Workflows

Parts 4-6 (1)

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

Credits: Jannetta

Requirement 1 and 3 (1)

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

Credits: Jannetta

Requirement 3 (1)

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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