Workflows

EBI_dbfetch_fetchBatch (1)

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Sample workflow illustrating the use of EBI's WSDbfetch service with Triana.

Created: 2009-08-28

Credits: Hamish McWilliam

EBI_dbfetch_fetchData (1)

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Sample workflow illustrating the use of the EBI's WSDbfetch service in Triana.

Created: 2009-08-28 | Last updated: 2009-08-28

Credits: Hamish McWilliam

Spreadsheet Importer (1)

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This workflow is designed to import a spreadhseet from a local computer. The imported spreadsheet is parsed to extract the first two columns, A and B, for all rows in the spreadsheet. These are returned as two separate outputs.

Created: 2009-08-24

Credits: Paul Fisher

/me is having Bioclipse/XMPP/RDF fun.js (1)

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Created: 2009-08-21

Credits: Egon Willighagen

Retrieve details on genetic marker by UniS... (3)

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The workflow retrieves the marker's primers and the organism name - if available. The organism name may not be unique for a given marker. The primers should be. It would be nice if some good soul could investigate how to retrieve the various mappings from the site. The retrieval of the primers is thought to prepare for a manual mapping of the marker's chromosomal location.

Created: 2009-08-19

Credits: Steffen Möller

SubGraph Filter (2)

This workflow filters a given Ondex graph to return a new ondex sub-graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph. Optional parameter. If no output graph is specified filtered items will be removed from the input graph. ConceptID - The root concept to start at. Valid value range is 1 to 2147483647. FirstRelationType - RelationType limitation for depth 1 (Optional). FirstConceptClass - C...

Created: 2009-08-19

Credits: Paul Fisher

Genomic Filter (1)

This workflow filters a given Ondex graph according to a chromosomal region, or QTL region. The result is a new Ondex graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph (Optional). If no output graph is specified filtered items will be removed from the input graph. ContextID - The Concept ID of the Context (Chromosome). From - The start position on the chromosome, e.g. 100. To - The stop pos...

Created: 2009-08-19

Credits: Paul Fisher

CV Filter (1)

This workflow filters a given Ondex graph according to a controlled vocabulary specified by the user. The result is a new Ondex graph with only those concepts that passed the filter. The parameters that can be used with this service graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph. Optional parameter. If no output graph is specified filtered items will be removed from the input graph. CV - A CV to include/exclude Concepts and Relations of (see Exclude param). R...

Created: 2009-08-19

Credits: Paul Fisher

Clean GO Filter (1)

This workflow filters an Ondex graph, by cleaning up any GO terms within the Graph (?). The result is a new Ondex graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph (Optional). If no output graph is specified filtered items will be removed from the input graph.

Created: 2009-08-19

Credits: Paul Fisher

KEGG Pasrer (1)

This workflow parses a KEGG species database into an Ondex Graph graphId - the ID of the Graph. inputDir - the plugin input directory Species - Use this parameter to specify the species to be loaded from the kegg database. Default value is all. ParseSequences - KEGG species code. Default value is false (boolean) ImportOrthologFillers - Import Ortholog Pathway Fillers. Default value is false (boolean)

Created: 2009-08-19

Credits: Paul Fisher

Rank Phenotype Terms (1)

This workflow counts the number of articles in the pubmed database in which each term occurs, and identifies the total number of articles in the entire PubMed database. It also identified the total number of articles within pubmed so that a term enrichment score may be calculated. The workflow also takes in a document containing abstracts that are related to a particular phenotype. Scientiifc terms are then extracted from this text and given a weighting according to the number of terms that ...

Created: 2009-08-10

Credits: Paul Fisher

Cosine vector space (1)

This workflow calculates the cosine vector space between two sets of corpora. The workflow then removes any null values from the output. The result is a cosine vector score between 0 and 1, showing the significance of any links between one concept (e.g. pathway) to another (e.g. phenotype). A score of 0 means there is no or an undetermined correlation between the two concepts. A score approaching 1 represents positive correlation.

Created: 2009-08-10 | Last updated: 2009-08-10

Credits: Paul Fisher

An example workflow with WSRF service (1)

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An example workflow with WSRF service The service used is http://sidgrid.ci.uchicago.edu:8100/wsrf/services/CounterService The service is included in Globus toolkit installation (ws-core). If the it is down you can host your own and modify the workflow definition file to point to your own. The workflow first creates a counter instance and adds the value 10 for two times to the same counter. Therefore the result should be 20.

Created: 2009-07-28

Credits: Wei Tan Stian Soiland-Reyes

BioQuali asynchronous workflow (1)

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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, ...

Created: 2009-07-06 | Last updated: 2009-07-06

Credits: abretaud GenOUEST Platform

Pipelined list iteration (1)

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Perform multiple iterations of services in order to show pipelining

Created: 2009-07-03

Credits: Stian Soiland-Reyes Ian Dunlop

GBSeq test (1)

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This workflow retrieves nucleotide and protein sequences with the literature and references associated to them given a protein and a nucleotide id.

Created: 2009-07-03

Credits: Stian Soiland-Reyes

Attributions: GBSeq test

Tuiuiu asynchronous workflow (1)

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Tuiuiu removes from a sequence or from a set of sequences areas as large as possible that do not contain researched repeats. Tuiuiu is used as a preliminary step before applying a multiple local aligner tool. Modeling and algorithmic details are provided in the following paper. Please, cite this paper if you use Tuiuiu. P. Peterlongo, G. Sacomoto, A. Pereira do Lago, N. Pisanti, M.-F. Sagot Lossless filter for multiple repeats with bounded edit distance BMC Algorithms for Mole...

Created: 2009-06-29 | Last updated: 2009-06-29

Credits: http://osallou.myopenid.com/ GenOUEST Platform

getOntologyTerm (1)

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This service takes a MIRIAM compliant URI and looks up all the synonyms for that URI using ChEBI and other services. Service developed and maintained by Neil Swainston at the MCISB in Manchester.

Created: 2009-06-09 | Last updated: 2009-06-09

Credits: Duncan Hull

getSynonymsFromSBML (1)

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This service takes an SBML file (for example from the Biomodels database) and extracts synonyms for each of the SBML species in the file, using ChEBI. Service is written and maintained by Neil Swainston at the MCISB.

Created: 2009-06-09 | Last updated: 2009-06-09

Credits: Duncan Hull

Test SoapLab Service Availability (1)

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This workflow tests for all Taverna workflows stored at myExperiment wether theS oapLab services used still exists. For each SOAP/WSDL service it checks wether the SoapLab service can still be accessed. The output is among others a report of accessible SoapLab services inaccessible SoapLab services

Created: 2009-05-29 | Last updated: 2009-05-29

Credits: Wassinki