Revvity Signals Research Suite - What's New

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.

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Releases By Year

2024 2023 2022 2021 2020

24.10 December 2024 (Update to E3 in March 2025)

What's New

This version 24.10 release of Signals brings a series of enhancements to the ChemCharts capability in Signals Inventa, to the Search Tables in Inventory, to privileges in Signals VitroVivo and to workflows in Signals Synergy. We have added some more options for admin configuration including new Measures and Naming Sequences, along with an ability to let users overwrite calculated values in Tables. We have added a new beta capability for an animal management app in Signals VitroVivo, which is available on request. Finally, we have also fixed a number of small bugs.

The following improvements are available for users, administrators and developers on the Signals platform. Certain features may only be available with appropriate licensing and/or with enablement by an administrator.

Fundamentals
– Replace contents of a Text Element
– Spotfire Connector Microsoft SQL available
VitroVivo
–    Animal Selection & Group Assignment App with Randomization capabilities (beta)
–    New privileges to manage Grid Plate Editor designs, Data Import and Calculations Explorer templates
–    New privileges to access Signals VitroVivo Apps in the Spotfire for Signals Apps page
Inventa
–    Integrated Summary App now accepts more separators in criteria (copy/paste from CSV)
–    Support for MDL RXN format
–    Antibody Developability Data Functions in ChemCharts
–    Cluster Card Visualization in ChemCharts
–    Kinome Visualization in ChemCharts
–    Enhancements to exact match substructure search in ChemCharts
–    Quick structures search in ChemCharts
–    Smart cells can be used in a control in form-based visuals in ChemCharts
–    Formatting preserved when exporting to Excel in ChemCharts
Synergy
–    Notifications for the CRO user
–    Quick Add for easy addition of chemicals to Chemical Drawings in Synergy Experiments from chemical databases and External Chemical sources enabled for CRO users
–    Download Work Order Reference Tables to SDF or CSV
Admin Defined Tables & Variation Tables
– Allow users to overwrite calculated values
Inventory
–    Update to Status on Containers Search Table
–    Search and Export Locations with Sub-Location from Containers Search Table
–    Add and Print Container Descriptions on Labels
Administration
–    Addition of Length and Area Measures
–    Insert attribute list value into Naming Sequences
–    Search for events made by System in Admin Audit Trail
–    Spotfire for Signals privileges available
–    Spotfire for Signals Custom Apps Configuration available for Private Cloud
–    ChemDraw Preferences chirality setting is now observed with ChemDraw (vNext) renderer in Inventa
Integrations & APIs
–    API Endpoint for fetching Synergy Work Types
–    API Endpoint for fetching Synergy CRO, CRO Department information, and Collaborations
–    External Notifications for Synergy Creation and Signing Events
–    SDF API Endpoint for retrieving measurements data

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

Principles for Populating a Materials Library by Asset

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 March 2025.

Further Details

Fundamentals

End users can now replace the contents of a Text Element using a new text file.

Spotfire Connector Microsoft SQL is available within Spotfire for Signals. Data Connection information must be embedded in analysis file. Authoring, editing, and creating new is supported in Spotfire for Signals Analyst while Spotfire for Signals Online can consume existing.

VitroVivo

Administrators can grant Data Import Templates, Calculations Explorer Templates and Grid Plate Editor Designs management permissions to specific User Roles:

These management permissions allow publishing and deleting Templates or Designs shared in Signals. The users without these permissions will not be allowed to publish or delete Templates or Designs in Signals.

Users without these permissions will not see the buttons allowing them to publish or delete in the respective Apps, as illustrated below in the context of the Data Import App:

Administrators can also grant access, or not, to the Spotfire Screening Apps to specific User Roles:

Users without this permission will not see the Apps in Spotfire for Signals, as shown below for the Data Import App.

Inventa

The Integrated Summary App now supports tabs, commas, and paste from Excel as inputs with the “Is Any Of” search criteria

Inventa now has improved support for MDL RXN content, including compatibility with Structure Rendering, Structure Filtering, Structure Copying, and Exporting to ChemDraw for Excel

Inventa’s ChemCharts introduces a major upgrade including two new visualizations, new antibody data functions, enhancements to structure search, and new configuration options.

Multiple Antibody Data Functions have been added to ChemCharts, including Relative Accessible Surface Area, Developability Metrics, and Structure Prediction. An Antibody Dashboard Data Function automatically chains all of them, plus the Antibody Numbering and Sequence Liabilities Data Functions.

The Cluster Card Visualization in ChemCharts allows user to create groups of small molecules or other entities via interactive drag-and-drop. Clusters are represented in a hierarchical tree, with an optionally defined representative structure. Cluster information, like group statistics, is displayed in a form-based view with various organization options.

The Kinome Visualization in ChemCharts displays qualitative and quantitative data in a kinase phylogenetic tree, with extensive configuration options for branch and nodes.

ChemCharts Structure Search has been enhanced with a Quick Search method to allow searching directly from a Details, Gallery, or Table Visualization.

The Exact Match and Substructure Search options in ChemCharts now include additional configuration options. Exact Match supports normalization prior to matching, which will remove explicit Hydrogens, disconnect metal ions, standardize stereochemistry, etc. Users can also specify Exact Match criteria beyond just Structure (e.g.: SMILES, InChi key, Molecular Formula). Substructure Searching now supports additional Bond Matching criteria, including Exact, Tautomer, and Relaxed.

Newly introduced Configuration options for ChemCarts Visualizations include the ability to use Smart Cells as controls in From-Based Visualizations, an option to turn off atom labels in the RDKit renderer when the image is small, and the ability to export number and color formatting to Excel.

Synergy

CRO users can now receive Notifications about Work Order assignment, Synergy Experiments, comments, and other relevant changes. CRO users can configure their notifications by clicking on Notifications in the User Menu. Email notifications will send an e-mail each time a selected event occurs. In-app notifications appear in the bell icon in the Synergy CRO application.

CRO users can now utilize Quick Add functionality in Chemical Drawings to easily add common chemicals (“generic add”), chemicals by CAS number from ChemACX, and chemicals from External Chemical Sources that are Enabled for CRO Users by the Admin. In Signals Configurations under Data Sources, the Admin can choose which External Chemical Sources to Enable for CRO Users. Enabled sources will appear for CRO users to the left of the Quick Add toolbar of Chemical Drawings in Synergy Experiments. Sources not enabled will not be accessible to CRO users.

In Synergy Work Orders, both Sponsor and CRO users can now download Reference Tables to SDF or CSV files. If a Chemical Structure or Design Structure is included, the structure will be included in the downloaded SDF or CSV (as SMILES). For Reference Tables with Materials assets or batches, exported files will contain both the Material ID and ExID for the Sponsor, but only ExIDs for the CRO.

Finally, given the appropriate privileges by the Admin, Sponsor users can now Share their Work Orders and Synergy Experiments with other Sponsor users in the parent Collaboration, allowing them to elevate or reduce access level (e.g., from Write to Full Control) to a specific entity. Work Orders and Synergy Experiments can only be shared to other Sponsor users who already access, never to CRO users. This functionality allows Sponsor users to share amongst other Sponsor users without risking leakage outside the organization.

Admin Defined Tables & Variation Tables

Configuration Admins can now define that calculated values in Admin Defined Tables and Variation Tables can be overwritten by the end user, by deselecting the “Read Only” setting. If the field is not set to Read Only, the end user can write in their own value. There is a reset option in order to reset to the calculated value.

Inventory

Status can now be updated via the Containers Search Table.

Users with privileges to Final Dispose will see the option, all others with appropriate privileges will see Dispose. To change container status to In Use, assign the container(s) a Current User. To change the container status to Available, set the Current User to unassigned:

To change the container status to Exhausted, update the Amount to zero.

Sub-Location can be searched and exported from the Containers Search Table.

When searching for locations, users can automatically include sublocations by checking the box. The results will show the selected location and its sublocations, which can then be exported.

Descriptions can be added and printed on Labels.
Each container type has a system property called Description.

Administrators can choose to add the Description property to label templates.

Creating, Copying or Editing a container will display the Description property.

If the Label Template has been configured to print the Description property, the users will see it on the label.

Administration

We have added new Measures for Length and Area. These Measures can be selected when adding new properties of type Number With Unit to Admin Defined Tables and other objects that support the Number With Unit property type.

