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Fetch PDB flatfile from RCSB server (1)

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Given an identifier such as '1crn' fetches the PDB format flatfile and returns the corresponding 3D image of the protein.

Created: 2009-07-03 | Last updated: 2009-07-03

Credits: Stian Soiland-Reyes

Attributions: Fetch PDB flatfile from RCSB server Fetch PDB flatfile from RCSB server

Analysing workflows (3)

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This workflows analyses workflows stored at the myExperiment site. It is used in the paper submitted to the Workshop on Scientific Workflow 2009. The workflow shows the task usage in the Taverna workflows stored at the myExperiment site The amount of services used The amount of local processors used The amount of scripting tasks The amount of sub workflows Furthermore it classifies the local services based on their intended function. The workflow has two inputs: ...

Created: 2009-05-06 | Last updated: 2009-05-06

Credits: Wassinki Pieter Neerincx Katy Wolstencroft Marco Roos

AffyArrayNormalization (2)

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The AffyArrayNormalization web services normalise raw Affymetrix GeneChip data. They are wrappers around Philip de Groot's normalization R script to provide remote programmatic access. This example workflow demonstrates the use of the AffyArrayNormalization services. The flow is as follows: A client executes the AffyArrayNormalization_submit service with two inputs: a User object and a collection of URLs linking to CEL files. The User object contains a user ID, a password and an ...

Created: 2009-02-16 | Last updated: 2009-02-16

Credits: Pieter Neerincx Philipg

MediGRID FEAT Workflow (1)

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This workflow is a translation of the VLeMed workflow to the GWorkflowDL format, which is used in MediGRID. The translation of the "cross product" iteration strategy is currrently under work and not yet finished. So this workflow only varies the parameters p1, p2, and p3.

Created: 2009-02-13

Credits: Andreas Hoheisel

Attributions: feat_workflow

FLOSS Communication Centralization Plot, U... (2)

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The analysis in this workflow represents the basis of the analysis in our paper, Social dynamics of FLOSS team communication across channels. This workflow uses WSDL components to select periodized data from the FLOSSmole database and generate sociomatrices. The workflow parses the threaded list structure into a communication network based on reply-to relationships. In the analysis process, an unit weighting is applied to the edges. The weighted sociomatrices are then dichotomized according ...

Created: 2009-02-07

Credits: Andrea Wiggins Crowston James Howison

What is known about HIV using Bio2RDF's SP... (2)

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To answer this question Bio2RDF Atlas about mouse and human genome sparql endpoint available at http://atlas.bio2rdf.org/sparql is searched.  The selected URIs are then loaded into your local Virtuoso triplestore at http://localhost:8890/sparql. You must enable insert mode into the graph. Once the mashup is built, two SPARQL queries analyze the obtained graph.  Finally you can submit queries to the RDF mashup about HIV as you like.  Enjoy. This is the queries present in t...

Created: 2009-02-05 | Last updated: 2009-02-05

Credits: Francois Belleau

BlatBlastCombi (2)

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This workflow combines the blat and blast workflows. It takes as input a database name (Danio_rerio_Genome for Zebra Fish for example) and and a set of Fasta sequences. It first tries to perform a blat (at www.bioinformatics.nl). When this service returns nothing, a blast is done (also at www.bioinformatics.nl). The resulting reports are combined.   To run this workflow, a certificate to access www.bioinformatics.nl needs to installed (Some services use an SSL connection). Look at the ...

Created: 2009-02-03 | Last updated: 2009-02-03

Credits: Wassinki

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

Retrieve_bio_documents (2)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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

Demo of statistics webservice invoked from... (1)

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Created: 2009-03-29

Credits: David De Roure

Workflow Pattern - Structured Discriminato... (1)

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This workflow is an alternative 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. The pattern is resets if both, A and B have been invoked. Please note that the transitions "C", "ignore", and "release" have different priorities (not shown in the graph) that make the net deterministic (except the occurrence of "A" and &q...

Created: 2009-01-19 | Last updated: 2009-01-20

Credits: Andreas Hoheisel

Using CQL to query protein sequence data (1)

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To query protein sequence infomation out of 3 caGrid data services: caBIO, CPAS and GridPIR. Scientific value To query protein sequence information out of 3 caGrid data services: caBIO, CPAS and GridPIR. To analyze a protein sequence from different data sources. Steps Querying CPAS and get the id, name, value of the sequence. Querying caBIO and GridPIR using the id or name obtained from CPAS.    

Created: 2008-12-05 | Last updated: 2009-07-14

Credits: Wei Tan

Workflow Pattern - Simple Merge (XOR-Join) (1)

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This workflow is a GWorkflowDL representation of a simple merge (XOR Join) that invokes C when either A or B has been invoked. The structure of the GWorkflowDL representation of a simple merge is identical to the multi merge pattern!

Created: 2008-12-03 | Last updated: 2009-01-19

Credits: Andreas Hoheisel

Blast against ENSEMBLE Danio_rerio_Genome (1)

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This workflow invokes the blast service provided at www.bioinformatics.nl, written by Pieter Neerincx. The workflow takes as input a database name (Danio_rerio_Genome for Zebra Fish for example) and a set of sequences in fasta format. The blast service is invoked (using polling) and the result is a tab separated blast report.   To run this workflow, a certificate to access www.bioinformatics.nl needs to installed (Some services use an SSL connection). Look at the link below how to ins...

