Workflows

Run on amazon cloud (1)

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 Execute commands on amazon cloud machines Manual and documentation at: http://www.students.ncl.ac.uk/g.georgiou/newweb/

Created: 2012-05-04 | Last updated: 2012-05-04

Credits: Georgeg9 BioGreen Ltd.

FINAL VERSION (1)

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 From genome to genbank file and annotations Manual and documentation at: http://www.students.ncl.ac.uk/g.georgiou/newweb/

Created: 2012-05-04 | Last updated: 2012-05-04

Credits: Georgeg9 BioGreen Ltd.

Attributions: Convert to KEGG ID NCBI Gi to Kegg Pathways EBI_NCBI_BLAST EBI_InterproScan_NewServices

Get top blastx hit of a list of contigs (1)

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This workflow takes a contigs.fasta file , gets all the ORF's present in it , runs blastx on each ORF, gets the FASTA file of the top blastX hit and its GI number.

Created: 2012-05-04 | Last updated: 2012-05-04

Credits: BioCo Consultants

generateWholeSeqAnnotation (1)

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 This work flow is used for genereating all the known genes together to annotate a whole or a large region of genome sequence.   outputfilrURL:  the location of the output file Ginumber:   the input gi gene number wholeGenomeSeq:    the whold sequence annotation information output:    the output of genbank text

Created: 2012-05-04 | Last updated: 2012-05-04

Credits: BioCo Consultants

ConcatStringTogether (1)

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 This workflow is as simple as you can imagine! It can be used to remove the information tags in a fasta file and concat the sequence together   fastaURL :  the input fasta reads file location seqURL : the outcome sequence file location wholeSeq : the output sequence as an entire string

Created: 2012-05-04 | Last updated: 2012-05-04

Credits: BioCo Consultants

filterDifferenceInLists (1)

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 This workflow output a list of the protein or any string hits in the first list but not in the second list.    output : output file location com : comparision protein list our : interested protein list out1: output as a string

Created: 2012-05-04 | Last updated: 2012-05-04

Credits: BioCo Consultants

extractGInumber (1)

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 This workflow uses regex pattern to compare the identity percentage of each hits against the input sequnece and return the whole information of the hits and the GI number of them (if they including the GI number as a sub information)   inputfileURL:  the location of the Gi number   outputText  : the list of all the hits and the GI number of them

Created: 2012-05-04 | Last updated: 2012-05-04

Credits: BioCo Consultants

Check Java Cryptography Unlimited Strength (1)

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Checks if Java Cryptography Extension (JCE) Unlimited Strength Jurisdiction Policy Files is installed, and redirects user to correct download page and relevant lib/security folder if not.

Created: 2012-05-08 | Last updated: 2012-05-08

Credits: Stian Soiland-Reyes

Attributions: Find/show Taverna's home directory

Find workflow ancestors (2)

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Given a t2flow file (Taverna 2 workflow), extract ancestor workflow UUIDs and search myExperiment for matching workflow entries. Note that this will also match the workflow itself and nested workflows, but does not match against other workflows having the same ancestors (but newer UUIDs).

Created: 2012-05-08 | Last updated: 2012-07-09

Credits: Stian Soiland-Reyes

Simple image migration (1)

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Then starts a migration action on an image and extracts properties from the original and migrated image. The properties are compared and a QA algorithms is started on the image data itself .

Created: 2012-05-08 | Last updated: 2012-05-08

Credits: Markus Plangg