Assay Custom Resource Publication Guide

Last Updated: Jun 01, 2019 07:13AM PDT

Summary: A guide to preparing ScienceCloud Assay custom resources for publication to production or sandbox

Covered Topics

The following topics are covered in this article. Clicking a link will scroll the page to the relevant section.

Introduction to ScienceCloud Assay Custom Resources

You can customize ScienceCloud Assay by creating custom resources as Pipeline Pilot protocols. A custom resource for ScienceCloud Assay can be created from a Pipeline Pilot client connected to ScienceCloud Authoring (authoring.sciencecloud.com), and published for registration in your team's Assay Administration page.

Customizable resources for ScienceCloud Assay are:

  • Readers: capture direct output of plate readers and manage data complexity
  • Sample Information Mappers: associate barcode information to plate data
  • Calculators: normalization procedures that transform raw data into normalized results and generate statistics
  • Post Transformations: sample and reference analysis procedures that perform data analysis on aggregated groups in order compute elaborated data
  • Viewers: visualization templates for using visual analytics capabilities to exclude outliers on control wells and identify deviation patterns
  • Reader Computations: used to compute well data from the raw field data in HCS runs.
  • Well Mapping:
  • Publishers: map protocol information and publish results on central repository

When creating any of these custom resources in Pipeline Pilot, protocol-level parameters should be created on your protocol so that the publishing process configures the protocol correctly in your team's Assay Administration page. Valid protocol-level parameters and values for each resource type are described below in the section for that resource. In many cases, the absence of any of these protocol-level parameters will result in the protocol being published with a default value for that parameter.

For all ScienceCloud Assay custom resource protocols, the resource name matches the protocol name and the resource description comes from the protocol summary. In the following screenshot from Pipeline Pilot's File->Save Protocol screen, the custom resource is a reader and the resource name is "BIO PDA Reader Matrix Format1". The description is "Plate Data Analytics Reader - Matrix Format 1".

Readers

A reader is a custom resource that captures direct output of plate readers and manages data complexity. In other words, a reader parses raw data from a file uploaded by the ScienceCloud Assay user and creates the plates and wells in ScienceCloud Assay.

The following protocol-level parameters are valid for sending configuration information for your reader to ScienceCloud Assay. For any parameter with a Default Value, you can omit the protocol-level parameter if the default value is appropriate for your custom reader.

For the Is Smart parameter, a reader is smart if it generates the plates and wells directly from reading the raw data files.

Parameter Name Parameter Type Legal Values Default Value
Plate Format String

1 (1x1)

4 (2x2)

6 (2x3)

8 (1x8)

12 (3x4)

24 (4x6)

48 (6x8)

96 (8x12)

384 (16x24)

1536 (32x48)

3600 (60x60)

384 (16x24)
Data Type String

Cross Run

End Point

High Content Screening

Kinetic

End Point
Is Hidden Boolean

True

False

False
Is Smart Boolean

True

False

False
File Fragment String    

The following screenshot provides an exmaple of where to set a protocol-level parameter on the Parameters tab in Pipeline Pilot client, using the parameter Plate Format as an example. Your protocol must be open in your Pipeline Pilot client with none of its components selected in order to set a protocol-level parameter.

Sample Information Mappers

Sample Information Mappers associate barcode information to plate data.

The following protocol-level parameters are valid for sending configuration information for your sample information mapper to ScienceCloud Assay. For any parameter with a Default Value, you can omit the protocol-level parameter if the default value is appropriate for your sample information mapper.

Parameter Name Parameter Type Legal Values Default Value
Is Hidden Boolean

True

False

False

Calculators

Raw data can be normalized using one or several normalization procedures, or calculators.

The following protocol-level parameters are valid for sending configuration information for your normalization to ScienceCloud Assay. For any parameter with a Default Value, you can omit the protocol-level parameter if the default value is appropriate for your normalization.

For the Is Inheritable parameter, by default, normalizations are inherited when using a run as a template. However some normalizations are dependent on the data of the run used to construct the template. This happens, for example, when corrupted input data needed corrections. Put this value to "No" to avoid copying this normalization from template.
Warning : When a normalization is not inheritable do not use the readout created from this normalization as input for another inheritable normalization.

Currently, a custom normalization created in Pipeline Pilot will support one parameter of the normalization.

Parameter Name Parameter Type Mandatory? Legal Values Default Value
Calculation Alias String Yes    
Data Type String No

Cross Run

End Point

High Content Screening

Kinetic

End Point
Calculation Type String No Find valid calculation types in your Assay Administration page Administration->Normalization Procedure Types Normalization
Is Hidden Boolean No

True

False

False
Is Inheritable Boolean No

True

False

True
Mandatory Well Types StringArray No    
Parameter 1 Name String No    
Parameter 1 Type String No

kinetic readout

number

readout

text

well_type

 
Parameter 1 Default Value String No    
Parameter 1 Is Mandatory String No

True

False

True

Post Transformations

Post transformations are sample and reference analysis procedures that perform data analysis on aggregated groups in order compute elaborated data.

