Workflows

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User: Rafael C. Jimenez
Original Uploader

Workflow Get models from BioModels including the in... (3)

Created: 22/08/12 @ 06:18:53 | Last updated: 24/08/12 @ 02:30:55

Credits: User Rafael C. Jimenez

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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A service to look for models in BioModels using a UniProt accession as input. If the input protein is found in one model the workflow will provide the BioModels Id, the SBML and a link to the BioModels database. Please use taverna 2.4 or above.

Rating: 0.0 / 5 (0 ratings) | Versions: 3 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 8 times | Downloaded: 0 times

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Original Uploader

Workflow Select redundant accessions (1)

Created: 31/01/11 @ 15:32:23 | Last updated: 31/01/11 @ 15:32:24

Credits: User Rafael C. Jimenez

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Simple workflows to select accessions which appear more than once. Chose threshold to specify how many times an accession has to appear to be selected. This workflow uses a list of Comma-separated values as input. The accessions selected is the result which is presented in a String of Comma-separated values.

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

Viewed: 11 times | Downloaded: 8 times

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Original Uploader

Workflow DAS sequence retrieval and parsing with JDAS (1)

Created: 30/05/11 @ 03:12:23 | Last updated: 30/05/11 @ 03:14:03

Credits: User Rafael C. Jimenez

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Retrieve Protein or Genome sequences 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: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 15 times | Downloaded: 8 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 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 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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