PerkinElmer Signals™ Notebook - What’s New

PerkinElmer Signals™ Notebook - What’s New

Signals Notebook is an intuitive and effective scientific research data management solution. Write up your research data and experiments, then drag and drop, store, organize, share, find and filter data with ease.

Check out the latest improvements.

September 2021 Monthly Update (Update to E3 in March 2022) -
What’s New

This release of Signals Notebook brings an initial release of handling of molecular sequence files in experiments, a capability to transfer configuration between tenants and a method to lock Spotfire files while they are being edited. We have provided improvements to parallel experiments, plates in experiments, Materials Library, Reagents and some usability enhancements. We have also fixed a number of small bugs.

The following are available for users of Signals Notebook Individual Edition, Signals Notebook Standard or Signals Notebook Private Cloud

  • Usability Improvements
    • –  Microseconds added to supported time units
    • –  Replace file in elements
    • –  Back calculate volumes from total reaction molarity
  • Spotfire file locking
The following improvements are only available for users of Signals Notebook Standard and Signals Notebook Private Cloud

  • Usability Improvements
    • –  Aliased hyperlinks support ftp
    • –  Remember most recently used attributes
  • Integrations & Administrative Enhancements
    • –  Audit trail records user system access
    • –  Icons for External Actions
    • –  Stoich APIs include Total Solvent Volume and Total Reaction molarity
    • –  POST/entity extended to allow creation of grid in Admin defined objects
    • –  POST/entity extended to allow creation of Sample
    • –  POST Material endpoints extended to allow definition of synonyms
  • Parallel Experiments
    • –  Sample summary table available to all tenants
    • –  Cherry-picking of SubExperiments applies to bulk sample creation
    • –  Cherry-picking in SubExperiment tables and sample summary tables applies to download, copy to clipboard
    • –  Cherry-picking in SubExperiment tables and sample summary tables applies to external actions
  • Samples
    • –  Addition of documents to Sample Templates
    • –  Cherry-picking in Sample tables applies to download, copy to clipboard, external actions
  • Materials Improvements
    • –  Safety fields in Materials Library
  • Inventory
    • –  Containers
      • •  Edit and Delete
    • –  Reagents
      • •  Bulk Import for Reagents (SNB)
      • •  Export for Reagents (SNB)
      • •  APIs for Reagents (SNB)
  • Configuration Transfer (beta)
    • –  General framework
    • –  Autotext
    • –  External Data Sources
  • Plates (beta)
    • –  Activation
    • –  Navigation
    • –  Copy and Delete
    • –  List
    • –  Link
    • –  Add Materials from Current Experiment
    • –  Add Materials with Containers
    • –  Add Custom Layers
    • –  Plates Search
  • Biological Sequence Element (beta)
    • –  DNA and Protein sequences viewed in experiments
    • –  SnapGene Integration
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
  • Settings for Permanent Deletion of Trashed Items
  • Learn to How Setup Samples
The following OnDemand videos for end users are now available
  • Chemical Drawing: Drawing Reactions with ChemDraw
  • What your History Tells You
  • Learn to Create and Record Sample Details
  • Task and Request: Working Through the Basics
This content is anticipated for release on our Production E3 environments, and for Private Cloud customers on our deferred release schedule, in March 2022.

Administrators should note that we have made some changes to resolve some inconsistencies in autonumbering of notebooks, experiments and other objects. A description of the behavior is provided in the administrative updates section.

Administrators should note that we are updating some of security controls which necessitates removing support for a number of older cyphers. The only two cyphers which will continue to be supported are:
  •   TLS_ECDHE_RSA_WITH_AES_128_GCM_SHA256
  •   TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384
This change will only have an impact if you have an integration that specifies one of the unsupported cyphers, in which case your connection will fail. If, as is most common, you do not specify a cypher, then your connection will be unimpacted.

Further the planned change to our back end IP addresses has been delayed. We will ensure adequate notice before we make the planned changes.

Further Details

Usability Improvements

We have added microseconds to our list of supported time units. All time values are normalized to minutes for search.

Usability Improvements

Certain elements now allow the file stored within the element to be replaced without needing to delete the element and add the new file separately. Image, MS Office, PDF, Spotfire, Molecular Sequence and attached files can be replaced. Any custom preview will be retained. Automatically generated previews will be replaced.

Usability Improvements

The stoich tables now allows the user to define an intended reaction molarity, upon which the system will calculate the desired solvent volume. The Limiting Moles/Solvent Ratio field is displayed if a solvent is added, and the moles of the limiting reagent are entered or calculated. If a solvent volume is already defined it will be overwritten with the new solvent volume to achieve the desired reaction molarity.

Usability Improvements
Spotfire File Locking

Spotfire files added to experiments can now be locked before launching in the Tibco Spotfire client via round trip editing. The lock prevents signing actions from being completed and prevents other users from launching the file in the Tibco Spotfire client and potentially overwriting changes. The lock can be removed by the same user. Other users with edit permissions can also remove the lock but are warned who created the lock.

