ScienceCloud Release Notes - November 2017

Last Updated: Dec 13, 2017 06:46AM PST

Project Data Enhancements


SAR Table

Enhanced SAR Table functionality with:

  • Batches can now be sorted, similar to as on the Project Data search results page
  • Social – comments, favorite, and like are available, similar to as on the Project Data search results page
  • More batch information, including a batch tooltip, is available
  • A selection checkbox allows for filtering SAR Table data to be exported or sent to a task
  • Templates can now be shared with specific team members (instead of the entire team)
  • Multiple value display now includes number of values and standard deviation

Project Data Entry Enhancements

Entity Type Data Migration
  • Compound type has been renamed to Entity Type
  • During entity type data migration, all specifically defined entity type within a team will be preserved and set to entity type representation “Chemistry Representation”
  • Previous default and unused entity type will change to SMM entity type 
  • A new list of default entity type will be created

Project Data Entry Home
  • A redesigned home page provides easier navigation
  • Custom registration and data entry protocols, if available, are shown on the homepage

My Registrations
  • A view of current and historical registrations
  • Currently running registration statuses are constantly updated
  • Currently running registration can be canceled
  • Validated registrations can be registered from this page
  • Registration reports and original data files can be downloaded

Register Entities – Online
  • The Entity Type field determines new structure representation inputs for:
    • Compounds via the already existing sketcher choices or SMILES
    • Biologics via HELM or Sequence
  • Enabled custom properties addition at registration for Entity, Batch, Sample, Shipping, and Assay Results

Register Entities – From file
  • A new page to register entities from file instead of using Project Documents
  • Registration of biologics through HELM or Sequence representation
  • Interactive creation of mappers from your raw data to ScienceCloud’s data fields
  • New options to register a file only when all records in the file have passed validation, or for any record without error
  • Enabled custom properties addition at all levels: Entity, Batch, Sample, Shipping, and Assay

Add Data To Entities – Online
  • Enabled custom properties addition for each Assay Result

Add Data To Entities – From file
  • A new section to register assay results from CSV Files
  • Interactive creation of mappers from your raw data to ScienceCloud’s data fields
  • Enabled custom properties addition for each Assay Result

Project Data Search Enhancements
  • A new option has been added to enable searching by Entity Type along with all the previously available options

ScienceCloud Administration

Project Administration
  • Added the ability to view and edit project/batch group relationships and folder information from within the project add/edit window
  • Added the ability to view and edit project/assay group relationships in the project add/edit window

User Administration
  • Team Permission Administrators are now able to invite new users to their team via an email link.
  • Team Permission Administrators are now able to manage users in their team.

Assay Group Administration
  • Added the ability to view and edit assay group/assay relationships in the assay group add/edit window

Project Data Component Collection

New Features


New data type: Entity

As part of new ScienceCloud features related to Entities, the Entity data type has replaced the Compound data type.
This change is backward-compatible:

 

  • The Compound data type still exists and components manipulating this data type are still present, though they have been deprecated.
  • The Entity data type’s properties have been kept identical if they already existed on the Compound data type. For example, Entity IDs are stored in a property named COMPOUND_ID, as was the case for Compound IDs in the past.
  • Components impacted by these changes, either because they were expecting Compounds in input or output, or because some of their parameters were referring to Compound data type, have been deprecated and replaced by a new component, with appropriate names, parameter names, and input/output data types. (See the “Deprecated” section at the end of this document for more information).

 

Retrieve data types by events

A new component Components/ScienceCloud/Project Data/Administration Data Types/Event Query is available to allow users to query for lists of SCIDS of Batches, Entities, Samples, Shipping and/or Assay Results that have been created, updated, or deleted in a given date and time range, with precision down to the second. 


The Team Administrator role, Data Quality Manager, is required to use this component.
Results can also be filtered based on project assignment. Note, however, that the list of results returned by the component is not restricted by the explicit project read permissions of the user. In other words, there is no need for users to have read permissions on all projects to access the list of SCIDs created within a Team across all projects.
Output records include properties for the SCID, the data type the SCID relates to, the date and time of the event, the event type, and an internal event ID to be able to group SCIDs involved in the same event.

 

Note that the similar (but not equivalent) feature available on the Batch/Entity/Sample/Shipping/Assay Result Query component has been removed from the latest version of these components. This feature will cease to function in existing protocols in the very near future. We strongly advise users to stop using that feature and replace it with an implementation based on Event Query as soon as possible.

 

New component: Delete Sample

A new component is available to delete Sample data types (Components/ScienceCloud/Project Data/Data Types/Sample/Delete Sample). The component has no parameters. It expects records of the Sample data type as input. The records provided as input will be deleted from Project Data if possible (according to current user permissions).

