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Taverna 2

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Team A

Antibiotic resistance profiling (1)

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A workflow that takes a user defined genomic sequence and queries a third party database of genes encoding antibiotic resistance through a BLAST search for matching sequences. The accession IDs from the matches are extracted and the Entrez webservice is used to retrieve genbank records for the antibiotic resistance genes found. A python script is essential in the functioning of this workflow and this can be found at www.bioinformatix.co.uk along with a user and maintenance manual whic...

Created: 2013-03-08

Credits: Team A

Taverna 2

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Team A

Identification of Virulence Factors from a... (1)

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This workflow takes a user specified genomic sequence and, via BLAST, queries a database containing genomic sequences of virulence factors. The database and genome sequence must be held locally. A python script is associated with this workflow and should be downloaded from www.bioinformatix.co.uk. A user and maintenance manual relating to this workflow can be found at www.bioinformatix.co.uk and should be consulted before this workflow is utilised.

Created: 2013-03-08

Credits: Team A

Taverna 2

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Team A

Metabolic profiling from NCBI GIs (1)

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This workflow will take NCBI GIs and produce the following output: KEGG identifier corresponding to the NCBI GI Information about the gene corresponding to the NCBI GI Pathway IDs corresponding to the the KEGG identifier Images of the pathways that the proteins defined by the NCBI GIs are involved in.

Created: 2013-03-08

Credits: Team A

Taverna 2

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Team A

Three Microbase responders used for the Id... (1)

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Three microbase responders are used to take .sff data from IonTorrent and report on the organisms present within the data. It also takes three JSON input messages. The first calls sff_extract python script, the next calls MIRA or Ray and the final responder calls BLAST. For more information including a user manual visit www.bioinformatix.co.uk

Created: 2013-03-07

Credits: Team A

Taverna 2

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Markus Plangg

imagemagick-convert-tiff2tiff-compression (1)

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Migration of tiff2tiff with compression action

Created: 2013-03-06 | Last updated: 2013-03-06

Taverna 2

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Stian Soiland-Reyes

Visualize PAV provenance as SVG (2)

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VoID descriptions are fetched as Turtle, cleaned up to be valid OWL ontology and include useful labels, processed through the OWL reasoner Pellet; this adds inferred PROV statements to the RDF, which is then fed to the PROV Toolbox, generating an SVG visualization of the provenance. Note that this workflow downloads CWM, Pellet and ProvToolbox on demand, and uses UNIX command line tools like wget and md5 which are unlikely to work in Windows. This workflow has been tested on Ubuntu 12.10 wit...

Created: 2013-03-05 | Last updated: 2013-04-05

Credits: Stian Soiland-Reyes

Taverna 2

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Magnus Palmblad

Calculate_Isotopic_Distribution (1)

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This small workflow takes as input a peptide sequence and calculates the elemental composition of the peptide (Calculate_Elemental_Composition). This is then transferred as a numerical vector to the Rshell Calculate_Isotopic_Distribution, that calculates the (integer mass) isotopic distribution using the FFT method. To shift to approximate real masses (or m/z values), transpose the distribution with the difference between the integer and real monoisotopic masses (both easily calculated using ...