Admins can now also include Attribute List values into Naming Sequences, such as those used to autoname Experiments. The Admin chooses from the available Attribute Lists, whereby on Experiment creation, the value selected for that Attribute List is included within the Experiment Name.

If the Attribute List is not present or doesn’t have a single value nothing is inserted into the name.

System Admins can now selectively view system managed events in the Admin Audit Trail.

User Roles VitroVivo section renamed Spotfire for Signals and includes an expanded set of privileges.

Access Spotfire for Signals Analyst privilege controls whether a user has access to the local Analyst installer within the Home App as well as the launcher. Users without this privilege will be limited to Spotfire for Signals Online use.

New manage privileges for Screening Apps include Manage Published Workflows, Manage Data Import Templates, Manage Calculation Explorer Templates, and Manage Grid Plate Editor Designs. The InVivo Data Model Designer App has a new Manage Data Model Designer Templates privilege. These privileges control which users can create, edit, and delete items that other users can access.

Additionally, new share privileges for Inventa include Share Inventa Search, Share SAR Groups, and Share SAR Layout.
Control which users can access and substantiate an App via new privileges, including Access Screening Apps, Access Surface Plasmon Resonance Apps, Access InVivo Apps, and Access Data Model Designer App. Users without these access privileges can still leverage the Apps within shared Workflows and DXPs.

Signals Research Suite Private Cloud environments now have the availability to manage and deploy Spotfire for Signals Custom Apps. Once enabled, a new privilege, Manage Spotfire for Signals Custom Apps, will be available in the tenant to control access to the new Spotfire for Signals Custom Apps Configuration available within Home. Also once enabled, all tenants within the environment will have a new Access Spotfire for Signals Custom Apps privilege that controls which users can substantiate Custom Apps.

The ChemDraw Preference setting for chirality is now observed in Inventa. When selected, the top-level chiral flag is ignored for mol files while using the ChemDraw (vNext) renderer in Inventa.

Integrations & APIs

This update brings our first set of endpoints for Synergy customers. Only sponsors have access to APIs and configuration of external sources.

The initial set of API endpoints is focused on fetching of details about Synergy entities and work types. A new Synergy section has been added to Swagger that includes these endpoints.

Endpoints are available to fetch details about CROs, collaborations, departments, and work types.

External Notification for Synergy Experiment, Idea, and Work Order creation have been added to the “Top Level Entity Creation” notifications events. Signing events for Ideas and Synergy experiments have been added to “All Signing Events” notifications.

A new endpoint for the Signals Data Factory has been added for retrieving measurements data. You must specify the id of the measurement you are interested in and can optionally provide a projectId in the request body.

Note: To fetch mTypeId you can use: GET /api/v1/info-design/measurement-types. To fetch projectIds you can use: GET /api/v1/projects.

Further Details

The following capabilities are in beta and are available for users, administrators and developers on the Signals platform upon request. Please contact your account representative or our support team if you would like access to the following features.

VitroVivo

A new In Vivo Application called “Animal Selection & Group Assignment” is now available upon request. This multi-step application will allow users to capture baseline data, select animals according to study criteria and assign them to treatment groups using either manual or randomization methods.

This new application is an enhanced alternative to the current Baseline Capture app. Administrators can configure new user workflows by replacing the existing Baseline Capture app with the new app.

The new application will allow users to capture baseline data from animal cohorts using a form-based approach.

The application supports automatic selection of animals based on user-defined metric ranges. Built-in visualizations will inform the user about the list of animals excluded from the study and the reasons for exclusion. This is an interactive application that will allow users to manually include or exclude animals, if needed.

The application supports assignment of animals to treatment groups either manually or via randomization methods. If “Randomization needed” is selected in the Study Designer Application in the workflow, then the system will automatically present the Randomization options to the user in the Group Assignment step in this application. Based on the randomization criteria entered by user, the system will automatically assign animals to treatment groups.

Users can also assign new Cage IDs and Animal IDs to the grouped animals, if needed.

24.9 October 2024 (Update to E3 in March 2025)

What's New

This version 24.9 release of Signals brings an enhancement to our External Actions to allow admins to specify which Experiment or other templates show the Action. We have also added enhancements to the Inventory Search Table, and to add calculations in Headers of Admin Defined Tables. Our beta capabilities around refreshing material properties and assigning Tasks to Groups are now available to all systems. We have also made improvements to the admin management of users, to materials, Inventa and VitroVivo. Finally, we have also fixed a number of small bugs.

Fundamentals
– Clear Formatting in Text Elements and Worksheet Templates
VitroVivo
– Sequence of Events App now supports Dose Volume calculations according to Body Weight
Inventa
– Data Factory timeout obeys Signals Config timeout system setting
Synergy
–    Creation of Work Order directly from selected Designs in an Idea
–    Smart Folder and search capabilities for CRO users in Synergy
–    Sponsor administrators can now decide whether to select a CRO Administrator for a CRO
–    External Actions are now available in Synergy
Chemistry
– Definition line of a FASTA Peptide sequence added as an annotation when inserted or pasted into a Chemical Drawing
Admin Defined Tables & Variation Tables
– Calculations in Headers
Inventory
–    Update to Location Search
–    Internal Requests Initiated from Experiments, Admin Defined Objects
–    Search via CAS in Containers Search Table
–    Filter by Autotext List in Containers Search Table
–    Bulk Update Responsible Person in Containers Search Table
–    Autofill Grid Locations
–    New privilege that allows users to aliquot containers
Materials
– Export batch/lots of a material from the Batch/Lot page
– Refresh of calculated material properties available to all systems
Tasks and Requests
– Bulk creation of tasks from Samples table now associates Sample and Container information
– Assignment of Tasks to Groups available to all systems
Administration
– Sort, filter and bulk actions on Users
Integrations & APIs
–    Read-only Experiment properties can be updated via ExternalAPI
–    Users endpoints for license management
–    External actions by Template for all templated Entities
–    Enhancement to Task External Actions

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

HELM Notation: Guide to Add and Edit Monomers & Polymers

This content is anticipated for release on our Production E3 environments, and for Private Cloud customers on our deferred release schedule, in March 2025.

Further Details

Fundamentals

There is now an option to clear formatting from the toolbar in Text Elements, and in the Worksheet definition view. On occasion, when content is copied from websites and other third party sources, it can carry formatting information that disrupts the display of the data written in the Text content. This option, which is also available in the Format menu bar, clears formatting and should alleviate such issues.

VitroVivo

The Sequence of Events app will now support the calculation of dose volume and pump rates for dose administration. Dose volume is automatically calculated based on each animal's body weight measurement.

Inventa

Session Timeout now controls both Signals and Data Factory. Previously, the Data Factory timeout was fixed at 30 minutes. Now, the Data Factory timeout will follow the System Setting in Signals Configuration and can be set for up 1 day.

Synergy

In Synergy, users can now create a Work Order from within an Idea. After selecting a set of Design(s) to send to a CRO, select the + Work Order button. The created Work Order will contain a Reference Table with the selected Designs.

CRO users can now search for their Collaborations, Work Orders, and Synergy Experiments within their Smart Folders, allowing them to more easily find their experiments or filter their Kanban boards.

External actions can now be used in Signals Synergy, by both the Sponsor and CRO users. External actions configured for Samples, Samples Tables, PDFs, Microsoft documents, Chemical Drawings, and Worksheets are all available in Signals Synergy.

Finally, Sponsor System or Synergy Administrators can now choose whether to specify a CRO Administrator for a given CRO, allowing the Sponsor to choose whether a given CRO has a CRO Administrator with access to limited, self-service management of their CRO’s users.

Chemistry

When pasting a peptide FASTA sequence with header information into a Chemical Drawing, either directly or via the text tool of the HELM Editor, the FASTA header will appear as an annotation.

Admin Defined Tables & Variation Tables

Headers in Admin Defined Tables and Variation Tables can now have their values calculated via an equation. Headers of type Date/Time, Number, Number with Unit and Text can be configured to use equations using entries from other Headers.

Inventory

Update to Location Search is no longer alphabetized and instead will return the “best match” of the text entered without any additional filters:

Internal Request can be initiated from Experiments and Admin Defined Objects (ADO) by using the Internal Request option in the top right corner:

When creating an Internal Request, a modal will open with the Sample, Material and Containers that are in the Samples Table, Material Tables and Task to do Table in an experiment or ADO:

User should select the Sample, Material or Containers they would like to request and fill in the amount and location:

Additional Internal Requests can be made and users will see the status of the current Internal Requests:

Search via CAS in Containers Search Table:

Filter by Autotext List in Containers Search Table:

Bulk Update Responsible Person in Containers Search Table:

Select a current Signals Notebook user to be the new Responsible Person:

After the update, a report will be generated:

Autofill grid Locations If users have a series of containers that need to be placed in a gridded location, they can autofill the location with either a “Z” or “N” pattern. The Position column is available for any additional adjustments. The pattern will fill from Left to Right or from Top to Botton starting with A1 and will skip currently filled coordinates:

New Privilege that allows user to Aliquot Containers:

Users will need both the ability to Add Containers and the Aliquot Container to see the Aliquot Container button the Container Page:

Materials

Export batch/lots of material from the Batch/Lot page. Users with the privilege to Export Materials will also be able to export batches/lots:

In the top right corner will be an Actions area where the Export Lots options will appear:

Users need to choose the format for the export:

The export may take a few minutes, when finished, the user will get a notification and a download option:

Administrator controlled refresh of calculated Material properties is now available to all systems. This feature re-runs calculated properties for chemical and protein Materials, including calculated chemical names. The setting is available under Advanced Settings on the Materials Configuration page. Once the process is complete, the last update and number of Materials updated will be displayed. At this point the Administrator can update additional Material types if desired.

Tasks and Requests

Bulk creation of tasks from the Samples table now provides Sample and Container Information:

If the row has a reference to a Sample, Material ID, or Container, it will show in the row for the user to choose to associate with the Task:

The option to assign Tasks to groups is now available to all systems. Groups can be assigned during or after creation of a task or tasks. Only a single group can be assigned to a given task. If enabled in their user settings, members of the assigned group will be notified of a Task Assignment.

Administration

System Administrators can now make more easily bulk changes to users, managing Licenses, System Groups, Roles and Deactivation.

Licenses can be added or removed to all displayed users via an option in the license view.

Users can also be selected and changes made to the selected users, either deactivation, or changes to Licenses, System Groups and/or Roles. Bulk changes can be made to add, remove or update to the selected Licenses, Roles and/or System groups.

The System Admin can also sort by UserID, Last Login or Created, or filter to certain time ranges of Last LogIn or Created, to better narrow down on the users to select for bulk actions.

Integrations & APIs

The definition of “readOnly” an experiment type object (ie. Experiments, Parallel Experiments, ADOs, Requests, etc) has been updated to allow these properties to be updated by ExternalAPI but still be Read Only for users via the UI.

The Users endpoint PATCH /users/{userId} has been enhanced to allow activation/deactivation of a user’s license.

Note that you can only update a User’s attributes/roles/systemGroups OR their licenses, you cannot combine both operations in one API call.

GET /users/licenses is a new endpoint for fetching your tenants’ licenses information and their id’s for use when updating users.

External actions are now able to be set to only specific templates, similar to Admin Defined Tables, for all Entities that use templates such as Experiments and Plates.

Note that any existing External Actions for these Entities are set to "Apply to all templates" to maintain current functionality.

External actions are now able to be set to only specific templates, similar to Admin Defined Tables, for all Entities that use templates such as Experiments and Plates.

24.8 September 2024 (Update to E3 in March 2025)

What's New

This version 24.8 release of Signals brings a full release of the integrated summary app in Signals Inventa along with a host of additional improvements. We have also fully released the ability to add monomers to custom HELM libraries. We have extended our Materials and Inventory capabilities including adding a Mixtures Library under a beta release. We have also released other beta capabilities around assigning Groups to Tasks, and publishing data from tables to Signals Inventa. We have also extended capabilities in Signals VitroVivo, Synergy and around the export of data in grid views. Finally, we have also fixed a number of small bugs.

• Fundamentals
– Export the grid view to CSV

•   VitroVivo
–    Simplified and more consistent user experience in the Calculations Explorer
–    Remembering form information in the Study Designer App
–    Enabling autosave of the dxp file after adding or deleting Treatment Groups

•   Inventa
–    New query and data summarization tool, the Integrated Summary App available to all systems
–    Reorder material selection attributes in Integrated Summary App available to all systems
–    Bio Sequence querying in Integrated Summary App available to all systems
–    Reorder measurement selections in Integrated Summary available to all systems
–    Quick Query mode in Integrated Summary App available to all systems
–    Criteria Summary captures split summarizations in Integrated Summary App available to all systems
–    Integrated Summary App now supports multiple structures Quick Query mode available to all systems
–    Additional options to split summarization in the Integrated Summary App (ISA), including defining layout and specifying relevant experimental factors or attributes.
–    Option to run ISA query with only material criteria
–    Perform bulk selection on measurement attributes in ISA
–    Publish Measurement App is now compatible with measurement types designed for ISA
–    Preview biological sequences in the ISA Quick Query
–    Reorder SAR Analysis columns based on column groups
–    Shortcut to summarization methods and create new tags directly from a Measurement Type
–    Material Sync now supports synonyms

•   Synergy
–    Bulk Import of Designs from SDF or CSV files
–    Configuration Transfer for Synergy Data Exchange Transformations and Designs and Reference Table settings

•    Chemistry
–    Add new monomer to custom HELM libraries available to all systems
–    BILN support for peptides
–    HELM hotkeys for editing biopolymers

•    Admin Defined Tables & Variation Tables
–    Calculations on properties of type Number with Unit
–    Publish Admin Defined Tables to Inventa (beta)

• Samples
– Read Only Sample Properties

•    Inventory
–    Internal Request of Materials with Aliquot available to all systems
–    Bulk actions from the Container Search Table: Update Current User
–    Update to the Inventory Bulk Report page
–    Scan or paste list of barcodes into the Container Search Table
–    User Notifications

•    Materials
–    Show More on batch/lot page
–    Refresh of calculated material properties (beta)
–    Improved reporting for Bulk Import tasks
–    Increased file size limits for Bulk Import/Update tasks
–    Mixtures library (beta)

• Tasks and Requests
– Assignment of Tasks to Groups (beta)

• ELN Archive
– BioAssay/Structured Data content

• Integrations & APIs
– External Notifications for Task Status changes
– External Notifications for Material edit, transfer, and delete
– API Endpoints for Material Bulk Update
– API Endpoints for Normalized Compound Registration
– SDF APIs for creating, retrieving, and modifying SDF measurement types

Administrators should be aware that the dependency between Inventa Analysis privileges has changed, and they may need to update their User Roles accordingly. All users with “Create Analysis” must also have “Edit Analysis” privileges, and all users with “Trash Analysis” must also have “Edit Analysis” privileges.

Administrators should be aware that attribute names are now available alongside the attribute ID in the SDF audit log.

This content is anticipated for release on our Production E3 environments, and for Private Cloud customers on our deferred release schedule, in March 2025.

Further Details

Fundamentals

Users are now able to export their grid view searches in Smartfolders to csv. To export the search list to csv, a user should enter selection mode by clicking “Select Items” from the Actions menu.

The user can then select items or pick “Export Items” from the Action on All option to generate a csv export.

Once the export is complete, a bulk report is also available.

VitroVivo

The Calculations Explorer main panel now shows two simple and clearly identified groups for the visualizations and the calculations. Visualizations can be switched on or off using the eye icon and the formulas of the calculations are presented in the Details tab of the right panel.

The Calculations Explorer right panel has been updated at the level of the QA tab, which now contains clearly identified sections for manual or automated QA. Moreover, the information in the Details panel is now strictly read-only.

The Study Designer app now has a new feature, "Remember Form Data," that allows users to preserve form data by enabling a toggle switch. Once activated, this feature automatically retains the information entered in any form, thereby reducing the need for repetitive data entry. This functionality extends to all key forms within the Study Designer, including cohort definition, treatment definition, and treatment group definition forms.

Autosave is now enabled in the Study Designer app, ensuring that any added or deleted information is automatically saved if the application is closed without manual saving. This feature helps maintain data consistency and prevents the loss of data after an unexpected shutdown.

Inventa

The Integrated Summary App (ISA) offers a new query and data summarization experience. All previous ISA capabilities are now available to all systems. ISA is an alternative to the Global Search + SAR Analysis Apps. The Standard Query mode uses admin-defined settings to create a more streamline, templated search experience and allows for aggregation of any attribute (not just endpoints). The Quick Query mode returns all known information about a particular entity or measurement type with a single click.