 

New component: Delete Shipping

A new component is available to delete Shipping data types (Components/ScienceCloud/Project Data/Data Types/Sample/Delete Shipping). The component has no parameters. It expects records of the Shipping data type as input. The records provided as input will be deleted from Project Data if possible (according to current user permissions).

 

New components: Create Batch GroupDelete Batch GroupAdd Project to Batch GroupUpdate Batch Group

A new set of components (in the folder Components/ScienceCloud/Project Data/Data Types/Batch Group) is available for data type Batch Group allowing users with Team Administrator role to create, update and delete Batch Groups. These allow for complete automation of Batch Group management.

 

New component: Update Assay Group

Assay Groups can now be updated using a new dedicated component (Components/ScienceCloud/Project Data/Data Types/Assay Group/Update Assay Group). This will allow for complete automation of Assay Group management. The Team Administrator role is required to perform this operation.

 

New data type and components: Query

Saved queries created in the Project Data user interface are now available through the component collection as a new “Query” data type. A new set of components (in the folder Components/ScienceCloud/Project Data/Utilities/Query) is available. These allow for automated management and execution of saved queries.
Note that there is currently no component to create a new query. This operation must be performed in the Project Data user interface.

 

New Templates for Tasks protocols

Templates for all types of task protocols that can be used in Project Data Search, Project Data Entry, and Project Documents are now provided as part of the collection. They can be accessed from Pipeline Pilot Client by opening a New Protocol From Template… from the File menu.

 

New components: utility component for SAR table tasks

The SAR Table task protocol, received as input parameters, a representation of the content of the table along with a representation of the format settings of the table, as defined in Project Data SAR Table. The component SAR Table Data Set Reader and SAR Table Template Reader (in folder Components/ScienceCloud/Project Data/Utilities/Export Tools) provide the capability to parse this information, as demonstrated in the protocol template ScienceCloud/Project Data/SAR Table Task Template.



Enhancements


Registration of entities and assay results using SCID references

New parameters on Define XXX Components or  Edit XXX Components allow references to other objects SCID rather than ID, Tag or Name. If an ID, Tag or Name is provided along with an SCID, SCID will take priority.

For example, when registering a new sample using Define New Sample, one can refer to the parent batch using the new parameter Batch SCID instead of Batch ID. If both SCID and ID for the parent batch are provided, only the SCID will be considered at registration time.

In the same way, when registering Assay Results, Units can now be referred to by SCID instead of names.

 

Define New Assay Results based on sample

In previous versions, Assay Results prepared for registration using Define New Assay Result had to be associated with a Batch directly. While this is still possible, a new Assay Result created with Define New Assay Result can now be associated with a specific Sample of that Batch. (This has been possible in the Project Data user interface for a long time.) In order to associate the Assay Result to a Sample, use the new set of parameters labeled “Sample Information.” ScienceCloud will accept either (1) Sample SCID, or (2) either Batch ID or Batch SCID combined with both Sample container and Sample well.

 

Enhanced support for custom properties

In previous versions of ScienceCloud, custom properties were exposed for all objects in Project Data and Project Document with a SCID.

Previous versions of the collection provided a specific set of components (in folder Components/ScienceCloud/Project Data/Utilities/Custom Properties) to create, retrieve and manipulate custom properties of individual objects. Additionally, query components for assay-related data types (Assay, Assay Parameter, Assay Result Type, Unit) were enhanced to retrieve custom properties of these data types upon query.
Support for custom properties has been enhanced so that:

 

  • Query components for all data types now automatically retrieve custom properties of objects.
  • Registration and update components for Batches, Entities, Samples, Shipping and Assay Results support manipulation of custom properties. For other data types, custom property manipulation is still performed using components in Components/ScienceCloud/Project Data/Utilities/Custom Properties.

 

Cross-application features on data types

Batches can now be explicitly associated with a ScienceCloud Experiments experiment number.
Assay Results can now be explicitly associated with a ScienceCloud Assay Run ID.
Query, Registration and Update components have new parameters to support this new field.

 

ScienceCloud Connection: error handling when password expired

In previous versions, for any failure in the attempt to connect to ScienceCloud using ScienceCloud Connection, a generic error message was returned.
In this version, if login fails because the user’s password has expired, a specific error message is returned clearly explaining the situation.

 

New Registration options on registration components

Registration and Update components for Batches, Entities, Samples, Shipping and Assay Results can now specify that if there is an error in any of the registration data, none of the data should be registered. The default behavior is to register as much data as possible, skipping data with errors.

 

Query Documents and Document folders by SCID

Documents and Document Folders can now be queried by SCID instead of Path. This is especially useful in the Project Documents Task protocol, which receives as input parameters arrays of SCIDs for the selected files and folders.

