Workflows

Cross-references search, duplicated genes ... (1)

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This workflow is composed of 3 steps: -First, it search for Ensembl gene Ids matching a list of identifier, using the GenOuest Xref webservice. -Then it uses the Duplicated Genes Database webservice to search for duplication information about each found gene. -Finally, it uses the GenOuest Xref webservice to fetch external identifier for each found gene (GO term in this example).

Created: 2010-03-16 | Last updated: 2010-03-16

Credits: abretaud

[untitled] (1)

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No description

Created: 2010-03-16

Credits: Paul Fisher

Split multi-sequence FASTA file into list (1)

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Splits a flat file containing multiple fasta sequences into a list of fasta sequences.

Created: 2010-03-16

microRNA to KEGG Pathways and Abstracts (1)

Workflow takes in a text file of microRNAs from microCOSM (at the EBI) and outputs a list of KEGG pathway information, including genes in pathways and pathway abstracts from PubMed. The results can then be used in various text mining applications/workflows to rank the results against a given disease.Workflow takes in a file of microRNAs

Created: 2010-03-17

Credits: Paul Fisher

Attributions: Pathways and Gene annotations for QTL region

Log into Alitora system (1)

A nested workflow to be used for logging into Alitora

Created: 2010-03-17

Credits: Peter Li

Log out from Alitora system (1)

A nested workflow to be used for logging out of Alitora

Created: 2010-03-17 | Last updated: 2010-03-17

Credits: Peter Li

Test workflow for logging into Alitora and... (1)

No description

Created: 2010-03-17

Credits: Peter Li

Convert to KEGG ID (1)

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Convert another database ID to a KEGG ID. Valid namespaces are NCBI_gi, GebBank, UniProt, UniGene, PMID or OMIM.

Created: 2010-03-17 | Last updated: 2010-03-17

Credits: White duncan100

Visualise KDA output data with Cytoscape (2)

This workflow retrieves a data file on a web server directory and launches Cytoscape to visualise it.

Created: 2010-03-18 | Last updated: 2010-03-18

Credits: Peter Li

Part 2 (1)

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Created: 2010-03-18

Credits: White duncan100

Parts 4-6 (1)

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No description

Created: 2010-03-18 | Last updated: 2010-03-18

Credits: White duncan100

Square A List Of Numbers (1)

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Simple workflow which squares a list of numbers.

Created: 2010-03-19 | Last updated: 2010-03-19

Credits: Paul Miller

Requirement 1 (1)

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No description

Created: 2010-03-19 | Last updated: 2010-03-19

Credits: Jannetta

Requirement 1 and 3 (1)

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No description

Created: 2010-03-19 | Last updated: 2010-03-19

Credits: Jannetta

Requirement 3 (1)

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No description

Created: 2010-03-19 | Last updated: 2010-03-19

Credits: Jannetta

Invocation of Gene Pattern modules using R (1)

 A workflow to invoke a Gene Pattern module using an R script. Note that a FTP URL for the data to be analysed is required, not the data itself!

Created: 2010-03-19 | Last updated: 2010-03-19

Credits: Peter Li

BlastandParse1 (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: 2010-03-19

Credits: Baywatch Solutions

Attributions: fetchEnsemblSeqsAndBlast

BlastandParse2 (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: 2010-03-19

Credits: Baywatch Solutions

Attributions: fetchEnsemblSeqsAndBlast

Compare genome, extract proteins which are... (1)

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  Takes GI number for source (non-pathogenic) and target (pathogneic) genomes, extracts list of all proteins from each genome using GenBank database. Outputs prtoeins in FastA format. Creates database from source proteins using formatdb (locally installed) and blasts (local installed) proteins from target against this database. Extracts protens which are unique (no blast hits) to the target (pathogenic) genome based on eValue set by user. Takes unique proteins from target and blasts aga...

Created: 2010-03-19 | Last updated: 2010-03-19

Credits: Ian Laycock nclteamc

Attributions: fetchEnsemblSeqsAndBlast NCBI Gi to Kegg Pathways color_pathway_by_objects

Fetch EMBL File (1)

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Fetches an EMBL file using the EMBL id. Creates file to a specified location.

Created: 2010-03-19

Credits: Baywatch Solutions