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Type: Taverna 2 User: Rafael C. Jimenez
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Workflow Split string into string list, new line se... (1)

Created: 15/08/11 @ 13:05:14 | Last updated: 15/08/11 @ 13:05:16

Credits: User Rafael C. Jimenez

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Split string into string list using new line as separator. Should work in Linux, Mac and Windows.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 19 times | Downloaded: 13 times

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Workflow Get homologous from NCBI homoloGene using ... (1)

Created: 14/10/11 @ 17:45:28 | Last updated: 27/10/11 @ 10:39:21

Credits: User Rafael C. Jimenez

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Get homologous from NCBI homoloGene for a lsit of UniProt protein accession. Use PICR to convert UniProt to RefSeq, get homologous from homoloGene and convert RefSeq results to UniProt. Be patient, the workflows has to bring a file around 11Mb. ftp://ftp.ncbi.nlm.nih.gov/pub/HomoloGene/README

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

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Workflow EBI PICR, find cross-references for protei... (2)

Created: 18/05/11 @ 09:36:26 | Last updated: 29/05/11 @ 17:35:20

Credits: User Rafael C. Jimenez

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Find cross-references (based on 100% sequence identity) for protein accessions from more than 95 distinct databases. For instance input a list of IPI accessions and find cross-references for Swissprot and Ensembl. Mappings can be limited by source database, taxonomic ID and activity status.

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Workflow DAS features retrieval and parsing with JDAS (2)

Created: 01/06/11 @ 18:06:35 | Last updated: 02/06/11 @ 10:24:13

Credits: User Rafael C. Jimenez

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Retrieve Protein or Genome features using the Distributed Annotation System (DAS) and create your own text output by modifying the JDAS component. To be able to use this workflow with JDAS copy this file … http://www.ebi.ac.uk/~maven/m2repo/uk/ac/ebi/das/jdas/1.0.3/jdas-1.0.3.jar … to the lib folder inside the Taverna application. This jar file is a dependency needed to parse DAS outputs.

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

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Workflow PSICQUIC Registry (Molecular Interactions ... (1)

Created: 20/07/11 @ 11:04:26 | Last updated: 20/07/11 @ 14:55:44

Credits: User Rafael C. Jimenez

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Query the PSICQUIC registry to retrieve information about services providing molecular interactions

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Original Uploader

Workflow Retrieve Molecular Interactions from PSICQ... (1)

Created: 05/10/11 @ 00:40:20 | Last updated: 05/10/11 @ 00:40:22

Credits: User Rafael C. Jimenez

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Retrieve Molecular Interactions from PSICQUIC Services for a list of Protein Accessions in PSI-MITAB format

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

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Workflow Parse QuickGO "proteinList" file format (1)

Created: 20/02/12 @ 23:28:03 | Last updated: 20/02/12 @ 23:28:04

Credits: User Rafael C. Jimenez

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Parse QuickGO "proteinList" file format. http://www.ebi.ac.uk/QuickGO/reference.html

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 14 times | Downloaded: 6 times

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Original Uploader

Workflow Find Reactome pathways and reactions by GO (1)

Created: 29/05/11 @ 19:09:23 | Last updated: 29/05/11 @ 19:09:25

Credits: User Rafael C. Jimenez

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Find Reactome pathways and reactions (names and accessions) in Human querying by a Gene Ontology term. This is an example of how to use the Reactome Biomart service in Taverna. Many other possibilities are possible by modifying the filters and attributes options of the service.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

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Workflow Get a PSICQUIC REST URL from a PSICQUIC SO... (1)

Created: 22/07/11 @ 11:30:30 | Last updated: 22/07/11 @ 11:31:05

Credits: User Rafael C. Jimenez

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Get a PSICQUIC REST URL from a PSICQUIC SOAP URL

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 12 times | Downloaded: 7 times

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Original Uploader

Workflow Find orthologs using a list of uniprot acc... (1)

Created: 14/10/11 @ 13:12:36 | Last updated: 14/10/11 @ 13:12:39

Credits: User Rafael C. Jimenez

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Find orthologs based on ensembl information using as input/output uniprot accessions

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 12 times | Downloaded: 6 times

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