Users can now run an ISA Standard Query using only material criteria

Users can specify which experimental factors are used to split aggregations. They can also specify whether the split aggregations be organized as columns instead of rows.

When defining measurement parameters, users can now take advantage of bulk attribute selection.

Quick Query mode now supports previews of sequences

The Publish Measurement App is now compatible with measurement types designed for either Global Search or the Integrated Summary App

In the SAR Analysis App, columns can now be reordered into different ChemCharts column groups.

Material Sync now supports synonyms

For Data Factory administrators, shortcuts within a Measurement Type Definition page allow admins to quickly update attributes or create new tags.

Synergy

In Synergy, users can now bulk import Designs from SDF and CSV files with SMILES or InChl structure info (UTF8 encoding). On a Designs Table, select Import Designs.

The user can then upload an SDF or CSV file and map the columns to the Design fields.

When import completes, the user can view the results, including the number of successful and/or failed designs, in the modal. Designs will be added to the Designs Table and the Designs Smart Folder.

On the administrative side, Transformations from the Synergy Data Exchange Library, as well Designs and Reference Table definitions, can now be transferred from one tenant to another using Configuration Transfer in Signals Configuration. After uploading a Configuration File, available Data Exchange Transformations from the source tenant Data Exchange Library will be shown under Synergy Settings > Data Exchange Settings. Selecting a Transformation will transfer the Details, Examples, Attachments, and other configuration settings for that Transformation. In addition, under Synergy Settings > Designs & Materials, selecting a Material Type will transfer the Design Definition, Designs Table settings, and Reference Table settings for Designs, Material Assets, and Material Batches for the selected Material Type. (Note that the Material Record Definition, Material Table settings, and other non-Synergy settings for the Material Type will not be impacted by this selection. Those settings can be transferred by selecting the Material Type under the general Materials section above the Synergy Settings.)

Chemistry

Adding a single monomer at a time to a custom monomer library in the HELM Monomer Curation (HMC) application, previously available in beta, is now available to all systems. Monomer structures can be drawn and edited directly within HMC, and all monomer properties defined in the ‘Add New Monomer’ form.

BILN format, a human readable line notation for complex peptides, is now supported. Users can create complex peptides by pasting a BILN string to the ChemDraw canvas or by inserting a BILN string using the text tab in the HELM editor. Additionally, ‘Copy As’ support has also been added allowing users to generate a BILN string from a peptide sequence drawn on the canvas.

Hotkeys are now supported when using the HELM editor. When editing a sequence on the canvas, any monomer from the selected monomer library with a single-letter symbol can be inserted by pressing the corresponding key on the keyboard. Similarly, any selected monomer while in HELM edit mode can be replaced by pressing a valid single-letter monomer from the selected library. For example, when the 'Peptide' tab is active in the HELM Editor and the 'Natural Monomers' library is selected, pressing 'a' will either insert monomer A (Alanine) or replace existing monomer with A (Alanine). HELM hotkey support is available in the Peptide, DNA/RNA and Blob/Chem tabs of the HELM editor.

Admin Defined Tables & Variation Tables

Configuration admins can now define new calculations incorporating properties of type Number With Unit. The function GETVALUE allows for the conversion of a Number with Unit into a Number which can be used in subsequent calculations. The function has two arguments. The first argument is used to identify the property of type Number with Unit. The second argument is used to identify the unit used for the conversion.

Samples

Admins can now make properties Read-Only for users in the UI. It is important to note that these Read-Only properties can still be updated systematically via the APIs. Under Sample Settings a new option is available.

Admins can simply select the Read Only Option on a property. For existing properties, the Read Only selection would make that property Read Only for all live samples.

Inventory

The Internal Request of Materials with Aliquot is now available to all systems.
We have added Update Current User to the Bulk actions from the Container Search Table.

When updating the Current User, the name of a Signals Notebook user can be typed in or set to unassigned:

Once completed, a report will be created:

The Inventory Bulk Report page has been updated to show the reports on the left side panel instead of across the top of the screen to make room for more bulk actions.

You can Scan or paste list of barcodes into the Container Search Table.

The search will update to return results on the specified barcodes.

User Notifications for Inventory can be found in the User Settings/Notifications/Inventory.

Materials

When there are more than 30 batches/lots a Show More option will appear at the bottom of the screen so that the additional batches/lots may be displayed.

Three options are now provided for materials library Bulk Import reports – one containing information only for registration failures, one for failures and/or duplicates, and one containing information for all outcomes. A new ID column in the report now contains the Material ID for items successfully registered to the library. For duplicates identified during a bulk import, a Duplicate ID column references the registered material ID that was considered a match.

Bulk import and bulk update tasks now allow for a file with maximum size of 300MB.

ELN Archive

The ELN Archive is a capability to import data from E-Notebook as archived content within Signals Notebook. Note that ELN archive required additional licensing and setup. The following enhancements require data extraction from E-Notebook using EN Data 2.8.

BioAssay/Structured Data is an application that helps biologist store, analyze and create reports on biological assay data. BioAssay/Structured Data is optimized for handling data related to high throughput screening. However, it can be effectively used to manage data related to low throughput and in vivo studies. Bioassay data in E-Notebook can now be fully displayed in the ELN Archive, and the original content downloaded as .csv.

Integrations & APIs

This update brings two new External Notification triggers, Task status changes and Material edit/transfer/delete.

For Task status changes you will see the “startState” and “endState” in the “properties” object.

For edits or deletes to Assets or Batches you will see a “type” of “edit” or “trash” respectively. The “included” object will include the entity.

Batch transfer notifications will be of type “move” and will include the source asset and destination asset in the “included” object.

New endpoints to mimic the Bulk Update functionality of the UI have been added.

This is an asynchronous API which is started with “POST /materials/{libraryName}/bulkUpdate”. This API supports update data in a ZIP file. The ZIP file should contain a summary SDF file or CSV file and attachments.

The response from the POST will contain a jobId for checking, delete, and viewing failures of a bulk update job.

An API to download an example ZIP has also been added.

The bulkImport API for materials has been enhanced to handle Normalized Compounds.

A new rule is available as a parameter:

“USE_ASSET_AND_BATCH_MATCHES”

Using this rule the server will check the item with uniqueness check, if duplicated will imported as new batch with existing batch type of an existing asset.

This update includes APIs for managing measurement types in Signals Data Factory.

The APIs are used to fetch existing measurement types, create new ones, fetch details of a specific measurement type, and update an existing measurement type.

Admin Defined Tables & Variation Tables

Users can publish data from Signals Notebook experiments to Inventa. To enable the data push there is administrative set up that will need to be done for both Inventa and Signals Notebook. Prerequisites for Inventa are a Project and defined Measurement Type. Prerequisites for Signals Notebook are an Admin Defined Table (ADT) and either (or both) an Admin Defined Object (ADO) or Experiment Template. Navigate to the ADT to be published. Click the Settings in the top left corner to expose the Template Settings menu:

Under the Data Factory Mapping header, choose + Add New Map. Associate the map with the Inventa Project:

Select a Data Factory Measurement Type or if previous maps exist, the Copy Map From button will be available:

Map the ADT Column Name to the correct Measurement Type Attribute. The Column Type will match with the Measurement Type Attribute automatically. If the Batch ID is required by the Measurement Type Attribute, there will be a warning. The Batch ID can be set on the ADT or from the ADO/Experiment Template.

Save the map. Additional maps can be created, on a per Inventa project basis. As each project is selected, the list of available projects will be updated. Once all maps have been created, activate the publishing by selecting the Publish Activation page:

Before users can Publish from the ADO/Experiment, a corresponding Project Map needs to be created. Navigate to the ADO/Experiment template. In the top right corner, click on Data Factory Maps:

Choose + Add New Map and select desired project. Click Save and Continue:

If desired (not required) additional fields from the ADO/Experiment Template can be mapped to the Measurement Type Attribute. This additional data will be appended to the ADT data when published:

Save Map. Additional maps can be created on a per project basis. Navigate to Publishing Activation to select when the user must fill in the Project:

There are 3 options. Unspecified means that users can navigate to the properties in the ADO/Experiment and select the project at any time. Click the Enable Publish to Data Factory when finished to allow users to publish from an ADO/Experiment:

Users will be prompted to fill in the Project if the selection is set to On experiment creation:

Users will see a Publish button in the top right corner of the ADO/Experiment when the configuration is correctly enabled:

User can add as many ADTs as needed to the ADO/Experiment. Only the ADTs that have been mapped to the same project as the ADO/Experiment will show in the screen for selection to be published. The first time the table(s) is/are published, the Last Published… will be blank:

Click on the grey Publication button to see if there are any errors:

If there are errors, a report will be available for download:

If no errors occurred, the Status will show as green:

Once the data is published, users can navigate to the Inventa Analysis to view the data:

Compounds that do not exist, will be created automatically. Batches with Compounds will be created automatically if they have not been created. Batches without Compounds will not be created and will show in the error report.

