PerkinElmer Signals™ Notebook - What’s New

What’s New
This version 22.5 release of Signals Notebook brings a capability to our Materials Libraries to allow for libraries without batches (beta). We have also enhanced other material capabilities around PubChem, Containers and Requests. We have extended our Task & Request capabilities with some improvements, (beta) and extended our ongoing Configuration Transfer (beta). We have also fixed a number of small bugs.


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

• Usability Improvements
• • –  Indication of number of search hits

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

• Inventory & Materials
• • –  Materials without batches/lots (beta)
  • –  Improved DNA sequence uniqueness checking
  • –  Updates to Container Permissions
  • –  Updates to PubChem Link Activation
  • –  Updates to Material Request Page
• Integrations & APIs
• • –  Download materials as SMILES
  • –  Transition objects from Active or Approved to Closed
  • –  GET status of bulk upload file
• Parallel Experiment layout
• • –  Available to all administrators without request
• Tasks & Requests (beta)
• • –  Updates to the Task Table
  • –  Updates to the Samples Table
  • –  Updates to the Task Folder
  • –  Assign Analyst in the Task Folder
  • –  Create Experiments from the Task Folder
  • –  Assign Analyst in the Task Folder
  • –  Updates to the Task To Do Table
• Configuration Transfer (beta)
• • –  System Settings – Workflow
  • –  Parallel Experiment settings
  • –  Notebook settings
  • –  Dependency checking

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

Administrators should note that we will soon be changing our IP addresses for our back end services. If you have integrations using External Sources, or use our Notifier APIs, and limit access to our provided IP ranges, please contact our support team for updated IP addresses.

The following OnDemand videos for Inventory are now available

• How to Add Locations
• Order Reagents with Material Requests
• Steps to Add Containers

This content is anticipated for release on our Production E3 environments, and for Private Cloud customers on our deferred release schedule, in November 2022.

Administrators should also note that we have replaced our notification Service Signals Notebook Pulse with the following site here. Administrators should bookmark or can subscribe to this site for notification of any planned or unplanned outages on Signals Notebook and other PerkinElmer products. This site is part of a larger support news site found here, which contains more information about releases and other pertinent product information.

Administrators should note that we will changing a Security Setting in Signals Inventory in our next release. If you have users that currently have Edit permissions to Containers through Inventory Security, they will not be able to edit the properties after the June 2022 release and will require Full Control instead. If Administrators would like to keep users being able to edit Container properties, they can update the Security Policy now or after the update to be:

RULE "Inventory Security"
IF attribute "Inventory Security" match
THEN grant "entity.full_control"

Some systems may already have the above Security Rule in place, and no further action is required.

Further Details

Usability Improvements

Users will now be able to see the total number of search results at the top of the search window.

In the event your search returns higher than our maximum allowed results you will see the message below with your count estimate.

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

Inventory and Materials

Uniqueness checking of DNA libraries has been enhanced to account for plasmids that are identical but may have different start sites due to user action. Such plasmids will now be detected if uniqueness checking rules are enabled and users will be asked to resolve duplicates during registration.

Container Permissions have been updated so that Users that have Write permissions through a Security Policy will be able to Update Amount in containers, Check In/Out, Dispose, Copy Containers and Print Barcodes. Only users with Full Control will be able to update container properties. An example of the Security Policy to set full control is shown below.

The PubChem Link is available to all Materials Libraries that have a CAS field. To better reflect this, the location of the PubChem Link Activation page has moved to Material Types:

The Material Request Page has been updated so that Order Requests on the Materials Request Page that are in the Received or Cancelled status will be removed from the page automatically when they are over 30 days old from the Date Requested.

Requests that are in the Backordered, Recognized at dock, Pending or On Order will remain, even if they are older than 30 days.

Integrations & APIs

The endpoint GET /materials/{eid}/drawing has been extended to allow download of chemical materials in SMILES or InChI format.

The endpoint POST/entities/{eid}/reviews/close has been added to allow developers to Close Experiments, Parallel Experiments and Admin defined Objects, from Active or Approved. The developer can optionally add a comment.

The endpoint GET/materials/bulkExport/reports/{reportID} has been added to check the status of the report requested via the POST/materials/{libraryName}/bulkExport endpoint.

Sub-Experiment Layout

The SubExperiment Layout is now available to all users where the administrator has enabled Parallel Experiments. This capability is now no longer considered as in beta and does not need to be requested.

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

Materials

Materials Libraries that do not have associated batches can now be created by administrators. This provides further flexibility in modeling your data to reflect how information is tracked in your organization. These Assets can be added to containers and referenced in Materials tables. Custom, DNA, or Protein libraries can be created. Note that a new container tab is present to track the inventory of these items.