Spotfire File Locking
Spotfire File Locking

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’ve expanded the aliased external hyperlink options to support links of type FTP and SFTP in addition to HTTP and HTTPS. This applies to all areas those links can be created, namely stoich properties, tables, samples, tasks, material tables, materials (assets and lots) and properties on Experiments and similar objects.

Usability Improvements

For creation of experiments and similar objects, where attributes are defined, the most recently used attribute values will be remembered to ease attribute entry. These values are stored locally and will not be remembered across browsers or terminals.

Usability Improvements

Integrations & Administrative Improvements

Administrators can now monitor which users access the SNB system in the Audit Log.

Integrations & Administrative Improvements

To improve usability of External Actions, admins can now “promote” an external action to an icon on the associated element.

The SNConfig page has been updated to ease this process, sorting the External Action by element. Also, admins can now reorder actions for a specific element in the External Action dropdown list.

Administrative Improvements

Admins can select one of the provided icons or upload one of their own for their action.

Materials Improvements

The new icon now appears at the top of element both in the experiment view

Materials Improvements

And in the individual element view

Materials Improvements

This new feature excludes Signing Actions as they are triggered by an action and would not require an icon to be triggered.

We have extended a number of our public API endpoints as follows. The Stoich APIs have been extended to include Total Solvent Volume and Total Reaction molarity, the POST/entity extended to allow creation of grid in Admin defined objects and to allow creation of Samples, and the POST Material endpoints have been extended to allow the definition of synonyms.

Materials Improvements

We have resolved some issues and some inconsistencies around object auto numbering behavior. The following behavior should be expected when creating a new instance of an object. When Global Numbering is ON, for all object types, the new object will take the next number in sequence for that object type regardless of the defined string and regardless of the location. When Global Numbering is OFF, and the Object Type is Notebook, Experiment, Admin Defined Object, Parallel Experiment or Request, the new object will take the next number in sequence for that defined string in that location regardless of the object type. When Global Numbering is OFF, and the Object Type is Sample, Task or SubExperiment, the new object will take the next number in sequence in that location regardless of the object type and the defined string.

This behavior does lead to updated recommendations for clients that want to ensure a combination of unique naming and/or consecutive numbering.

If Global numbering is ON and unique names are desired, the string formats for each object type should be different. If Global Numbering is OFF and sequential numbering within the object type and location is desired then the string formats should be different. If consecutive numbering across objects is desired, such as multiple objects sharing a sequential string within a notebook, then we recommend either requiring those objects to only be created within notebooks and/or ensuring that notebooks have a different string format to avoid non sequential numbering of notebooks.


Parallel Experiments

All parallel experiment capabilities are now available to all customers where parallel experiments have been activated. Customers no longer need to request activation, the features added in beta last release are now generally available.

The cherry-picking capability added in the previous release has been extended to support download to file, copy to clipboard, external actions and bulk create samples in the sub experiment summary, and download to file, and external actions, in the sample summary table. When the user is in selection mode in these tables, these actions will occur on only the selected objects. Specifically for the External Actions, the payload of the call now includes a section to identify the eid’s of the selected objects. External Actions must be configured as a POST event to be supported for this action.

Parallel Experiments
Parallel Experiments

Samples

Admins can now add content to the Sample Templates. Documents added to the template will be added to the Sample when the user creates a Sample of that type.

Parallel Experiments

The selection mode changes to the Sample Summary table above also apply to Sample Tables in Experiments and other objects. External actions, when the method is POST, copy to clipboard and download to file will operate on the selections when in selection mode.

Materials Library Improvements.

GHS Safety fields are now available for every Materials Library. Administrators will need to add the fields and select the appropriate Attribute List in the drop down. Please note that Precautionary and Hazard statements have Multi Select and Show Description options. GHS Hazard has Multi Select, Show Icon and Show Description. You may have 1 of each of the GHS Safety Fields so be certain that they have been configured correctly.
Attribute List with GHS Safety Fields:

Materials Library Improvements

Multi Select and Show Description are below the Attribute List selection:

Materials Library Improvements

For GHS Hazard Multi Select, Show Icon and Show Description are below the Attribute List selection:

Materials Library Improvements

GHS Safety fields are available for users to update upon edit of current materials or when new materials are created:

Materials Library Improvements

Inventory

Edit and Delete button has moved to the top 3 dots in the top right corner:

Inventory

Deleted containers have a red Deleted icon in the top right corner:

Inventory

Reagents

Bulk Import is now available for Reagents (SNB) under that Add New menu:

Reagents

Export Reagents is available from the gear icon in the top right corner:

Reagents

The Materials API updated with CAS, Safety Fields, Concentration and Density for Reagents:

Reagents

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

Administrators can now transfer configuration between tenants. When the admin chooses to download the configuration from the System Settings of a tenant, the system provides an asynchronous download of a .snb file into the preferred download location. This proprietary file can then be loaded into the same or a different tenant. Once loaded the admin can select which portions of the configuration are to be loaded. Transfer is limited to between two tenants that are running the same version of the application, transfer to an older or newer version is disallowed. The current release supports transfer of External Sources and of Autotext. Subsequent releases will support additional configuration settings.