Materials

Administrators can now automatically refresh the calculated properties for a selected type of Materials. This will run calculated properties for chemical and protein libraries, including calculated chemical names. The setting is available under Advanced Settings on the Materials Configuration page. Administrators can designate the library and confirm that they wish to recalculate the fields of that set of Materials. Once the process is complete the last update and number of Materials updated will be displayed. At this point the Administrator can update additional Materials.

Administrators can now set of libraries to describe Mixtures. The Mixtures Library type can be selected when setting up a new library.

The library allows the administrator to define properties, uniqueness rules, activation as they do for other custom libraries. The admin can also define a table for the compositional data for the Mixture.

Once the library has been defined and activated, users can create new entries, completing both asset and batch level properties, in addition to populating the table based compositional data.

Tasks and Requests

It is now possible to assign Tasks to User or System Groups using the system reserved field, Assigned Group. Groups can be assigned during or after creation of a task or tasks. Only a single group can be assigned to a given task. If enabled in their user settings, members of the assigned group will be notified of a Task Assignment.

It is also possible to unassign an analyst or group from a Task in the Submitted, Canceled, or New states. This action can be taken from the Task table or the Task Smart Folder. Tasks that are In Progress must be unassigned from the Task-to-do table.

24.7 August 2024 (Update to E3 in November 2024)

What's New

This version 24.7 release of Signals brings improvements to Signals Synergy, Inventory and new Spotfire file handling. We have also added a new aggregate calculation into Variation Tables, and enabled the addition of internal references into Text elements. We have continued to work on our ongoing beta capabilities for the Integrated Summary App in Signals Inventa, the prior beta capabilities around Inventory linked ADTs and Variation Tables in now available to all systems. Finally, we have also fixed a number of small bugs.

•    Fundamentals
–    New Spotfire for Signals Information Item
–    Spotfire File removed from Add Content menu
–    Insert Internal Reference into the Text Element

•   Inventa
–    Criteria Summary captures split summarizations in Integrated Summary App (beta)
–    Integrated Summary App now supports multiple structures Quick Query mode (beta)

•   Synergy
–    Configuration Transfer for Synergy templates
–    On Hold status for Work Orders
–    References from Work Order Reference Tables can be referenced by CRO users in ADTs

• Chemistry
– Improved HELM sequence navigation

•    Admin Defined Tables & Variation Tables
–    Inventory linked properties in ADTs and Variation Tables available to all systems
–    Aggregate calculations from Variations to Components

•    Inventory
–    Inventory Bulk Results page displays 20 reports at a time
–    Home Location shows grid coordinates
–    Location page sublocations sorted alphabetically
–    New 40 x 18 label template
–    Grid Locations displays available spaces
–    Bulk actions from the Container Search Table: Delete and Update Status

• Materials
– Reverse order of batch/lots

•    Administration
–    Spotfire Setting to select Spotfire File opener, on-prem or Spotfire for Signals included with Signals Research Suite
– Privilege to add Spotfire for Signals opener option to Spotfire Files (when Spotfire Setting set to on-prem)

•    Integrations & APIs
–    New PUT endpoint to replace uploaded files
–    New endpoint to trigger "Update from PubChem"
–    New endpoints to allow usage of Parallel experiments Enumerator

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

Understanding Variation Tables - Basics of Chemical Formulations

The following OnDemand videos for Signals Notebook Administrators are now available

Enabling HELM Libraries & Creating Custom Libraries

Developers in Signals Notebook and Signals Research Suite should note that the behavior of endpoint PATCH /adt/{eid} has been updated. This update is to align the API behavior to match that of the UI, specifically regarding the display data in the key/ID value column for Tables utilizing an internal data source. The value of the column will now always be the name of the referenced entity, as in the UI, for update/create actions via the API.

Administrators should be aware that the legacy feature ‘Attachments’ in SDF has been deprecated.

Administrators should be aware that the “Project” and “Sample” tabs have been removed from the SDF interfaces.

Developers should note that we have published a new Developers Guide, found at https://revvitysignals.com/revvity-signals-developer-guide-overview

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

Fundamentals

New Spotfire for Signals available for Signals Research Suite licensed users for exclusive use with the Spotfire included with Signals Research Suite. Spotfire for Signals is the new default and is available in the Add Content menu (creates a blank Analysis file).

Spotfire File is no longer in the Add Content menu. Spotfire File can still be created with Drag and Drop or File Upload depending on licensing and/or Admin Setting.

Users should now be able to insert an internal reference into the text element using two methods. First, a new text element toolbar option allows users to search for and insert an internal reference buy clicking the magnifying glass icon.

Users are now also able to insert an internal reference into a text element by copy/pasting the url for an SNB entity.

Synergy

On the administrative side, Synergy templates for Ideas, Work Orders, and Synergy Experiments can now be transferred from one tenant to another using Configuration Transfer.

In Synergy, both the Sponsor user and the CRO user can put a Work Order On Hold. When placing the Work Order On Hold, the user can enter a reason. While On Hold, the Sponsor can edit the Work Order as required to provide additional information and resume when (if) the issue has been resolved.

In addition, CRO users can now pull external identifiers (ExIDs) for shared materials from the associated Work Order into internal reference fields in admin defined tables (ADTs). This avoids the error-prone process of copying and pasting identifiers into tables for capturing results. CRO users can report results related to the ExID, while the Sponsor can view and use both the ExID or internal material IDs.

Chemistry

Usability enhancements are available for working with biopolymer structures. When editing a HELM structure, a click selection of a monomer will select it for replacement. Similarly, a click selection of the bond will select if as an insertion point for a new monomer to be added. The buttons at the bottom of the HELM Editor have been removed and replaced with a badge that indicates ‘Insert’ or ‘Replace’ mode. Additionally, it is now possible to traverse a HELM structure by using keyboard arrow navigation. Once a monomer or bond is selected, directional arrows on the keyboard can be used to alternate between monomer and bond selection through the entirety of the sequence.

Admin Defined Tables & Variation Tables

The ability to add Inventory related columns to Admin Defined Tables and Variation Tables, previously available in beta, is now available to all systems.

We have also added the ability to calculate a SUM of values in the Variants in the Components. The SUM function calculates the sum of a given row across all the Variants, displayed in that row in the Components.

Inventory

Inventory Bulk Results page displays 20 reports at a time with a Show more option:

Home Location shows grid coordinates in Container Details page:

The Home Location grid coordinates print on the labels:

Home Location grid coordinates appear in Containers Search Table:

Location page sublocations sorted alphabetically:

New 40 x 18 label template:

When selecting a Grid Location, the drop down will display available spaces when doing a move:

User with Delete Container privileges will be able to bulk delete containers from the Containers Search Table:

Deleted containers cannot be restored. A toast will appear at the bottom of the screen, followed by a notification under the bell after the delete is completed. A report can be found in the Inventory Bulk Results - Container Delete:

Users with the appropriate privileges will be able to bulk update the status of containers from the Container Search Table:

Containers in the Final Disposed Status will not be updated as Final Disposed Status is a Read Only status that can not be restored. Disposed containers can be restored on an individual basis.
Once a selection has been made, a confirmation screen will appear:

A toast will appear at the bottom of the screen. A report will be generated, and a notification can be found under the bell icon. The report can be found in the Inventory Bulk Results  Container Status Update:

Reports are removed after 30 days.

Materials

The Batch/Lot page of a material shows the batches/lots in the reversed order with the most recent batch displaying in the list first:

Administration

A new Spotfire Setting allows the use of hybrid Spotfire, both OnPrem Spotfire and Spotfire for Signals, within Spotfire File Information Items. These settings do not affect the new default Spotfire for Signals information item that is for exclusive use with the Spotfire included with Signals Research Suite.