Tasks and Requests

Our existing Task and Request Workflows have been enhanced with improvements to the Task Table, Samples Table, and the Task Folder.

Additional columns have been added to the Task Table for Creator and Created Date. The Reference ID can also now have multiple references for each task. Users can add additional references by using the magnifying glass. Users can remove individual references by using the break link icon or remove all references by using the x next to the last listed reference:

Users can select multiple tasks at a time with check boxes at the front of each row or they can use the checkbox at the top to select all the tasks. After tasks are selected, the Bulk Actions drop down will be available. Bulk Actions adjust based on the status of a task (Submit, Delete, Duplicate and/or Cancel).

Additional Tasks can be created by using the Create Task button. A new window will open, and users can fill in the appropriate information.

If users would like to have all the references in 1 task, the check box needs to be checked.

The Task Table can now be added to an experiment through the Add Content drop down.

The Samples Table has been enhanced so that Tasks and a Task Table can be created through actions taken directly on the Samples Table. The Samples Table now has checkboxes and the Bulk Action drop down. When users select Create Tasks with selected samples the Task creation window will open.

Users can create tasks on an individual row in the Samples table as well.

Once the tasks have been created, the Task Table will automatically appear in the experiment.

Tasks created in experiments inherit their security from the experiment. Only users that have access to the experiment in which the tasks were created in, have access to the task. The tasks created in the Request Folder will continue with the current security model.

The Task Folder has been updated so that the Task Folder cards have been replaced with a table view. New columns for Creator and Date Created have been added. New functionality has been added: Multi-Select, Update Status, Create Experiment, Assign Analyst and Filtering.

Users can select up to 10 rows at time to perform an action on. The selection and the action will vary depending on the status of the task. New tasks can be deleted (users should submit the tasks from the experiment or the request).

Submitted tasks can be completed or canceled.

In Progress and Completed tasks cannot be updated from the Task Folder.

Filters can be applied to the Task Folder by using the text box at the top of the page. Filtering terms will show below the text box:

User may remove the filters by clicking the x next to the text or using the Clear All button next to the text terms.

Users can search in the User columns (Analyst and Creator) by clicking in the column header for an additional filter.

Users can search by a Date or a Date Range in columns that have dates, like Created Date.

To change to a Date Range, use the drop down next to Date.

Enter the date range you would like to filter by.

Analysts can be assigned to tasks in the Submitted state from the Task Folder. Select the tasks that should be assigned and click the Assign Analyst option. A window will open to search for a user.

Use the type ahead feature to find the user.

The table will update with the newly assigned Analyst name.

Note that assigning an Analyst to a task is not a requirement for the task to be completed. If a different Analyst puts the task in a Task To Do table, the Analyst field will update automatically.

Users can also now create Experiments directly from the Task Folder. Users can select the tasks they would like to have in a new experiment. They then can select the Create Experiment option.

The new Experiment window will open.

When the new experiment is created, a new Task To Do table with the selected tasks will appear in the experiment.

The Task To Do Table has been updated so that users can select multiple tasks in the Task To Do table to perform an Update Status on.

Depending on the task Status, the options in the drop down will change. Once the Status has been updated, it will show in the Task To Do table.

It will also show in the original experiment’s Task Table.

Configuration Transfer

We have extended our configuration transfer capability to support transfer of Workflow settings from System Settings, Parallel Experiment settings and Notebook settings. We have also added an indication on import of any missing dependencies.

What’s New
This version 22.4 release of Signals™ Notebook brings an ability to print a selected portion of the experiment, some changes to Internal References, an enhancement to make it easier to find Notebooks when creating experiments, some updates to Inventory, and enhancements in ongoing beta capabilities around Parallel Experiment layout and Configuration Transfer. We have also fixed some small bugs.


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

• Usability Improvements
• • –  User with Full Control can delete comments
  • –  Limit of printed History in PDF increased to 500 items
  • –  Partial PDF printing
  • –  State Modified field extended to capture additional state transitions
  • –  Notebook description can be used to find Notebooks when creating experiments, etc.
  • –  Update to Contact Support link

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

• Usability Improvements
• • –  Internal reference enhancements
• Inventory & Materials
• • –  Creation date in Containers Details page
  • –  Update Amount on containers
  • –  Associate containers with registered material from Samples table and print multiple barcodes
• Integrations & APIs
• • –  Bulk update Samples table
  • –  Bulk update Sample Summary table
• Parallel Experiment layout (beta)
• • –  Plate, Well, Row, Column included in GET entity for SubExperiment
• Configuration Transfer (beta)
• • –  Plates
  • –  Sample settings
  • –  Experiment settings
  • –  External Actions
  • –  Task and Request settings

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

Administrators should note that we will soon be changing our IP addresses for our back-end services. If you have integrations using External Sources, or use our Notifier APIs, and limit access to our provided IP ranges, please contact our support team for updated IP addresses.

