique and valid to successfully be used to create new Materials in Bulk. Internal references that do not meet these criteria will be included in an error report.
Users may include internal reference values in bulk updates. Values must be unique and valid to successfully be used to update Materials in bulk. Internal references that do not meet these criteria will be included in an error report.