Note that if the tenant has never been licensed for Signals Research Suite, Spotfire Settings are unavailable and only OnPrem Spotfire is available within Spotfire File. The creation of new Spotfire Files is available with Drag and Drop or File Upload.

When the Spotfire Setting is enabled (default), legacy Spotfire Files open with Spotfire for Signals included with Signals Research Suite. The creation of legacy Spotfire Files is blocked and defaults to the newly available Spotfire for Signals. Users not licensed to Signals Research Suite will have no openers available.

By disabling the Spotfire Setting, Spotfire Files will open with OnPrem Spotfire for all users. The creation of legacy Spotfire Files is available with Drag and Drop or File Upload for all users.

If the Spotfire Setting is disabled, additional Spotfire for Signals options are available if Open Spotfire File with Spotfire for Signals privilege is granted. This privilege is useful during the transition from OnPrem Spotfire to Spotfire for Signals included with Signals Research Suite as the user will have all opener options available.

Integrations & APIs

There is a new endpoint available to replace uploaded entities with new files.

This endpoint can be used to replace an uploaded file, as you can via the UI, while preserving the entity id for Microsoft Office Files, Images, Generic Files, PDFs and Spotfire Files.

The Content-Type should be set in the header when utilizing this request to define the type of entity/the file type you are replacing. Full details can be found on the Swagger page. 

There is also a new endpoint available to trigger the “Update from PubChem” functionality on a material within a Reagents material library.

The material must be part of a Reagents material library with “Import from PubChem” enabled in System Configuration. Additionally, the material must have a valid CAS number.

A new set of endpoints have been created to allow for usage of a Parallel experiment’s enumerator programmatically.

These endpoints allow for:

Fetching of an enumerators content.
Adding a compound to an enumerator. Single compounds can be added via: cdxml, mol, smiles, or InChI. multiple compounds can be added via a sdf file. Column fields are mapped by the exact name match, using appropriate Content-Type (see Swagger page for more details)
Refreshing an enumerators group.
Kicking off an enumeration job to generate sub experiments, where the parallel experiment requires a chemical drawing to use as the Generic Reaction, the chemical drawing requires at least one Reaction, and only one reaction can be enumerated at a time. To use the enumerator again you must delete all existing sub experiments.
Checking the status of an enumeration, where IN_PROGRESS: Enumerator is attempting to create sub experiments; COMPLETED: Enumerator successfully created sub experiments; and FAILURE: Enumerator failed to create sub experiments. The API Response will return details on the failure/errorThe enumeration job is asynchronous and requires that no existing sub experiments exist. Parallel experiments sub experiments can be reset with pre-existing endpoints:

Inventa

The Integrated Summary App (ISA) allows users to split their results based on experimental factors. Now, the Criteria Summary also these reflects these search settings.

The Results Preview section of ISA’s Quick Query mode now supports multiple structures, which users can navigate between.

24.6 July 2024 (Update to E3 in November 2024)

What's New

This version 24.6 release of Signals brings a series of calculations to Admin Defined Tables and Variation tables. We have also improved Inventory with a display of the history of Containers and an archiving process, plus made some improvements. We have made a series of improvements to our Signals VitroVivo, Inventa and Synergy products. The recent beta capabilities on stereochemical annotation and web based Spotfire analyses are now available to all systems. We have continued working on our beta capabilities in the Integrated Summary App, and added a new beta capability to link Admin Defined Tables and Variation Tables to Inventory. Finally, we have also fixed a number of small bugs.

The following improvements are available for users of Signals Notebook Standard, Signals Synergy, 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
–    Allowing selection and export for Grid view
–    Option to remove page breaks in PDF printing
–    Option to edit and view Spotfire Files and Inventa Analysis Objects in your web browser available to all systems
–    Adding a Spotfire File creates a blank Analysis file available to all systems

•   VitroVivo
–    Enhancements to the Editable Data Grid handling of tables selected in the Notebook Experiment
–    Better row sorting for 1536 wells plates

•   Inventa
–    Add Inventa Analyses directly to a Notebook
–    Multi-select measurement attributes when defining Measurement Types
–    Reorder measurement selections in Integrated Summary App (beta)
–    Quick Query mode in Integrated Summary App (beta)

•   Synergy
–    License allocation per CRO for Synergy CRO user licenses
–    Configuration Transfer for Synergy Roles and Privilege and CROs and CRO users
–    Reopen and Recall Work Orders
–    Improvements to tracking of Work Orders on Designs

•   Chemistry
–    Enhanced Stereochemical Annotation tool available to all systems
–    Complimentary Strand Generation

•    Admin Defined Tables & Variation Tables
–    DateAdd function
–    Concatenate function
–    Round Up/Down function
–    Row offset function
–    Limit External References selection in Variation Tables to entities in the same experiment
–    Inventory linked properties in ADTs and Variation Tables (beta)

•    Inventory
–    History on Containers page
–    Archive a Location or Container type

•    Administration
–    Signed SAML response for external IdP authentication workflows

•    Integrations & APIs
–    New endpoints for deprecating and restoring deprecated monomers
–    New endpoints for creating and managing Plate annotation layers
–    Enhanced export API to allow Plates to be exported as CSV

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 or updated

Using Hierarchical Attributes on Experiments and Tables
ELN Archive Deeper Dive – Finding Collections

The following OnDemand videos for Signals Notebook Administrators are now available or updated

First Time Administrators - Where to Start
Enabling Chemistry Settings

Due to a change to a third party component used in Signals Notebook, image editing capabilities in our Text Editor are no longer available. All images will need to be appropriately formatted prior to addition to such elements.

Developers in Signals Notebook and Signals Research Suite should note that the behavior of endpoint PATCH /adt/{eid} is being updated. This update is to align the API behavior to match that of the UI, specifically regarding the display data in the key/ID value column for Tables utilizing an internal data source. The value of the column will now always be the name of the referenced entity, as in the UI, for update/create actions via the API. This change will be made in a future release.

Administrators should note that our updated licensing service, previously only made available on tenants with licenses to Signals Research Suite and/or ChemOffice+, is now being applied to all tenants. Although this change is being rolled out in the same approximate timeline to the current release it does not involve changes to the underlying code and is not release dependent. Once this change is applied to a given tenant, license assignment can be set on the main user page, on the create and edit user pages, as well as with the bulk update.

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

Fundamentals

Existing export functionalities in the Search Smartfolders Card view are now available in the grid view. Exactly as is currently available in the Card view, users can enter selection mode using the right side Actions icon and selecting “Select Items”

Once in selection mode, the user can execute available External Actions in the available Smartfolders or other additional currently available export options in Materials.

When printing an experiment to PDF, users now have the option to skip page breaks for a shorter report view.

Users now have the option to edit and view Spotfire Files and Inventa Analysis Objects within their web browser, previously available in beta, is now available to all systems. 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), previously available in beta, is now available to all systems. 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.

VitroVivo

To improve the user experience, and reduce the number of clicks: Signals VitroVivo workflows containing an Editable Data Grid App pulling data from an ADT in a Notebook Experiment will see the content of the data grid refreshed automatically when the name of the ADT selected in the workflow matches.

The default Spotfire alphabetical ordering was inadequate for labelling rows of 1536 wells plates and has been replaced in the Data Import App by the order corresponding to the plates labels expected by the scientific community (A -> Z followed by AA -> AF).

Inventa

Users can now directly add a new Inventa Analysis to a Notebook via the Add Content menu.

Admins can add multiple measurement attributes at once when modifying measurement types.

Synergy

On the Administrative side, System and Synergy Administrators (Sponsors) can now allocate Synergy CRO licenses on a per CRO basis. As a result, a given CRO (or other external partner) cannot license more users than their assigned allocation, allowing the Sponsor to reduce the administrative burden of managing user turnover and dynamic business needs often experienced when working with external partners.

In addition, Synergy-related Roles and Privileges, as well as CROs and CRO users can now be transferred from one tenant to another using Configuration Transfer.

In Synergy, the Sponsor user can now recall a Work Order that has been sent to a CRO as well as Reopen a Rejected Work Order.

Chemistry

The “Enhanced Stereo Annotation” tool is now available to all systems.

Complimentary strands of DNA/RNA can now be generated in ChemDraw via the HELM editor Text tab with sequence types FASTA DNA and FASTA RNA. The template strand will be inserted in the 5’ to 3’ direction on the canvas, with the compliment being aligned underneath in the 3’ to 5’ direction.