The following OnDemand videos for Inventory are now available

• Container – From Create to Dispose and Everything in Between

This content is anticipated for release on our Production E3 environments, and for Private Cloud customers on our deferred release schedule, in November 2022.

Administrators should also note that we have replaced our notification Service Signals Notebook Pulse with the following site here.
Administrators should bookmark or can subscribe to this site for notification of any planned or unplanned outages on Signals Notebook and other PerkinElmer products. This site is part of a larger support news site found here, which contains more information about releases and other pertinent product information.

Further Details

Usability Improvements

Users with Full Control on Experiments or other objects can now delete any comments. Any user can still edit or delete comments they added themselves.

The limit for History items included in the PDF export has been increased to 500 items.

Additionally, users can now generate PDF exports for selected portions of their experiments by deselecting the Print Entire Experiment option, then selecting the content they would like to include in the PDF.

The State Modified property on objects has been extended to cover all state transitions, including Close and Reopen.

On Experiment creation, users can now search for the Notebook by description as well as by name. This will ease Notebook selection.

The Contact Support option on the login page and under the User Menu will now link directly to the main Support page instead of routing to an account login page.

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

Usability Improvements

Admins may now configure any internal reference field to allow users to input multiple internal reference links and predefine a query.

The predefined query streamlines user selection of the desired internal reference/s. In the example below the administrator is restricting users to select Projects from a specific Notebook.

Users are then able to populate multiple values using admin desired internal references. Users may not change the admin defined query but may further refine it prior to selection.

Inventory and Materials

Creation Date in containers details page
Creation Date was added to the Container Properties tab in the container details page:

Update Amount on containers
When you are on a container and you have edit permission, there is an Update Amount button that can be selected to update the amount of material in the container. When the button is clicked a new window will appear.
The Update Amount window has been updated to be more streamlined and focused:

Associate containers with registered material from Sample table and print multiple barcodes.
We have extended the ability for creation of containers from the Samples Table to automatically associate a new container with a Material ID if the Sample has been registered:

We also continued the workflow so that if more than one container is created, all the labels can be printed at once:

Integrations & APIs

We have added two endpoints to facilitate the bulk updating of data within Sample tables and Sample Summary tables. The two endpoints, GET/samplesTables/{samplesTableId}/rows and PATCH/samplesTables/{samplesTableId}/rows allow bulk editing of up to 50 samples at a time.

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

Sub-Experiment Layout

The Plate, Well, Row, and Column data captured on each SubExperiment via the SubExperiment layout is now reported via the public API when retrieving the SubExperiment entities.

Configuration Transfer

We have extended our configuration transfer capability to support transferring External Actions, Plate settings, Sample settings, Experiment settings, and Task and Request settings.

What’s New
This version 22.3 release of Signals™ Notebook brings archived and approved states and transitions. We’ve enhanced our biosequence library, reagents, and inventory and ordering workflows. We’ve extended the beta capability of Configuration Transfer to cover more areas of configuration and added a beta capability to lay out parallel experiments in plates or grids. We’ve also fixed a number of small bugs.


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

• Usability Improvements
• • –  Description field available as a search filter

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

• Usability Improvements
• • –  Optional fields are not collapsed
• Materials Library
• • –  Containers in Quick Add look up from Stoichiometry Table
  • –  View biological sequences in dynamic mode without editing
  • –  Search for features and properties in registered biological sequence files
• Inventory & Ordering
• • –  Orders with Material ID linked go directly to Lot Choose/Create page
  • –  Received Orders with multiple containers display all containers in Materials Request page
  • –  Bulk Action: Bulk Dispose Containers
  • –  Set default unit for properties
• Administrative improvements
• • –  AuthnContextClassRef property added for SAML configuration
  • –  Option to allow reviewers to edit content they are reviewing
  • –  Optional Approved state
  • –  Optional Archived state
• Integrations & APIs
• • –  GET/DELETE comments
  • –  Change state from Closed to Archived
  • –  Import materials via ZIP file
  • –  GET contents of grid from ELN Archive
• Parallel Experiment layout (beta)
• • –  Manual layout
  • –  Systematic layout
  • –  Ability to define grid dimensions
  • –  Ability to block out selected wells
• Configuration Transfer (beta)
• • –  Chemistry settings
  • –  Users
  • –  Table Templates
  • –  Group associations
  • –  Reporting of import successes and failures

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

The following OnDemand videos for administrators are now available

• Basics to Setup Unrestricted Access to Signals Inventory
• How to Add Access Restriction to Signals Inventory

The following OnDemand video for end users is now available

• Explore Advantages to Including Biological Sequences

This content is anticipated for release on our Production E3 environments, and for Private Cloud customers on our deferred release schedule, in July 2022.

