Close Problem with query expression: Error parsing query expression

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Pack Taverna 1.7 starter pack


Created: 2008-07-17 21:06:12 | Last updated: 2018-01-28 19:42:32

Everything to get started with Taverna 1.7 - latest version is 1.7.2

19 items in this pack

Comments: 0 | Viewed: 740 times | Downloaded: 263 times

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Workflow Success-Abandonment-Classification (3)

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Retrieves data from FLOSSmole and from the Notre Dame SourceForge repository to compute project statistics based on releases, downloads and project lifespan. Project statistics are then used to classify projects according to the criteria set up in English & Schweik, but comparison criteria are parameterized so that a different set of criterion thresholds can be used to evaluate the project characteristics.

Created: 2008-02-06 | Last updated: 2008-07-02

Credits: User Andrea Wiggins User James Howison

Workflow Add Mesh String to Biological Process (2)

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This workflow is designed to add the following MeSH term to the end of a KEGG pathway name: AND "Metabolic Networks and Pathways" [MeSH Terms]   Example input for this service is as follows:   VEGF signaling pathway Hematopoietic cell lineage GnRH signaling pathway Type II diabetes mellitus  

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

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Pack Taverna 2.2 starter pack


Created: 2010-06-11 13:40:05 | Last updated: 2012-01-03 15:46:09

The Taverna team are pleased to announce that Taverna 2.2.0 workbench and command line tool are now available for users to download. Taverna 2.2.0 includes improvements to the workbench user interface and gives users greater control over the workflow engine.  Here are a few of the new features in the workbench:     * Loading and sharing of service sets     * Ability to load and edit workflows that contain services that are offline     ...

20 items in this pack

Comments: 0 | Viewed: 872 times | Downloaded: 209 times

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Workflow Mapping OligoNucleotides to an assembly (7)

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Version info The former version of the workflow expected that results from BioMART only report transcripts when the query (the probe in our case) are entirely encapsulated in an exon of that transcript. However, the BioMart service also returns transcripts when the query is not or only partially overlapping with an exon in the stretch on the assembly on which a transcript is defined. This resulted in too many oligos classified as having multiple transcripts or having multiple genes. ...

Created: 2009-02-13 | Last updated: 2009-02-13

Credits: User Wassinki User Pieter Neerincx

Attributions: Workflow Blat against ENSEMBLE Danio_rerio_Genome Workflow BlatBlastCombi Workflow Blast against ENSEMBLE Danio_rerio_Genome Workflow AppendToFile Blob Test Input for Mapping oligonucleotides to an assembly Blob Input for Mapping oligonucleotides to an assembly

Workflow KNIME workflow used to collate data for th... (1)

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KNIME workflow used to collate data from different sources (Open Data, in-house data) for certain protein targets of interest; further the data is filtered for certain activity endpoints, erraneous data is removed and data overlap between the different sources as well as the targets under study is determined and given as an output;Requirements:- Knime v2.11- Open PHACTS Knime nodes version 1.1.0: https://github.com/openphacts/OPS-Knime- KNIME additional community nodes: 'Trusted Community...

Created: 2015-11-02 | Last updated: 2016-03-29

Credits: User Barbara Zdrazil User Daniela Digles Network-member Open PHACTS

Workflow Nucleotide_InterProScan (4)

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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 InterProScan using a...

Created: 2008-10-26 | Last updated: 2011-04-01

Credits: User Hamish McWilliam

Attributions: Workflow EBI_InterProScan Workflow EBI_NCBI_BLAST Workflow Nucleotide_ORF_translation Workflow Fasta_string_to_fasta_list Workflow Sequence_or_ID

Creator

Pack Taverna 2.5 Enterprise Starter Pack


Created: 2014-04-02 12:54:33 | Last updated: 2017-01-09 12:01:51

This is a Starter Pack for Taverna 2.5 Enterprise edition - it contains a number of example workflows to showcase various features of Taverna 2.5 Enterprise and help you get started using it.Workflows from this Starter pack can also be found in the myExperiment perspective of the Taverna Workbench.Tutorials for Taverna are available under the Taverna 2.x documentation on the Taverna Web site.Also check out the Taverna User Manual.

18 items in this pack

Comments: 1 | Viewed: 220 times | Downloaded: 176 times

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Workflow BioAID_ProteinDiscovery_filterOnHumanUnipr... (11)

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This workflow finds proteins relevant to the query string via the following steps: A user query: a single gene/protein name. E.g.: (EZH2 OR "Enhancer of Zeste"). Retrieve documents: finds 'maximumNumberOfHits' relevant documents (abstract+title) based on query (the AIDA service inside is based on Apache's Lucene) Discover proteins: extract proteins discovered in the set of relevant abstracts with a 'named entity recognizer' trained on genomic terms using a Bayesian approach; the AIDA serv...

Created: 2009-05-28

Credits: User Marco Roos User Martijn Schuemie Network-member AID Network-member AID_myGrid_collaboration

Attributions: Workflow BioAID_DiseaseDiscovery_RatHumanMouseUniprotFilter

Workflow blast_simplifier.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: User Paul Fisher

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