Configuration Transfer
Configuration Transfer

Plates

Activation:
Administrators can activate Plates under the System Settings: Other:

Plates

When Plates are activated, users will be able to add plates to experiments under the Add Content menu. If Plates are not activated, users will not be able to add plates to experiments. If Plates was activated, content was created and then Plates were deactivated, experiments with plates can see and update the existing plates, but no new plates may be created.

Navigation:
In the plate grid, users can use the tab key to move from left to right. When the cursor moves to the end of the row, it will start at the beginning of the next row below. Users can use the Enter key to move from top to bottom in the plate grid. Once the cursor gets to the bottom of a column, it will move to the top of the next column to the right.

Plates

Copy and Delete:
Use the copy icon in the top right of the plate element to copy the plate from one experiment to another:

Plates

Once the copy button has been selected, navigate to a different/new experiment and under the Add Content button at the bottom of the list, choose the Paste Plates:

Plates

Use the delete icon in the top right of the plate element to delete the plate element from the experiment. A warning message will appear before the delete will be completed:

Plates

List:
A new feature of plates is the List feature. The List name and contents will change depending on the layer/tab you are on. Users can copy and paste a list of values into the List or type values directly into the box and then select the “Add to … List” under the values.

Plates

The values will move to the space above the text box and below the Legend. The values will remain when moving from one plate to the next. To add items from the list to the plate grid, use the copy button on the right of the value. To remove an item from the list, use the delete icon to the left of the value.

Plates

When items are moved from the list to the plate grid, they will appear in the legend with a corresponding color:

Plates

List in the Materials layer/tab will automatically link to Materials, Materials Batch/Lot, Samples, Barcodes and Container ID’s. The appropriate icons will be associated with the value:

Plates

Links
Values typed directly into the plate grid can be linked via the Legend to a Material, Material Batch/Lot, Sample or Container:

Plates

Select the Material Batch/Lot from the window:

Plates

The value in the Legend is updated with the link and the selected Material Batch/Lot name:

Plates

If there are Materials, Tables and/or Sample tables in the experiment, the “Add From Experiment” link will provide a window to select the Materials and Samples to be added to the Material List. Materials, Sample and Table in an Experiment:

Plates

Window to select Samples and Materials:

Plates

The Materials List shows the added items:

Plates

Add Materials with Containers:
If more than one container of the same Material is added to the Material List, a hover will appear over the icon that will note the Container ID:

Plates
Plates

When the containers are added to the plate grid, they will have different colors and in the table below the plate grid, the container ids are reflected in the Container column:

Plates

Add Custom Layers:
Plate elements automatically create Well Format, Concentration, Material, Amount, Replicate and Deviation layers/tabs. To add additional layers/tabs, select the + icon to the right of Deviation:

Plates

A window will open to enter the Name:

Plates

Select an Annotation Class:

Plates

When you select an Annotation Class from any of the default layers/tabs (Amount, Concentration, Deviation, Material, Replicate, Well Format) the layer/tab will look and behave like the default layers/tabs:

Plates

The table below the plate grid will reflect the added layer/tab:

Plates

If the default layers/tabs are not accurate for the data that needs to be added to the plate, there is an “Other” option:

Plates

If Other is chosen, a Data Type drop down will be presented. Integer is for whole numbers; Real Number is for decimals and Text (String) is for text. These Data Types correspond to the Data Types used in Signals VitroVivo™.
The Other layer/tab is reflected in the table below the plate grid:

Plates

Search
Searching for a Material, Material Batch/Lot, Sample, Container Name or a typed value in the Materials layer/tab will return the plate it is associated with in a Search query:

Plates

To reduce the search to just plates, under the Type choose Plate:

Plates

Biological Sequence Element

Users may now insert via add content or drag and drop biological sequence files (e.g. Genbank) into Experiments in Signals Notebook and render a preview of the sequence map.

Plates

Full entry into the Element splits the read-only view into the annotated map versus more detailed features such as the sequence.

Plates

An integration with SnapGene enables users to change the sequence and save the updated file back to the underlying experiment. We also support an upload and replace of files created with nearly any sequence design tool.

Plates
August 2021 Monthly Update (Update to E3 in November 2021) +
July 2021 Monthly Update (Update to E3 in November 2021) +
May 2021 Monthly Update (Update to E3 in November 2021) +
April 2021 Monthly Update (Update to E3 in July 2021) +
March 2021 Monthly Update (Update to E3 in July 2021) +
February 2021 Monthly Update (Update to E3 in July 2021) +
January 2021 Monthly Update (Update to E3 in July 2021) +
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