Further Details

Usability Improvements

Users can now filter their search by the entity description. This will help when the entity name is not descriptive.

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

Usability Improvements

The optional Additional Fields section will now be expanded by default on the entity creation form to ease entry of Additional data. This section is still collapsible. It will now just default to expanded as opposed to collapsed.

Materials Library

Registered proteins and DNA sequences can now be viewed in dynamic mode without having to first enter edit mode. Users can toggle modes to inspect sequences in detail and utilize other functions such as copying sequences.

Users may now find registered biological sequences via a simple text search. General properties, features, and primers can all be surfaced by a text search. The search can be used in combination with others to quickly find any sequence.

Expanding on the Quick Add functionality in the ChemDraw Document Stoichiometry table, if users type in the full or partial Chemical name of a material, the Quick Add drop down will show containers available:

If there is more than one container available, a page will open for the user to select the container:

The container will be added to the Chemical Drawing as well as the stoichiometry table:

Inventory

When users receive an order where the material is already identified in the Order Request, the receiving workflow will start with the Choose Lot page and not the Choose Reagent page:

Received Orders with multiple containers display all containers in the Materials Request page:

Containers can now be disposed using a bulk action. Navigate to the Bulk Action page by clicking the barcode icon in the top of the Inventory page:

Users can scan, copy/paste, or type in barcodes of containers that they would like to add to the table below. By clicking the Add button the containers will appear in the table:

If an invalid barcode is scanned, copy/pasted, or typed the user will see a Barcode Not Found message:

Users may also add containers to the table by using the Search option in the top right corner:

There are filters available to narrow the search for containers:

Users can use the Select All in the top right corner to quickly select all or the clear selection to deselect the containers. Once the containers have been selected, click the Add Selected button to add the containers to the table:

In the table, users can use the Clear List to remove all the containers from the table. By clicking on the checkbox next to the Barcode column, users can quickly select all the containers. To remove only select containers from the table, the Remove button is available on the far right:

Once the containers are selected for Disposal, the Dispose Selected button will become available. Once clicked, the user will get a confirmation message. Upon confirmation, the user will see the containers in the table Status column is updated to Disposed:

An additional Barcode option of 76 by 25 mm has been added in the Print Dialog drop down:

The new option will print: Material Name, Barcode, Location, Safety Icons, Size, Creator, Received Date, Expiration Date, RM #, Description, Additional Info/Safety (text field):

Administrators of Signals Notebook can navigate to the SN Config → Inventory page to access the Properties for Containers and Locations:

After selecting a property, the administrator can set the default units that they would like for the property:

Administrative Improvements

The SAML AuthnContextClassRef property has been added as an optional parameter for configuration. This property is used to support signing workflows when the admin requires the signer to reenter their password at sign off which supporting single sign on. This addition is available only when a system is using an external SAML compliant IdP.

When defining workflows for Experiments, Parallel Experiments and Admin Defined Objects admins can now optionally allow Reviewers temporary edit privileges on the object while it is in review.

Experiments, Parallel Experiments, and Admin Defined Objects can now optionally be Approved. Approving of these objects is a State change, whereby a Reviewer can move it into the Approved state from In Review. When it is in the Approved state a user with Full Control or optionally the Creator can move the object to the Closed state. The Admin can require the reviewer to comment when Approving, Rejecting, or Accepting (ie. Closing) an object and set predefined comments for each.

Experiments, Parallel Experiments, and Admin Defined Objects can also now optionally be Archived. Archiving of these objects is a State change, whereby a user with an Archive privilege and a minimum of View on the object can move it into the Archived state from Closed. When it is in the Closed only a user with the Return from Archive privilege can return the object back to the Closed state.

An object in the archived state cannot be directly Reopened. New comments cannot be added, nor existing comments edited or deleted, when the object is in the Archived state. Administrators can define rules in the security policy specific for the Archived state.

Approve, Archive, and Return From Archive state transitions can also be used to trigger external actions. This can be used to intercept signing events to check the content against specific business rules. This extends existing capability already available for other signing events.

Integrations & APIs

We have added three endpoints to be able to retrieve and delete comments from a given entity.

Comments can be deleted by the original creator of the comment or anyone with Full Control on the object via the API; currently only the creator of the comment can delete or edit comments directly through the UI.

We’ve added an endpoint that allows an application to programmatically move objects from the Closed to the Archived state. This endpoint allows an optional comment to be added to the audit trail entry.

The POST/materials/{libraryName}/bulkImport endpoint has been extended to support import via ZIP file.

An additional endpoint was added to be able to retrieve the expected formatting for the ZIP file.

