Workflows

Workflow Pattern - Structured Discriminator (2)

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This workflow is a GWorkflowDL representation of a structured discriminator (1-out-of-M Join) that invokes C after the first invocation of A or B (M=2). All next (M-1) invocations of A or B are ignored. This is only one out of various possibilities to model this workflow pattern. Notice alternative representation of this pattern at http://www.myexperiment.org/workflows/632

Created: 2009-01-19 | Last updated: 2009-01-19

Credits: Andreas Hoheisel

REST access of xml.nig.ac.jp (WABI) (1)

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This workflow has a beanshell script for composing the REST URL for the services at xml.nig.ac.jp  (WABI) This URL is passed to the local worker Get_web_page_from_URL that fetches the requested data. Note: This is a proof of concept of accessing REST services through Taverna. All of WABI's services can more easily be browsed and used in Taverna by adding their WSDL, for instance http://xml.nig.ac.jp/wsdl/GetEntry.wsdl The example invokes the getDDBJEntry(accession) method of the getE...

Created: 2008-10-14 | Last updated: 2008-10-14

Credits: Stian Soiland-Reyes

color_pathway_by_objects (1)

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Color given objects on a pathway map with specified colors and return the URL of the colored image. In the KEGG pathway maps, a gene or enzyme is represented by a rectangle and a compound is shown as a small circle. Example of input: pathway_id: path:eco00260 object_list: (to add as list) eco:b0514 eco:b2913 fg_color: (to add as list) blue orange bg_color: (to add as list) red orange

Created: 2008-10-01 | Last updated: 2008-10-01

Credits: Franck Tanoh

Sequence_or_ID_or_GI (1)

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Get a sequence in fasta format given one of: An NCBI GI number (e.g. 75251068). An entry identifier in database:identifier format (e.g. uniprot:Q96247). 3. A sequence entry in a format supported by EMBOSS seqret.

Created: 2008-06-07

Credits: Hamish McWilliam

Attributions: Structure_or_ID

Structure_or_ID (1)

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Given a structure or structure entry identifer (e.g. PDB:1crn), return the structure in PDB format. If a structure identifier, in database:identifier format, is input the EBI's WSDbfetch web service (see http://www.ebi.ac.uk/Tools/webservices/services/dbfetch) is used to retrive the structure in PDB format. Otherwise the input is assumed to be a formated structure and is passed through to the output.

Created: 2008-06-06

Credits: Hamish McWilliam

EBI_MaxSprout (2)

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Generation of protein backbone and side chain co-ordinates from a C(alpha) trace using the MaxSprout tool. The EBI's WSMaxsprout service (see http://www.ebi.ac.uk/Tools/webservices/services/maxsprout) is used to access the tool.

Created: 2008-06-05 | Last updated: 2008-06-06

Credits: Hamish McWilliam

Attributions: Structure_or_ID

EBI_InterProScan_with_prompts (1)

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Note: the WSInterProScan web service used by this workflow is no longer available haveing been replaced by the EMBL-EBI's InterProScan (REST) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_rest) and InterProScan (SOAP) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_soap) web services. Thus the workflow described here no longer works, see the alternative workflows for the InterProScan (SOAP) service for workflows which use the new services. Run an InterProScan anal...

Created: 2008-05-31 | Last updated: 2011-04-01

Credits: Hamish McWilliam

Attributions: EBI_InterProScan

Staged iteration strategy (1)

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Consider two lists A and B, of equal size 3. A[1] corresponds to B[1], A[2] to B[2], etc, for instance A are image scans from 2007 and B from 2008, and the index indicates the patient number. A = [a0, a1, a2] B = [b0, b1, b2] There's then two lists of possible parameters P and Q, of different lengths, P has 2 and Q has 4 items. P = [p0, p1] Q = [q0, q1, q2, q3] Each of the A items should be processed in ap using each of the P parameters, and each of the B items ...

Created: 2008-05-07 | Last updated: 2008-05-07

Credits: Stian Soiland-Reyes

AffyArrayQualityAnalysis (2)

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The AffyArrayQualityAnalysis web services provide quality control for raw Affymetrix GeneChip data. They are wrappers around Philip de Groot's quality control R script to provide remote programmatic access. This example workflow demonstrates the use of the AffyArrayQualityAnalysis services. The flow is as follows: A client executes the AffyArrayQualityAnalysis_submit service with two inputs: a User object and a collection of URLs linking to CEL files. The User object contains a u...

Created: 2008-03-13 | Last updated: 2009-02-16

Credits: Pieter Neerincx Philipg

Human Microarray Analysis (1)

This workflow takes in probesets from and AffyMetrix  Affy HG U133A micorarray experiment and returns: genes ; gene start and end positions; chromosome where genes reside; ensembl trasncripts; SwissProt ids. The final output of the workflow is a list of candidate pathways which are linked to the genes expressed in the microarray data.   Example input for this workflow is: 212283_at 221634_at 220399_at  

Created: 2008-02-08 | Last updated: 2009-12-03

Credits: Paul Fisher