Created: 2008-10-15 | Last updated: 2008-10-15

Credits: Wassinki

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acetanilide comparison study (test)

Created: 2008-08-18 17:58:31 | Last updated: 2008-08-18 18:11:21

7 items in this pack

Comments: 0 | Viewed: 6842 times | Downloaded: 45 times

EBI_Fetch_InterPro_Matches_UniParc (1)

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For a UniParc (see http://www.ebi.ac.uk/uniprot/database/DBDescription.html#uniparc) identifier/accession fetch the assocated InterPro Matches from SRS@EBI (see http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-page+LibInfo+-lib+IPRMC_UNIPARC).

Created: 2008-06-08

Credits: Hamish McWilliam

selectworker (1)

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This workflow shows how the selectData beanshell script can be used to select items from a given list for analysis by downstream processors. Use Control and left mouse click to select multiple items.

Created: 2008-03-25 | Last updated: 2008-03-25

Credits: Peter Li

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From biologist to web service to Taverna to myExperi...

Created: 2008-03-21 19:00:12 | Last updated: 2008-03-23 10:39:27

Credits: Marco Roos Martijn Schuemie AID myGrid

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: AVI video

Comments: 1 | Viewed: 490 times | Downloaded: 381 times

GeneIlluminator_GetPubMedQuery (2)

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Example workflow demonstrating how to use GeneIlluminator_GetPubMedQuery, a synchronous BioMOBY service for gene symbol disambiguation. If a gene symbol is ambiguous this service uses GeneIlluminator to create clusters describing which different genes, sharing the same symbol, exist in different parts of the tree of life. GeneIlluminator provides also aliases associated to the input gene symbol. Finally, using the cluster characteristics it creates a boolean PubMed query that could be used to...

Created: 2008-02-27 | Last updated: 2008-03-03

Credits: Pieter Neerincx Alako

GeneIlluminator_Disambiguate (2)

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Example workflow demonstrating how to use GeneIlluminator_Disambiguate, a synchronous BioMOBY service for gene symbol disambiguation. If a gene symbol is ambiguous this service provides GI_Clusters describing which different genes, sharing the same symbol, exist in different parts of the tree of life. Provides also gene symbol aliases associated to the input gene symbol. (This is the same output as the one from the GeneIlluminator_GetClusters service.) In addition this service takes an Organi...

Created: 2008-02-27 | Last updated: 2008-03-03

Credits: Pieter Neerincx Alako

ExampleWorkflow1 (2)

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This workflow was created based on the Leeds Taverna Workshop 2008-02-04 material developed by Katy.

Created: 2008-02-04 | Last updated: 2008-02-04

Credits: Katy Wolstencroft

Extract_proteins (2)

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This workflow filters protein_molecule-labeled terms from an input string(list). The result is a tagged list of proteins (disregarding false positives in the input). Internal information: This workflow is a copy of 'filter_protein_molecule_MR3' used for the NBIC poster (now in Archive).

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

Credits: Marco Roos

Discover_entities (2)

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This workflow contains the 'Named Entity Recognize' web service from the AIDA toolbox, created by Sophia Katrenko. It can be used to discover entities of a certain type (determined by 'learned_model') in documents provided in a lucene output format. Known issues: The output of NErecognize contains concepts with / characters, breaking the xml. For post-processing its results it is better to use string manipulation than xml manipulations. The output is per document, which means entities will ...

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

Credits: Marco Roos Sophia katrenko AID

TestIteratorStrategy_withCloning (2)

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This workflow implements a strategy for this problem: > I would like to perform an iteration including a dot product between > a list and a list of lists; example: > Input: > > [1] (1) > [A,B,C] (2) > [[a,b],[c,d],[e,f]] (3) > > Desired output: > > [1Aa, 1Ab, 1Bc, 1Bd, 1Ce, 1Cf] In this implementation a java beanshell is used to clone the items in list 2 as many times per item as there are items in the sublists of list 3. The iteration stra...

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

Credits: Marco Roos

kegg_gene_to_swissprot_identifier (1)

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Takes a KEGG gene identifier, e.g. sce:YAL038W (yeast pyruvate kinase) and converts to the corresponding Swissprot identifier.

Created: 2007-11-27 | Last updated: 2007-11-28

Credits: Sirisha Gollapudi

BioAID_Discover_proteins_from_text_plus_sy... (1)

This workflow discovers proteins from plain text and adds synonyms using Martijn Schuemie's proteins synonym service. Proteins are discovered with the AIDA 'Named Entity Recognize' web service by Sophia Katrenko (service based on LingPipe), from which output it filters out proteins. The Named Recognizer services uses the pre-learned genomics model, named 'MedLine', to find genomics concepts in plain text.

Created: 2007-11-15

Credits: Marco Roos Martijn Schuemie AID

Query Maxd microarray database (1)

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Retrieves data from the maxd database given name of data set

Created: 2007-11-14 | Last updated: 2007-11-22

Credits: Peter Li

pELM_getInstance_Return_Seq (2)

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Simple workflow to retrieve the sequence of a phospho.ELM entry given the Instance identifier. Input requires xml as the namespace is not correctly handled by the xml splitter. Example input: I000299 Further outputs can easily be added, most are text with some xml. See list in InstanceXML.

Created: 2007-10-03 | Last updated: 2008-05-02

Credits: Niall Haslam

getFragWithClosure (2)

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Bit of a hack, but it works now, adds trailing "%90" to the output.

Created: 2007-10-03

getFragWithClosure (2)

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getFragment with closure "workflow", actually just one service, but need example inputs for smiles string, group and closure parameters.

Created: 2007-10-03

MrBayesPPtest (13)

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robust connection

Created: 2013-12-11 | Last updated: 2014-11-27