Workflows

Protein_transmembrane_prediction (2)

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Note: the WSInterProScan web service used by this workflow is no longer available haveing been replaced by the EMBL-EBI's InterProScan (REST) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_rest) and InterProScan (SOAP)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. Transmembrane and signal...

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

Credits: Hamish McWilliam

Attributions: EBI_InterProScan_tmhmm_signalp EBI_Phobius tmap_single_sequence

EBI_InterProScan_tmhmm_signalp (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Note: the WSInterProScan web service used by this workflow is no longer available haveing been replaced by the EMBL-EBI's InterProScan (REST) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_rest) and InterProScan (SOAP)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. Use the TMHMM and Signal...

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

Credits: Hamish McWilliam

Attributions: EBI_InterProScan

Genome annotation pipeline demonstrator wo... (2)

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Part of a workflow by Hannah Tipney, adapted by Duncan Hull using GenScan, RepeatMasker and BLAST. http://dx.doi.org/10.1093/nar/gkl320

Created: 2007-10-03

fetchEnsemblSeqsAndBlast (1)

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This workflow allows you to configure a BioMart query to fetch sequences you want from Ensembl. These sequences are retrieved and a blast database of them is created (by default, in the directory you ran taverna from). Warning: This workflow assumes that you have blastall and formatdb installed on the machine, and that by default, these are both found or linked in /usr/local/bin. It also assumes that you have write permission to the directory you have run taverna from. The beanshells "creat...

Created: 2008-04-18 | Last updated: 2008-04-18

Credits: Bela

Download from ChemSpider using Accurate Mass (2)

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No description

Created: 2007-11-26 | Last updated: 2008-02-05

Credits: Egon Willighagen

Simplify a BLAST text file (2)

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This workflow simplifies a BLAST text file into identifiers, descriptions and values (P, E-values). In order to extract the relevant ids etc. you need to pass the relevant string into the corresponding port, e.g. the default port being used is gi. This has been passed "gi". For any other ports simply pass in the string the SAME as the port name, e.g. seq_id, p, per etc.

Created: 2007-10-03 | Last updated: 2009-07-28

KEGG pathways common to both QTL and micro... (3)

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This workflow takes in two lists of KEGG pathway ids. These are designed to come from pathways found from genes in a QTL (Quantitative Trait Loci) region, and from pathways found from genes differentially expressed in a microarray study. By identifying the intersecting pathways from both studies, a more informative picture is obtained of the candidate processes involved in the expression of a phenotype.   Example input for this workflow is given below (as newline separated values). qt...

Created: 2009-11-24 | Last updated: 2009-12-03

FLOSS Communication Centralization Plot, E... (4)

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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 edge weighting is applied so that older messages receive less weight using an exponential decay fun...

Created: 2009-02-07

Credits: Andrea Wiggins Crowston James Howison

EBI_PICR_Sequence_to_UniParc_and_InterPro (2)

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Given a protein sequence get some information about it: Does this protein sequence occur in any of the protein databases (e.g. UniProtKB, PDB, etc.). Using the PICR web service (see http://www.ebi.ac.uk/Tools/picr/) map the sequence to a UniParc identifer. Which entries in the protein databases have this sequence. Using the UniParc database (see http://www.ebi.ac.uk/uniprot/database/DBDescription.html#uniparc) a summary of the databases and the entries in those databases which have this s...

Created: 2008-06-08 | Last updated: 2008-06-08

Credits: Hamish McWilliam

Attributions: EBI_dbfetch_UniParc EBI_Fetch_InterPro_Matches_UniParc EBI_PICR_Sequence_to_ID

Fetch today's xkcd comic (1)

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Use the local java plugins and some filtering operations to fetch the comic strip image from http://xkcd.com/ Based on the FetchDailyDilbert workflow.

Created: 2008-03-05 | Last updated: 2008-04-07

Credits: Tomoinn Stian Soiland-Reyes

Attributions: