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BioQuali asynchronous workflow

Workflow Entry: BioQuali asynchronous workflow

Created at: 06/07/09 @ 10:08:10 Last updated: 06/07/09 @ 10:09:02

Version 1 (of 1)

Version created on: 06/07/09 @ 10:08:10 by: abretaud | Revision comments Expand

Last edited on: 06/07/09 @ 10:09:04 by: abretaud

Title: BioQuali asynchronous workflow

Type: Taverna 1

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Description

BioQuali: Network Compatibility and products variation inference in a biological network.

Help page: http://genoweb2.irisa.fr/claroline/claroline/course/index.php?cid=BIOQUALI

Reference: Carito Guziolowski, Annabel Bourdé, Francois Moreews and Anne Siegel BioQuali Cytoscape plugin: analysing the global consistency of regulatory networks
BMC Genomics 2009, 10:244 doi:10.1186/1471-2164-10-244

This web service is made available on GenOuest bioinformatics platform (Rennes, France) using Opal toolkit. A list of other web-services available on GenOuest platform can be viewed here.

This workflow uses BioQuali in an asynchronous way: the workflow will launch BioQuali and then regularly poll the server for results.

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Run

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Option 1:

Launch in Taverna

Note: you need to have both the WHIP Launcher and the Taverna myExperiment/WHIP plugin installed on your machine for this to work. See here for information.

Option 2:

Copy and paste this link into File > 'Open workflow location...'
http://www.myexperiment.org/workflows/830/download?version=1
[ More Info Expand ]

Workflow Components

Inputs (6)

Name	Description
nameGraphInput	Name of the input network file (usually something like input.net).
contentGraphInput	Content of the input network file, loaded from a file on your hard drive.
nameDataInput	Name of the input observations file (usually something like input.obs).
contentDataInput	Content of the input observations file, loaded from a file on your hard drive.
calculateCoreNetwork	Calculate core network. Set to 'true' or 'false'.
findAllInconsistentSubgraphs	Find all inconsistent subgraphs. Set to 'true' or 'false'.

Processors (8)

Name	Type	Description
PollStatus	workflow	This nested workflow is a loop which will regularly request the job status to the server until it is finished.
inputObservationsFileXML	local	This object represent the input observations file.
inputNetworkFileXML	local	This object represent the input network file.
launchJob	arbitrarywsdl	Requires all the parameters with correct type, and structures representing the input files. The structure contains the name of the input file and either the contents in Base64 encoded binary form or a MIME attachment, or simply a location (URL) to the associated file. The operation returns a Job ID that can be used to retrieve job status and outputs. See the Service entry for this web service.
launchJobInputXML	local	This is where you define all the input data to BioQuali webservice.
launchJobOutputXML	local	This object represent the output data produced by BioQuali.
getOutputs	arbitrarywsdl	returns the outputs from a job that is identified by a Job ID. The output consists of the urls for the standard output and error, and an array of structures representing the output files. The structure contains the name of the output file and the url from where it can be downloaded. See the Service entry for this web service.
getOutputsOutputXML	local	These are the files generated by Tuiuiu.

Beanshells (1)

Name	Description	Inputs	Outputs
IsFinished		code	isFinished

Outputs (1)

Name	Description
result	Result of the job. It includes exit status and URL to access output files. There are other operations defined in the WSDL to retrieve output data.

Links (14)

Source	Sink
calculateCoreNetwork	launchJobInputXML:calculateCoreNetwork
contentDataInput	inputObservationsFileXML:contents
contentGraphInput	inputNetworkFileXML:contents
findAllInconsistentSubgraphs	launchJobInputXML:findAllInconsistentSubgraphs
nameDataInput	inputObservationsFileXML:name
nameGraphInput	inputNetworkFileXML:name
getOutputs:getOutputsOutput	getOutputsOutputXML:input
getOutputsOutputXML:outputFile	result
inputNetworkFileXML:output	launchJobInputXML:inputNetworkFile
inputObservationsFileXML:output	launchJobInputXML:inputObservationsFile
launchJob:launchJobOutput	launchJobOutputXML:input
launchJobInputXML:output	launchJob:launchJobInput
launchJobOutputXML:jobID	PollStatus:JobID
launchJobOutputXML:jobID	getOutputs:getOutputsInput

Coordinations (1)

Controller	Target
PollStatus	getOutputs

Information Workflow Type

Taverna 1

Information Original Uploader

abretaud

Information License

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Information Tags (4)

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Information Shared with Groups (1)

GenOUEST Platform

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Information Statistics

393 viewings

544 downloads

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Citations (0)

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Version History

Earliest Version:
[1] - BioQuali asynchronous workflow

Created on: Monday 06 July 2009 @ 10:08:10 (GMT)

Created by: abretaud

Last edited on: Monday 06 July 2009 @ 10:09:04 (GMT)

Last edited by: abretaud

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Other workflows that use similar services (1)

Taverna 1

Original Uploader

abretaud

BioQuali synchronous workflow (v1)

Created: 06/07/09 @ 10:00:52 | Last updated: 06/07/09 @ 10:05:49

Credits: abretaud GenOUEST Platform

License: Creative Commons Attribution-Share Alike 3.0 Unported License

BioQuali: Network Compatibility and products variation inference in a biological network. Help page: http://genoweb2.irisa.fr/claroline/claroline/course/index.php?cid=BIOQUALI Reference: Carito Guziolowski, Annabel Bourdé, Francois Moreews and Anne Siegel BioQuali Cytoscape plugin: analysing the global consistency of regulatory networks BMC Genomics 2009, 10:244 doi:10.1186/1471-2164-10-244 This web service is made available on GenOuest bioinformatics platform (...

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 16 times | Downloaded: 7 times

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