The GET/entities/{eid}/export endpoint has been extended to allow the contents of Tables and Lists from ELN Archive to be downloaded as .csv files.

The following capabilities are in beta and are only available to users and administrators of Signals Notebook Standard or Private Cloud upon request. 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.

Sub-Experiment Layout

Chemists can now represent their grid, or plate, layout of their Sub-Experiments in a parallel experiment by adding a Sub-Experiment Layout element to their Parallel Experiment. This element will provide a list of all the Sub-Experiments, which can be manually or systematically laid out in grids.

The chemist can define dimensions for the plates and indicate wells that should not be filled during a systematic layout.

The chemist can select any well to see details of the Sub-Experiment in that position. The data that is displayed can be modified via a configuration screen. This can alternatively be set in a Parallel Experiment System Template by the administrator.

Configuration Transfer

We’ve extended our configuration transfer capability to support transferring Group Associations, Users, Table Templates, and Chemistry Settings.

The admin will also now be presented with a report on the successes and failures when importing configuration.

What’s New
This release of Signals™ Notebook brings improvements to our beta releases of calculations in Admin Defined Tables, configuration transfer. Plates are now no longer on beta release and available to all administrators, along with many improvements. We have also added PubChem integration, made some improvements to Orders and to Materials, and added or enhanced a number of API endpoints. We have also fixed some small bugs.


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

• Usability Improvements
• • –  Additional ChemDraw^® hotkeys
  • –  Copy selection as CDXML

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

• Usability Improvements
• • –  Hover over for internal reference fields
• Materials Library
• • –  Add Containers, Samples, Reagents & Compounds to the Stoichiometry Table
  • –  PubChem Pull- custom fields
  • –  Sequence based material libraries
  • –  Lineage tracking for Materials
  • –  Admin-defined internal reference query
  • –  Multiple internal reference links
• Inventory
• • –  Barcode font
  • –  Material Request Table update
  • –  Disposal Workflow
• Platess
• • –  Plate ID
• Samples
• • –  Append templates
• Calculations in Admin Defined Tables
• • –  Removal of beta flag, on general release
• Integrations & APIs
• • –  Delete single associations from group associations
  • –  Entity flags
  • –  Endpoint for Plate Summary Table
• Configuration Transfer (beta)
• • –  Attributes
  • –  Roles & Privileges
  • –  Salts/Solvates
  • –  Biological Sequences
  • –  External Notifications
  • –  System Groups
  • –  Security Policy

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

The following OnDemand videos for administrators are now available

• Export Materials with APIs
• Initial Launch Essentials
• Defining Locations

The following OnDemand videos for end users are now available

• Export Materials from Your Materials Library

The following OnDemand videos for Inventory are now available

• Getting Started with Signals Inventory

This content is anticipated for release on our Production E3 environments, and for Private Cloud customers on our deferred release schedule, in July 2022.

Administrators should note that we no longer support Tibco Spotfire ^® version 10.3.

Further Details

Usability Improvements

We have enhanced a few hotkeys in our embedded ChemDraw sketcher.

Ctrl-Alt-K (Cmd-Alt-K) will toggle between kekule and aromatic representation for selected aromatic systems.

The hotkeys “j” and “shift-j” will sprout a cyclopentadiene or a phenyl ligand orthogonal to a metal atom.

Shift-Up/Down/Left/Right Arrow moves the hotspot by 3 bonds. Shift-Alt (Option)-Up/Down/Left/Right moves the hotspot to the nearest fragment in that direction.

Alt (or Option)-Up/Down arrow will rotate a selected object 15 degrees counter clockwise/ clockwise. Alt Left/Right rotate 1 degrees counter clockwise/clockwise.

The toolbar also now has a new option to copy the selected part of the drawing as CDXML to the clipboard.

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

Usability Improvements

We have added a hover over preview for Internal References in Table type entities and in the entity fields/properties of Signals Elements. This will allow users to view a simple preview which includes a preview image and the Properties/Fields of the linked entity when they mouse of the i icon.

Materials Library

The Chemical Drawing Element in Experiments can look up Barcodes, Container ID’s, Reagents (SNB) and Samples. We’ve improved the Compound look up as well as added the ability to search different sources in the Magnifying Glass Icon next to the Quick Add toolbar.
Administrators need to set up the mapping for users to take advantage of this capability.
For mapping of Samples, administrators will need to choose Samples in the System Objects configuration:

A new section called Stoichiometry Mapping is available to map the fields from the Sample to the fields populated in the Stoichiometry table.

The administrator must not only map the fields, but also Enable the mapping and save the changes:

To set up the Reagents (SNB) and Compound libraries administrators need to navigate to the relevant Material Types, and set the Stoichiometry Mapping.