Admin Defined Tables & Variation Tables

The new function DATEADD allows addition of a time duration to a Date/Time. A statement such as TIMEADD([Start], [Duration], “unit”) is used, supported units include “Millisecond”, “Second’, “Minute”, “Hour”, “Day” and “Week”. The function must be set up on a Date/Time property, likewise the Start Time must be of type Time/Date. The duration must be of type Number, alternatively a property of type Number with Unit, with the Duration “measure” can be used in place of both the duration and units, following the format TIMEADD([Start], [Duration].

A CONCATENATE function allows multiple strings to be combined in a column of type Text. A statement such as CONCATENATE([ColumnA], “text”, [ColumnB]) will provide a results string with the relevant column values and strings as a single text string.

A ROWOFFSET function allows values from a differing row to be used in a given row based calculation. A statement such as ROWOFFSET([Column], offset) will provide the value from a previous or following row for the stated column, where an offset of -1 is the previous row.

ROUNDUP and ROUNDDOWN functions allows numbers to be rounded to the nearest unit, either Up (away from zero) or Down (towards zero). A statement such as ROUNDUP([Column], rounding), whereby the Column is a number and rounding is an integer, will round the number to the relevant unit A rounding of 0 rounds to ones, -1 to tens, -2 to hundred, 1 to tenths, 2 to hundredths etc.

Properties of type Internal Reference in Variation Tables can also now be limited to only return entities in the same Experiment.

Inventory

Users with access to containers will be able to see the history of the container by clicking on the History button in the top right corner:

A new page will open with the latest changes to the container. Users do not need access to the audit trail to see the history:

Administrators can now archive a location or container type. To archive a location or container type, navigate to the type and open the details view:

In the upper right corner will be the Archive option. If the type has already been archived, a Restore option will be available instead:

Archived types will prevent users from creating more instances. The Properties will be greyed out on the details view and will no longer be available for editing. The card view will display the archived status.

Administration

Organizations are now able to require that during authentication using an external Identity Provider (IdP, that the SAML request is signed. The administrator can configure their external IdP authentication workflow by selecting the “Sign SAML request” option, where a current Revvity certificate, to validate the request can also be downloaded.

Integrations & APIs

Monomers can now be deprecated and restored via the API. There is one new endpoint for each action.

A set of endpoints has been added to manage annotation layers on plates. There are endpoints for fetching, creating, updating, and deleting annotation layers of a plate container.

When creating a new annotation layer an annotation class must be specified in the POST body. The available classes are wellformat, concentration, material, amount, replicate, deviation, and other. When using “other” you must specify a data type of DECIMAL, TEXT, or INTEGER.

We enhanced the /entities/{eid}/export to allow for Plates to be exported as CSV, as opposed to .json by default, when specified in the “format” url parameter.

Inventa

The Integrated Summary App introduces two new enhancements. Users can now reorder measurement selections using the handles in the Criteria Summary panel.

Users can take advantage of the new Quick Query mode to retrieve data even faster. Quick Query mode can be accessed directly from the Inventa Dashboard or as an option when creating a new Inventa Analysis

Integrated Summary’s Quick Query allows you to quickly drill down into a particular set of data focused on a single asset, a batch/lot, or a measurement type. Use the type ahead to find an entity or measurement type of interest

Further limit your results based on a custom date range or use one of the convenient date shortcuts (today, last week, this year, all time, etc)

Retrieve an instant summary of your selected data

And the download the full set of results, complete with a Summarized Key Results table and individual measurement tables.

Tables can be conveniently toggled to best leverage viewing space.

Admin Defined Tables & Variation Tables

Admin Defined Tables and Variation Tables can now be linked to Inventory if the table template uses an Internal Data Source. The admin can choose to add inventory columns, which adds Barcode, Inventory Decrement and Container columns to the ADT, or Components. The scientist can then enter a barcode into the ID column and the related Material will be imported into the table along with associated data. The user can also change the container to another container with the same material.

24.5 June 2024 (Update to E3 in November 2024)

What's New

In this version 24.5 release we are excited to announce the release of SaaS Signals Synergy, a new product offering with Signals Notebook or Signals Research Suite for efficient and effective management of collaboration with contract partners. Signals Synergy provides simplified administration setup of CROs, powerful automated security features, kanban-style project management, Ideas and Designs for drug ideation, and the Synergy Data Exchange for parsing unstructured CRO reports into structured columnar data tables. Signals Synergy is built on the same platform as Signals Notebook and Suite for seamless integration of internal and external data.

Further, 24.5 delivers an improved ability to see the template that content was created from, and to export data from the Materials grid view. We have improved curve fitting in VitroVivo and improved the Material library integration in Signals Inventa. We have extended our calculation used in Admin Defined Tables and Variation Tables to include a time difference and improve our existing IF calculations. We have continued to work on our ongoing beta capabilities for the Integrated Summary App, and for Normalized Compounds, our prior beta capabilities around Tasks and Requests are now available for all systems. We have new beta capabilities around stereochemical annotation in ChemDraw Documents, and to add monomers to custom HELM libraries. 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, Signals Research Suite Private Cloud and Signals Synergy. Certain features may only be available with appropriate licensing and/or with enablement by an administrator.

• Fundamentals
– Origin Template displayed in Properties

•   VitroVivo
–    Include Multiparametric curve fitting constraints to the Calculations Explorer
–    Goodness-of-fit R-squared (R^2) measure is now available in all the fits, not only in the logistic fits

•   Inventa
–    Create measurement types using an example file
–    Material Library as source of truth in Data Factory
–    Reorder material selection attributes in Integrated Summary App (beta)
–    Bio Sequence querying in Integrated Summary App (beta)

•   Synergy
–    Synergy and Synergy Configuration are new applications for managing collaborations with contract partners (e.g., CROs). Available only to licensed systems.
–    Creation of CROs, CRO users, CRO Departments, and Collaborations with automatic security
–    New licensed user type “Synergy CRO User” with controlled access through Synergy CRO application
–    Security and IP protection features built-in for CRO users, such as automated CRO ring fencing, Hidden from CRO properties visible only to Sponsor users, and ExIDs for masking Material IDs
–    Ideas and Designs for gathering newly proposed structure designs prior to synthesis or registration
–    Work Orders creation and management via kanban-style boards for both internal (Sponsor) users and CRO users
–    Reference Tables within Work Orders allow for partial sharing of Material or Design properties and masking Material IDs
–    Synergy Experiments allow the CRO user to record their experimental record in response to Work Orders with dedicated workflows and security features
–    Synergy Experiment initially support the following content: Text, Chemical Drawings, Word, Excel, Powerpoint, Samples, Tables, Biological Sequence, Image, Spotfire File, Worksheets, and File Upload
–    Synergy Data Exchange provides excel-based CRO report parsing into structured data tables

•   Chemistry
–    Enhanced Stereochemical Annotation tool (beta)
–    Add new monomer to custom HELM libraries (beta)

•    Admin Defined Tables
–    Time duration calculations
–    IF calculations support empty values

•    Materials
–    Administrators can include internal reference properties in uniqueness check rules for Materials
–    Normalized Compounds (Beta)

•    Tasks and Requests
–    Assign an Analyst during Task Creation and from the Task Container available to all systems
–    Create Tasks from Materials in Experiments available to all systems
–    Notification for Task creator regarding assigned analyst access available to all systems
–    Notification for Analysts when assigned a Task available to all systems
–    Create an Experiment from a Task Container available to all systems

•    Integrations & APIs
–    POST/ endpoint for bulk import of monomers to custom libraries
–    GET/ endpoint to obtain an example file for importing monomers in batches
–    GET/ endpoint to get a report of a monomer bulk import job status
–    GET/ endpoint to obtain report of failed monomer bulk import jobs
–    New Endpoint for syncing entities with updated Template
–    Templates included in API Responses
–    New Endpoint for Batch/Lot transfer
–    Expanded Character set for Material/Lot naming via API

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

Developers in Signals Notebook and Signals Research Suite should note that Inventory is now updated to give more meaningful error codes, the error codes provided via the External API now align with the user interface, specifically regarding 4xx (400, 409 and 412) error codes. The following codes are now 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).

