Workflows

Workflow Pattern - Structured Discriminator (2)

• Download

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)

• Download

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)

• Download

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)

• Download

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)

• Download

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)

• Download

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)

• Download

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)

• Download

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)

• Download

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

Retrieve_bio_documents (2)

• Download

This workflow retrieves relevant documents, based on a query optimized by adding a string to the original query that will rank the search output according to the most recent years. The added string adds years with priorities (most recent is highest); it starts at 2007.

Created: 2007-12-10 | Last updated: 2007-12-10

Credits: Marco Roos Edgar AID

CloneItemsInList (1)

• Download

Utility workflow that clones an item copy_number times. You can use this to work around standard iteration strategies, e.g. in combination with the CountListItems workflow. Workflow examples: TestIterationStrategy_withClones. For an alternative approach see TestIterationStrategy_withNesting. Example I/O: input: A copy_number: 3 result: [A,A,A] input: [A,B,C] copy_number: 3 result: [[A,A,A][B,B,B][C,C,C]] input: [A,B,C] copy_number: [3,2] result: [[[A,A,A],[A,A]][[B,B,B],[B,B]],[[C,C,C],...

Created: 2007-11-29

Credits: Marco Roos

Fetch Dragon images from BioMoby v2 (3)

• Download

Use the local java plugins and some filtering operations to fetch the comic strip image from http://www.dilbert.com

Created: 2007-11-29 | Last updated: 2007-11-29

Credits: Yuwei Lin David De Roure Jiten Bhagat

1 (2)

• Download

Trivial workflow which will initially fail, retry twice then fall over to the alternative specified for the FailingThing process.

Created: 2007-11-06 | Last updated: 2007-11-20

Credits: Antoon Goderis Carole Goble A. Random Scientist try it out

Attributions:

Remove duplicate strings (2)

• Download

This workflow takes in two list of strings and then concatenates them together. Any duplicates that are present are then removed, and the resulting file is returned back to the user.

Created: 2007-10-03 | Last updated: 2007-11-13

Cow-Human Ortholog Pathways and Gene annot... (2)

• Download

This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in the cow, Bos taurus. The workflow requires an input of: a chromosome name or number; a QTL start base pair position; QTL end base pair position. Data is then extracted from BioMart to annotate each of the genes found in this region. As the Cow genome is currently unfinished, the workflow subsequently maps the cow ensembl gene ids to human orthologues. Entrez and UniProt identifiers are then identified...

Created: 2007-10-03 | Last updated: 2009-12-03

RetroPath2.0-Mods-metabolomics (2)

• Download

Set of workflows for the "Metabolome completion and metabolomics" use case:1) Produces a list of molecules using a user defined set of rules (RetroPath2.0 workflow).2) Takes as input the products generated by RetroPath2.0 and prepare the files to be read by OpenMS nodes.3) The last workflow finally searches for each produced compound the corresponding peak in some MS spectra.See [1] for details. How to useSee instructions embedded in the workflow.Usage specificationsThe workflo...

Created: 2017-06-30 | Last updated: 2018-11-14

Credits: Thomas Duigou BioRetroSynth

Attributions: RetroPath2.0 - a retrosynthesis workflow with tutorial and example data

User friendly data mining (7)

• Download

This scientific workflow was designed for the novice data miners to learn how mining algorithms behave when applied on their datasets. The workflow is the responsible for invoking the mining recommender, as well as using the datasets required by the user, thus returning the ranking of algorithms according to the design criteria of the recommender. 

Created: 2013-10-03 | Last updated: 2019-01-08

Credits: respinosa

Visualize Molecules from DBPedia as Molecu... (3)

• Download

Downloads entries from DBPedia which have a SMILES and creates a molecule table with 2D structures of the hits found with SPARQL.

Created: 2010-03-14

Credits: Egon Willighagen

Get pathways by external reference (3)

• Download

Finds pathways on WikiPathways by an external gene/protein/metabolite reference. See http://www.pathvisio.org/Help_1.1#Supported_database_systems for a list of supported database systems.

Created: 2010-01-13

Credits: Thomaskelder