If Administrators want to update the fields shown in the Stoichiometry tables, they can do so via the Chemistry Settings in the System Configuration:

The Barcode, Material ID and Container ID are hidden by default in both the Reactants and Products Tables.

Users can type, scan or copy/paste a barcode, container ID, Sample ID or Material ID, for Compounds or Reagents (SNB) into the Quick Add tool bar to add the structure and relevant properties such as Barcode, Container ID, Material ID and/or Sample ID to the Stoichiometry tables:

If users want to browse for the desired Compound, Reagents (SNB), Containers or Samples they can do so via the magnifying glass icon next to the Quick Add toolbar. When users click the magnifying glass icon, they will get a search window where the drop-down menu can be changed, and filters applied. Once the material of interest is located, the user can select where to place the compound in the scheme.

Users can type or copy/paste the name or part of the IDs, or the chemical name, into the Quick Add toolbar. When more than one option is available, the search window described above will open and the user can select which item to add and where to add it to the scheme.

Users who create content in the Reagents (SNB) Materials Library can pull additional custom data into the Reagent (SNB) that is publicly available from PubChem.
The administrators will need to add the custom fields to the Reagents (SNB):

Then the additional fields can be mapped for the PubChem Pull.
Click on the Mapping option under PubChem to set the field(s) that users can populate from PubChem:

To use the PubChem features, users can create a new Reagent (SNB) with a valid CAS number or choose a currently existing Reagent (SNB) and click the PubChem refresh icon in the top right corner. The data available will be populated in the table below and the date will be next to the refresh icon in the top right corner:

Biological sequence files are now supported in the Materials Library. Admins can define a new Material type as either Custom, DNA, or Protein. The sequence file itself can be defined as required or optional. Uniqueness checking by submitted sequences is supported during registration. Uniqueness is based on an exact match of the submitted sequence.

When registering, users may add supported sequence files. Sequence files can be previewed in static or dynamic modes with properties appearing below the sequence file.

Admins now have several enhancements when defining a Material internal reference property. The admin can allow for multiple internal references, may predefine the query the user will leverage, and can define if the internal reference will be for tracking the lineage of the underlying Material.

There are two types of Internal References. A General internal reference allows the admin to leave an open or defined query and users may select any object allowed by the admin for the internal reference.

The Lineage-Parent internal reference will only allow another activated Material to be focus of the internal reference. This will allow for tracking Parent-Child relationships between related Materials. The underlaying relationships will enable future enhancements for better search, analysis and understanding of Material lineages.

When configuring an internal reference field on a Material property field, the admin may now predefine the search query. This allows the user to easily pick the internal reference desired by the admin (e.g. Library). When selecting the appropriate internal reference/s during registration, the user may further refine the query but may not change the underlying query path for the internal reference.

When allowing for multiple internal references, uses may select more than one internal reference when registering a material. These references will also display in Materials Tables in Experiments and elsewhere.

Inventory

The Barcode font has been updated to be bolder with thicker lines to accommodate printers that use lower dpi print options. This will also aid scanners to be able to read the barcode more accurately.

The Material Request Table Request column has been updated from e-mail address to the user’s name with a hover over with additional information.

The Inventory Disposal Workflow is a 2-step process: Dispose and Final Dispose. Users can dispose containers, but only users with additional permission may move the disposed containers to final dispose. Disposed containers can be restored, final disposed containers may not be restored and can no longer be updated in any way. Final Dispose is for record keeping information of the containers and their materials have been removed from the premises.
To provide additional permission to a group of users, the administrator will need to navigate to the User Roles, Containers tab and check off the groups that should have Final Dispose permission:

Users can dispose of containers by navigating to a container and choosing the Dispose button:

Once confirmed, and the container has been disposed, the additional buttons are removed, and the status is displayed in the top right corner:

If the container was disposed by accident, the user can restore the container by clicking on the ellipse in the top right corner and choosing Restore:

If the user has navigated away from the container screen, but would still like to restore the container, they can navigate to a list of the disposed containers.
Under the User Name menu choose the Disposed Items option:

Select the container(s) to restore by using the checkboxes. If all containers are to be selected, use the checkbox in the top left next to the Restore button:

Final Dispose can be performed from the same location as the Dispose Restore if the user has permission. Select the container(s) to be Final Disposed and select the Final Dispose button:

Once confirmed, the container is Final Disposed and cannot be restored:

We highly recommend that a location for Final Disposed containers is created in the system and that all containers to be placed in Final Disposed be moved to that location prior to selecting the Final Dispose button. Locations cannot be deleted if containers are in them, this includes Disposed and Final Disposed containers. Containers that have been moved from Disposed to Final Disposed will disappear from the Disposed page and appear on the Final Disposed page.
Disposed and Final Disposed containers do not return in the Global Search. Users can see and filter by location for Disposed and Final Disposed containers in the Disposed Items pages only. To toggle between Disposed and Final Disposed users can use the radio buttons on the left side:

Users can filter by location and the text search within the results to narrow down results.