Due to a change to a third party component used in Signals Notebook, image editing capabilities in our Text Editor will no longer be available. All images will need to be appropriately formatted prior to addition to such elements. This change will take effect in a future release.

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 Origin Template is now displayed for objects derived from a System Template, including Experiments, Admin Defined Tables, Variation Tables and Worksheet. The Origin Template is displayed in the Properties and reflects the current name of the System Template used.

VitroVivo

The new multiparametric analysis is particularly important to simultaneously analyze data from instruments producing multiple readouts (e.g. multimodal plate readers or flow cytometry instruments). The settings of the fits can be edited, under the “Manage Fittings” tab of the Calculations Explorer Controls, based on names (parameters) included in a specific column of the data and the impacted curves are listed. Furthermore, the Calculations Explorer templates can now be saved in this new modality.

The goodness-of-fit R-squared (R^2) measure is now available in all the fits, not only in the logistic fits.
Until now, the R^2 measure could be added using the add coefficient toggle. However, this toggle was only present in the logistic fittings. Thus, in the rest of the fittings, the R^2 could not be added to the raw table. Adding the R^2 measure is now possible for all fits.

Inventa

Administrators now have the option to use an example file as a guide for simultaneously creating a new measurement type and a corresponding map.

When a Material Library has Inventa Sync enabled, it serves as the source of truth in Data Factory. Updates to synced materials must originate directly from the Material Library and cannot be overridden by user-added files. Mapped entity attributes will always reflect the most current material record definitions, even if the value is blank.

Synergy

Signals Synergy has a dedicated Synergy Configuration application for setting up Contract Research Organizations (CROs; or other contract partners), creating and licensing of Synergy CRO Users, and configuring Synergy related entities.

Inside the new Synergy app, Sponsor users can manage collaborative work with their CROs. First, users can request work from a CRO using a new system object, Work Orders. Work Orders are prioritizable, group assignable to CRO Departments, and contain traditional content elements such as Chemical Drawings. Progress of Work Orders can be tracked using built-in project management tools, such as Kanban-style Work Order boards.

Work Orders can also contain Reference Tables. Reference Tables allow the user to selectively share properties of Materials or Designs required for the requested work. Reference Tables allow the user to automatically mask the Material IDs using ExIDs and select only a subset of material properties to be seen by the CRO.

To fulfill a Work Order, Synergy Experiments allow CRO users to capture their experimental record and submit their work back to the Sponsor for review. Synergy Experiments are very similar to existing Experiments, supporting content such as Text, Chemical Drawings, Word, Excel, Powerpoint, Samples, Tables, Biological Sequence, Image, Spotfire File, Worksheets, and File Upload, but provide dedicated workflows for Sponsor users and CRO users, as well as specialized IP security features.

Synergy Experiments and Collaborations support a new property type, Hidden from CRO properties. Hidden from CRO properties (configured as Hidden from the CRO at the template level) are available for internal Sponsor users to organize and search for objects, but are always hidden from CRO users.

Synergy Experiments also support the new Synergy Data Exchange element, which automatically transforms excel-based CRO reports into structured data tables ready for publication to Inventa or download as CSV.

In addition, Ideas and Designs are new system objects for capturing drug ideas. Ideas contain Designs Tables, which allow the user to create, capture, and prioritize drug designs. Work Orders requested for each Designs are also captured at the Design level for track-ability.

Finally, CRO Users access and easily manage their Work Orders and Synergy Experiments through the dedicated Synergy CRO application. The distinct Synergy CRO User type and dedicated application allows us to provide automated ring fencing of CROs, filtering of proprietary information such as Material IDs and Hidden from CRO properties, and easy work prioritization through the Kanban Boards.

Admin Defined Tables

Admin Defined tables now support a time duration function and IF functions support definition of behavior when a referenced cell does not contain a value.
Reference of a cell in an IF function in an Admin Defined Table now allow the admin to define behavior if the referenced cell has no value. A statement such as [Column] = “” is used to refer to the condition whereby Column has no value in that row.

The new function DATEDIFF allows calculation of a duration between two Date/Time properties. A statement such as DATEDIFF([Start], [End], “unit”) is used, supported units include “Millisecond”, “Second’, “Minute”, “Hour”, “Day” and “Week”. The function can be set up on a Number property, alternatively a Number with Unit, with the Duration measure can be used. In such cases the units are not specified and the most logical unit is presented by the system.

These functions are also enabled in Variation Tables.

Materials

Administrators now have the option to include internal reference values in uniqueness check rules. To include an internal reference field in uniqueness check rules, the field must be set as single-select and required. The value of the internal reference name will be used in the uniqueness check rules once set:

Tasks and Requests

Several new Task functions, previously in beta, are now available to all systems. Analysts may be assigned during Task creation and from the Task Table. Tasks may be created from Materials Tables. Analysts have a new notification both in app and via email to inform them of when they are assigned a Task. Analysts may create an experiment directly from a Task table.

Integrations & APIs

Monomer libraries can now be bulk imported via the API. This is an asynchronous job and will bulk import monomers into an existing Monomer Library.

To begin the bulk import job, specify the .json file to bulk upload, and how to handle duplicates and use the endpoint POST /monomers/libraries/{libraryEid}/bulkImport. The response contains a Job ID. There are options for both symbol/polymer type/monomer type and structural duplicates to be treated as new monomers. These are the same options in the UI.

You can check the status of the job based on its ID using the endpoint GET/monomers/libraries/{libraryEid}/bulkImport/jobs/{jobId}. The status will be one of: READY, the job is ready to run; IMPORTING, the job is running; FAILED, the job is failed to run; or COMPLETED, the job is completed. If there is a failure you can get a report for the details via the endpoint: GET /monomers/libraries/{libraryEid}/bulkImport/jobs/{jobId}/failures.

Additionally, an example of a well formed .json file for importing is available via the endpoint GET /monomers/libraries/{libraryEid}/bulkImport/example.

For admin defined tables, worksheets, and variations tables who are out of date with the template they were created from can now be refreshed via the endpoint POST/entities/{eid}/syncWithTemplate.

Note that this will DELETE all existing content in the entity when updating to the new template version. This is same behavior as updating via the UI.

For entities that utilize templates the “systemTemplate” and the “template” are now returned in the “relationships” object for an entity in API responses.

The “systemTemplate” property returns the eid for the closest system template used in the creation of the object. The “template” returns the eid of the entity used to create the object.

The object “Test Table Template” shows the eid for the System Template “Test Table Template” for both “systemTemplate” and “template”

Whereby the object “copy of Test Table Template” shows the eid for the System Template “Test Table Template” for “systemTemplate” and the eid for the object “Test Table Template” for “template”

A new endpoint has been created to allow batches/lots to be transferred between assets as is currently possible via the UI, POST /materials/{eid}/transfer.

The originating asset and the target asset should be in same material library. When transferring the final batch of an asset to a new asset the originating asset will be deleted. 

A restriction on special characters, except for “/”, for material Batch/Lot naming during creation via API has been removed.

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

Integrated Summary App users can now rearrange material criteria, affecting the search order and resulting table layout

In the Integrated Summary App, users can now perform protein and nucleic acid sequence queries using BLAST or exact substring matching. Beyond the standard query output, these biosequence searches also provide alignment and annotation results.

Chemistry

Chemists can now view and annotate stereochemical information contained within their molecule using the “Enhanced Stereo Annotation” tool. This tool enables the assignment of enhanced stereo properties and the addition of chemically significant labels to stereocenters by applying rules that describe the stereochemical composition of each atom or bond. The chemically significant labels are recognized and honored in chemical searches, and if exported as a mol file, the labels will be included in the SGROUP portion of the file.

Users can now add a single monomer at a time to a custom monomer library in the HELM Monomer Curation (HMC) application. Monomer structures can be drawn and edited directly within the application, and all monomer properties defined in the ‘Add New Monomer’ form.

Materials

Normalized Compounds type libraries can be imported using the same method that is currently available for Compounds type libraries.

The user can select the bulk import option from the “Add New” menu.

Once a file is selected the user can map fields for import and select the duplicate resolution options. New for this library are the option to “Use Asset Matches, Treat Batches as Unique” which allows the imported compounds to match based on the normalized asset but still retain a unique batch type for each batch and “Use Matches for Asset and Batch” performs uniqueness checking on the Asset and Batch level allowing for duplicate batches to be registered with the same batch type.

The Import report is the same as what is currently available for Compounds library.

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