 

Edit Capabilities on Notification View

On top of displaying notifications from Project Notification, the reporting element created by Notification View can be set to Allow Edition, so that the user can reply to displayed notifications, delete them or create a new notification (depending on user’s permissions) directly from the generated HTML report. This is especially useful when using this component to display a notification in a custom web application.

 

Hit List to Batches optimized for Batch for Entity

Hit List to Batches now returns Batch data records optimized for input into the Batch to Entity component, similar to using the equivalent option on Batch Query. Using Batch to Entity downstream from this component will now perform better.


Fixed Defects

Remove references through token replacement of undefined global properties

Some components’ inner implementation was referring to undefined global properties through text token replacement, which populated log files with a new warning each time the component was used. This has been fixed.

 

Update Entity: submitting an array as entity name generates an error

Trying to update Entity name (and other properties) using Update Entity when a corresponding property was an array of more than one value was generating an error. This has been fixed.

 

Remove Batch Tag parameter on Edit Sample and Edit Shippings

Both Edit Sample and Edit Shipping components had a parameter to modify Batch Tags, but this parameter was ignored. The parameters have been removed, as manipulation of Batch Tags should be made using Batch-related components.

 

Edit Sample ignoring some parameter combination

Some combinations of parameters on Edit Sample were generating an error or creating unexpected results. This has been fixed.

 

Mapping tools example components were using deprecated property names

Some example mapping components in folder Components/ScienceCloud/Project Data/Utilities/Mapping Tools/Mappings were using field names that are no longer supported. They have been fixed to use default field names.

 

Add Batch ID generates an unexpected error with certain combination of parameter values

Some combinations of parameters on Add Batch ID were generating an error. This has been fixed.

 

Query components: unexpected results when combining Project/Batch Group filter and SCID/ID/Tag filters

When performing queries based on both a Project ID or Batch Group ID and an object SCID, ID or Tag, if the returned object was shared in multiple Projects/Batch Groups, the object was sometimes not returned even if the selected Project/Batch Group was part of the list of Projects/Batch Groups of the object. This has been fixed on all query components.

 

Sample and Shipping Query: combination of Batch Group and “maximum” parameters not working as intended

When performing a query on Samples or Shipping using Batch Group filters, the “maximum” parameter was not working as expected, causing the query to return an incorrect number of results. This has been fixed.

 

Batch Group to Batches not returning all expected results


Batch Group to Batches component was only taking in account the first batch group record in an input. This has been fixed.
 

Batch Group Query: parameter Project is case sensitive

Project parameter on component Batch Group Query was case sensitive, but it should not have been. This has been fixed.

 

Changes

Define New Assay Results does not require Project or Batch Group values anymore

In previous versions, providing a Project (and before that a Batch Group as well) was required by Define New Assay Results prior to registration in order to determine whether the user had sufficient permission to register the data. This isn’t the case anymore. In the current version, authorization to register is determined by user permission on projects where both the related batch or sample and the related assay are available.

 

Deprecated Components

Due to recent changes and improvements in the ScienceCloud Project Data data model, a number of components have been deprecated. They have been tested in the current version and will continue to work in this version. However, they may become unavailable in future versions. We strongly advise users to (1) stop using these deprecated in new protocol development, favoring new components that perform the same function instead, and (2) upgrade existing protocols to replace these deprecated components as soon as possible.

Please contact support if you need assistance on upgrading existing protocols.
All deprecated components in the Project Data Component Collection can be found under Components/ScienceCloud/Project Data/Utilities/Deprecated

 

Components with compound-related parameters

Following the introduction of the Entity data type replace the Compound data type, all components with compound-related parameters (the parameter name contains the word “compound”) have been deprecated and replaced with new versions, where parameters have been renamed using the word “entity.”

Note that components where “compound” only appeared in the name of the component have not been deprecated but simply renamed.

 

Batch/Entity/Sample/Shipping/Assay Query: parameters to retrieve data by event type and/or dates

Batch/Entity/Sample/Shipping/Assay Query components all had a parameter group “Data to retrieve” allowing the user to limit the data retrieved to only updated or deleted records in a given date range. This parameter group has been hidden and should not be used anymore.

Consider using the new component Event Query as a replacement for this feature.


V3 migration tools

Utility components provided to assist migration to the new version of ScienceCloud in December 2015. As all existing users have now completed migration, these components have been deprecated.

 

Custom properties emulation components

Before the implementation of custom properties in the ScienceCloud Project Data model, we provided components to emulate custom properties on batches using file attachments. These capabilities have now been completely superseded by a full implementation of custom properties in the data model. Therefore these components have been deprecated.
 

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