Plates

The Plate Element in an Experiment now has Plate ID’s that can be filled in by the user. The Plate ID is a text string that can be different for each plate.
Plate 1:

Plate 2:

The Plate ID is searchable in the Global Search interface:

Samples

Users can append sample templates to existing samples to add content from a sample template to an existing sample. This appends content only and does not alter the sample properties. This functions in a similar way to the “Append Template” function currently available for experiments.

Calculations in Admin Defined Tables

Capabilities enabling calculations in admin defined tables, released in beta over the last few months, are now available to all administrators without request.

Integrations & APIs

The endpoint PATCH/groups/{groupID}/associations has been updated to allow deletion of a single association.

We have added an additional parameter to our POST/entities/search endpoint to allow the results to include the CanEdit flag indicating if the user making the API call has edit on the given entity.

The CanEdit flag is also reported in the GET/entities/{eid} response.

We have added an endpoint GET/plates/{plateContainerID}/summary to export the contents of a plate. This provides access to the same data as the Summary Table/csv for the Plate element created in an Experiment

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

Configuration Transfer

We have extended our configuration transfer capability to support transferring Attributes, Roles & Privileges, Salts/Solvates, Biological Sequences, External Notifications, System Groups and Security Policy.

What’s New
This release of Signals™ Notebook brings improvements to our beta releases of calculations in Admin Defined Tables, configuration transfer. Plates are now no longer on beta release and available to all administrators, along with many improvements. We have also added PubChem integration, made some improvements to Orders and to Materials, and added or enhanced a number of API endpoints. We have also fixed some small bugs.


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

• Usability Improvements
• • –  Updated Notebook view
  • –  Bulk import of users works asynchronously
  • –  User alias is printed in exported PDFs
  • –  Default units
• Biomolecular Sequences
• • –  Search by property or feature
• Integrations & Administrative Enhancements
• • –  GET related items
  • –  GET/POST/PATCH/DELETE Materials attachments
  • –  GET User to include creation date
  • –  PATCH ID for Admin Defined Table linked to an External Data Source
• Materials
• • –  Bulk import including attachments from ZIP file
  • –  Update to Materials user interface
  • –  PubChem data pull
• Inventory - Orders
• • –  New Order tabs updated
  • –  Status updates on Order details page
• Plates
• • –  Plates available to all administrators
  • –  Print plates in an experiment
  • –  Export Summary Table to csv
  • –  Read only view of plates for experiments
  • –  Auto-update of Summary Table on small plates
  • –  Copy/paste into multiple cells
• Configuration Transfer (beta)
• • –  Print & Export, Deletion, Appearance, Timeout, File upload system settings
• Calculations in Tables (beta)
• • –  Define accuracy of calculated values
  • –  Show tooltips for formulas to end users
  • –  Added power based calculations
  • –  Capability for administrator to test table calculations
  • –  Export to csv/clipboard enhanced to include headers and SUMs

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

The following OnDemand videos for administrators are now available

• Chemistry Settings: Make Chemical Drawing Content Your Own
• Key Settings Needed to Register Samples into the Compound Material Library

The following OnDemand videos for end users are now available

• Filtering with Self, Parent, and Child
• How to Troubleshoot a Material Bulk Import
• Associate Materials to your Experiment
• Working with Microsoft Office Files

This content is anticipated for release on our Production E3 environments, and for Private Cloud customers on our deferred release schedule, in July 2022.

Administrators should note that we anticipate removing support for Tibco Spotfire^® version 10.3 in our next release.

Further Details

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

Usability Improvements

The Notebook details view has been updated to be consistent with the experiment, notebook and other folders. This adds improved performance, additional filters and the ability to view in a detail view in addition to the List/table and Card views.

The bulk import of users has been updated to work asynchronously. This change removes timeout issues when loading larger numbers of users.

When an Experiment is printed to PDF, the user Alias will now be included in the user information on the PDF cover page.

In the event there is no user alias, the cover page will be unchanged.

Admins can now set default units for Number w/ Unit fields in the SN Config of Signals Elements if the system standard default unit for a specific measure isn’t useful to their users. Number w/Unit fields will now have options for “Measure” and “Default Unit” as seen below in the Chemistry settings. The admin will be able to select the “Default Unit” from our list of available units for the selected measure.

If no unit selection is made, the field defaults to our current system default unit.

This change would only apply to user entered integers from the time the default is set. So when a user enters an integer without specifying the unit, the new default unit is used.

