Workflows

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Type: Taverna 2 User: Rafael C. Jimenez
Original Uploader

Workflow Molecular Interactions from IntAct PSICQUI... (2)

Created: 29/05/11 @ 01:32:18 | Last updated: 05/10/11 @ 00:20:00

Credits: User Rafael C. Jimenez

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Get molecular interaction data in psi-mitab25 from IntAct through its REST PSICQUIC service. As input you can use an Uniprot Acc like "P99999" or a MIQL query like "alias:KHDRBS1".

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

Viewed: 16 times | Downloaded: 9 times

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Original Uploader

Workflow EBI NCBI BLAST Multi FASTA (2)

Created: 16/07/11 @ 19:08:38 | Last updated: 16/07/11 @ 19:35:11

Credits: User Rafael C. Jimenez

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow performs multiple sequence similarity searches using the NCBI blast at the EBI. It uses the new EBI services, which are asynchronous and require looping over the nested workflow (Status) until the workflow has finished. Many of the EBI services now work in this way, so you can use this workflow as an example of the invocation pattern and looping configuration. If you want to make a blast search for more than 10 sequences I would recommend you to run the workflow using the comm...

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

Viewed: 44 times | Downloaded: 31 times

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Original Uploader

Workflow Biomart datasets for the Ensembl Genes mar... (1)

Created: 03/10/11 @ 10:17:40

Credits: User Rafael C. Jimenez

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Retrieve Biomart datasets for the Ensembl Genes mart service (one dataset per specie).

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

Viewed: 12 times | Downloaded: 10 times

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Original Uploader

Workflow Get homologous from an NCBI homoloGene.dat... (1)

Created: 20/10/11 @ 17:53:28 | Last updated: 27/10/11 @ 10:38:33

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. This workflow is useful if you have a long list of protein accessions. 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

Viewed: 43 times | Downloaded: 11 times

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Original Uploader

Workflow Find Biological Models by GO. (1)

Created: 29/05/11 @ 21:44:22 | Last updated: 29/05/11 @ 21:44:23

Credits: User Rafael C. Jimenez

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Find Biological Models (Ids and Names) from Biomodels querying by Gene Ontology terms.

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

Viewed: 19 times | Downloaded: 8 times

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Original Uploader

Workflow List of PSICQUIC services (names and URLs)... (1)

Created: 20/07/11 @ 14:10:30 | Last updated: 20/07/11 @ 14:58:43

Credits: User Rafael C. Jimenez

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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PSICQUIC provides access to molecular interaction databases. This workflow queries the registry and gets a list of available PSICQUIC services (names and URLs).

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

Viewed: 18 times | Downloaded: 7 times

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Original Uploader

Workflow Get homologous from NCBI homoloGene (1)

Created: 13/10/11 @ 18:35:58 | Last updated: 13/10/11 @ 18:36:01

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 list of Refseq protein accessions. 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

Viewed: 18 times | Downloaded: 5 times

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Original Uploader

Workflow Get a list of Protein Identification exper... (2)

Created: 21/02/12 @ 00:30:44 | Last updated: 22/02/12 @ 21:48:22

Credits: User Rafael C. Jimenez

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Get a list of Protein Identification experiments from PRIDE by a Gene Ontology query

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

Viewed: 12 times | Downloaded: 5 times

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Original Uploader

Workflow Molecular Interactions from IntAct PSICQUI... (2)

Created: 17/05/11 @ 07:09:30 | Last updated: 20/07/11 @ 15:14:56

Credits: User Rafael C. Jimenez

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Get molecular interaction data in psi-mitab25 from IntAct through its PSICQUIC service. As input you can use an Uniprot Acc like "P99999" or a MIQL query like "alias:(KHDRBS1 OR HCK)". This workflow finds by itself how many queries needs to make (SOAP service limited to 200 binary interactions per call) to be able to return all the results in one file.

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

Viewed: 28 times | Downloaded: 8 times

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Original Uploader

Workflow DAS features retrieval (2)

Created: 01/06/11 @ 17:10:43 | Last updated: 01/06/11 @ 17:57:45

Credits: User Rafael C. Jimenez

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Retrieve Protein or Genome features (annotations) using the Distributed Annotation System (DAS).

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

Viewed: 16 times | Downloaded: 8 times

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