Workflows

Untitled (1)

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Initial version

Created: 2013-03-15

Simulate_Mass_Spectrum (1)

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This 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 Simulate_Mass_Spectrum, that calculates the isotopic distribution using the FFT method and convolutes the theoretical (infinite resolution) distribution with a Gaussian peak shape. The building blocks can be used in any other workflows using the isotopic distribution of peptides or other molecul...

Created: 2013-03-12

Credits: Magnus Palmblad

Extract a column from a VOTable into a List (3)

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Snippet showing how to use AstroTaverna tool for extracting a column from a VOTable into a single List.

Created: 2013-03-08 | Last updated: 2013-04-22

Credits: Julian Garrido Susana

List all human metabolites in Wikipathways (1)

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Created: 2013-03-08

Credits: Egon Willighagen

List all Kegg identifiers used for metabol... (1)

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Created: 2013-03-08

Credits: Egon Willighagen

List all sources from which metabolite ide... (1)

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 List all sources from which metabolite identifiers are used, sorted by use.

Created: 2013-03-08

Credits: Egon Willighagen

List all Metabolites in WikiPathways (1)

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Created: 2013-03-08 | Last updated: 2013-03-08

Credits: Egon Willighagen

Microbase S3CMD and AWS Workflow to Analys... (1)

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 This workflow is designed to interact with the aws and a specific VM, to carry out commands and analsye next gen sequence data (SFF FASTQ)

Created: 2013-03-08

Credits: ROBSeq Tech. Ltd.

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

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