Biomolecular Sequences

Biological sequence files may now be found via quick or advanced search. Text contained in the file and found under the Properties tab in the Sequence Viewer (General, Features, and Primers) is now searchable.

Integrations & Administrative Improvements

We have added a new public API endpoint, GET/entities/{eid}/relationships, to get the related entities for an entity.

We added new endpoints for Materials to be able to GET, PUT and DELETE attachments for Materials.

The GET/users and GET/users/{userID} endpoints have been extended to report the creation time and date for the user.

We added a parameter to Admin defined table endpoints, POST/adt/{eid}, PATCH/adt/{eid} and PATCH/adt/{eid}/{rowid} to allow the developer to force a synchronization. This will enable the developer to enter an ID which is used to lookup an external data source.

Materials

The Materials Library interface has been updated to provide users with a clearer preview of images and chemical drawings and to clearly distinguish Asset and Lot properties. The Asset and Lot information are now on separate pages accessed with a simple toggle. The Batch page contains the same functionality and information that was previously located on the same page.

Users may now bulk upload new Materials with images or file attachments. Bulk upload of new Materials requires a single .zip file containing: (1) A CSV file named summary.csv with Material properties and mapping to file attachments and (2) File attachments that are mapped in the corresponding summary.csv file. An example .zip file can be downloaded from the Bulk Import page of any activated Material for guidance.

Users who create content in the Reagents (SNB) Materials Library can pull data into the material (asset) that is publicly available from PubChem.
The administrators will need to do a very small amount of initial set up to activate the PubChem Pull.
Go to the Materials SN Config area and choose the Reagents (SNB), click on PubChem and Activate the “Import From PubChem” option:

Then click on the Mapping option under PubChem to set the field(s) that users can populate from PubChem:

Click the Save button to save the Import options.
There is a PubChem Terms of Use that administrators should be aware of. Click the blue link called “PubChem Terms of Use” to read the document:

There is an option for users to read the Terms of Use under the username:

By selecting the “PubChem Terms of Use” users will be directed to a page where they can read the content:

To use the PubChem features, users can create a new Reagent (SNB) with a valid CAS number or choose a currently existing Reagent (SNB):

Fields that have had the Import option turned on will have a grey icon next to them so users are aware that those fields may be populated from PubChem.
At the top right corner, users with edit/create permissions will be able to click on the “Import from PubChem” refresh icon.
Once clicked, the user will be warned that the current data will be Overwritten:

Once the user Confirms this is acceptable, the user will see a message letting them know if the pull was successful:

Once the message is closed, the user will see the data that was available in PubChem is now populated in the Materials Library:

Users can still edit or update the data, even if there is data from PubChem:

Users should be aware that if they choose to pull the data from PubChem again, any data manually entered will be over overwritten when data is found in PubChem. If the user manually populates a field and that field is blank from PubChem, the users data will persist even after the PubChem update.

Inventory- Orders

The Inventory, On Order and Reorder tabs in the New Order Material Request webpage have been improved to have color every other row and a “Type to filter” option at the top:

If more than 20 results are returned on the Inventory, On Order or Reorder tabs, users will see a “Show More” link at the bottom:

The status of an Order Request can be changed in the Order Request Details page in the top right-hand corner:

Plates

Plates are no longer in beta and are available for all administrators. Please remember administrators will need to enable plates in SN Config:

When users choose to Print to PDF their experiment, the plates will print as a csv attachment to the PDF. When users open the PDF, they will see the name of the attached file they should reference to open the data file:

Users can export the Summary Table of the plate(s) in the experiment by using the download icon:

When the experiment is closed, users are able to see the plate data and legend as they click through the tabs:

Smaller plates will automatically update the Summary Table for users:

As the number of plates or tabs increase the users will still be given the update button to a manual update the Summary Table data.

Users can now select multiple cells or rows in the plate element and click the copy icon from the List causing the cells to be filled in with the selected value:

Fill the entire column in 1 click:

Fill rows and columns with one selection and one click:

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

Configuration Transfer

We have extended our configuration transfer capability to support transferring certain system settings. Currently we support transferring settings for Print & Export, Deletion, Appearance, Timeout, and File Upload settings.

Calculations in Admin Defined Tables

The administrator can now test out their calculations in admin defined tables prior to releasing the table templates to end users. The “Test In Out” button will launch an interactive table where the admin can enter representative data to verify the calculations are working as desired.

The administrator can also define the accuracy of calculated values. The administrator can define a maximum or absolute number of decimal points for any calculated value.

The mathematical operators have also been extended to include Power, for calculating squares, cubes etc., SQRT to calculate Square Root and √ to calculate other roots such as cube root.

We have also provided tooltips to the end users so they can see the equations being used to calculate the values in their tables.