The following protocol-level parameters are valid for sending configuration information for your post transformation to ScienceCloud Assay. For any parameter with a Default Value, you can omit the protocol-level parameter if the default value is appropriate for your post transformation.

The "Is Reference" parameter should be True if the custom post transformation is for reference analysis, and False for sample analysis.

Multiple Post Transformation parameters can be supplied to the parameters Parameters Name, Parameters Code, Parameters In Out, and Parameters Type. Those are arrays, so multiple values can be provided.

Parameter Name Parameter Type Legal Values Default Value
Is Reference Boolean

True

False

False
Is Hidden Boolean

True

False

False
Parameters Name String Array    
Parameters Code String Array    
Parameters In Out String Array

In

Out

 
Parameters Type String Array

String

Numeric

 

Viewers

Viewers are visualization templates for using visual analytics capabilities to exclude outliers on control wells and identify deviation patterns.

The following protocol-level parameters are valid for sending configuration information for your viewer to ScienceCloud Assay. For any parameter with a Default Value, you can omit the protocol-level parameter if the default value is appropriate for your custom viewer.

For the Is Default parameter, a default visualization template is pre-selected at the corresponding step.

The Show Side Region parameter can be used to embed the "validation" and "refresh computation" feature in the visualization template. The side panel will be hidden in the visualization pages.

Parameter Name Parameter Type Legal Values Default Value
Visualization Step String

Sample Analysis

Cross Run Analysis

Validation

Reference Analysis

Sample Analysis
Data Type String

Cross Run

End Point

High Content Screening

Kinetic

End Point
Is Hidden Boolean

True

False

False
Is Default Boolean

True

False

False
Show Side Region Boolean

True

False

True

Reader Computations

A reader computation us used in a HCS run with field raw data. They allow you to compute well data from the raw field data. Reader computations are launched a first time at the Raw Data File step and then whenever a field is validated or invalidated to update the corresponding well data.

The following protocol-level parameters are valid for sending configuration information for your reader computation to ScienceCloud Assay. For any parameter with a Default Value, you can omit the protocol-level parameter if the default value is appropriate for your custom reader computation.

Parameter Name Parameter Type Legal Values Default Value
Data Type String

Cross Run

End Point

High Content Screening

Kinetic

End Point
Is Hidden Boolean

True

False

False

Well Mapping

The following protocol-level parameters are valid for sending configuration information for your well mapping to ScienceCloud Assay. For any parameter with a Default Value, you can omit the protocol-level parameter if the default value is appropriate for your custom well mapping.

Parameter Name Parameter Type Legal Values Default Value
Is Hidden Boolean

True

False

False

Publishers

Publishers map protocol information and publish results on central repository.

The following protocol-level parameters are valid for sending configuration information for your publisher to ScienceCloud Assay. For any parameter with a Default Value, you can omit the protocol-level parameter if the default value is appropriate for your custom publisher.

The Procedure Unpublish parameter value should be the path to the location of the location of the Pipeline Pilot protocol for unpublishing results.

Parameter Name Parameter Type Mandatory? Legal Values Default Value
Publisher Code String Yes    
Procedure Unpublish String Yes    
Is Hidden Boolean No

True

False

False

Publishing Your Custom Resource Protocol

When publishing your ScienceCloud Assay custom resource protocol, the first step is to save the protocol to a valid folder location in Pipeline Pilot based on the corresponding Assay procedure. Valid folder locations based on Assay procedure are:

Folder Name Supported Synonyms
Readers  
Sample Information Mappers  
Calculators

Calculation

Normalization Procedures

Post Transformations

Post Transformation

Sample and Reference Analysis Procedures

Viewers Visualization Templates
Publishers  

These folders will be under Protocols/ScienceCloud/BIOVIA/Assay (replace BIOVIA with your team name).

To request publication of your protocol after saving the protocol to the appropriate folder, right-click on the protocol name and click "Publish to ScienceCloud" context menu option.

This will launch validation of your protocol, and if no validation errors are found the protocol will be submitted for review by personnel at BIOVIA, if the target environment is Production. If the target environment is Sandbox, the review process is skipped and post-processing occurs, which configures the protocol in your team's Assay Administration page, so that it appears under Administration Utilities for the specific procedure type.

Protocol review should be completed within 48 business hours. If the review finds no problems, the protocol is published by the reviewer. This initiates automatic post-processing.

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