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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

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

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

imagemagick-convert-tiff2tiff-compression (1)

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Migration of tiff2tiff with compression action

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

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

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 ...

Created: 2013-03-05

Credits: Magnus Palmblad

HGNC 2 Bio2RDF rdfizer workflow (1)

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Talend workflow to convert in RDF with Bio2RDF URIs, the HGNC description of genes available at http://www.genenames.org/cgi-bin/hgnc_stats.

Created: 2013-02-27

Credits: Francois Belleau

Test RShell (1)

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workflow hacked to include empty username and password elements

Created: 2013-02-27

Credits: Reinout van Schouwen Eleni

Attributions: workflow to test Rshell (for internal purposes)

Migration Imagemagick convert no compression (2)

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Converts an image using imagemagick convert -compress None

Created: 2013-02-25 | Last updated: 2013-02-26

Credits: Kraxner Markus Plangg

Attributions:

JP2 to TIFF file format migration with qua... (1)

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This workflow reads a textfile containing absolute paths to JP2 image files and converts them to TIFF image files using Kakadu's j2k_to_image command line application (http://www.kakadusoftware.com). Based on the input text file, the workflow creates a Taverna list to be processed file by file. A temporary directory is created (createtmpdir) where the migrated image files and some temporary tool outputs are stored. Before converting the files, the JP2 input files are validated using the SC...

Created: 2013-02-07

Credits: Sven

Annotate a gene list with disease concepts (1)

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Purpose: Currently, this workflow takes a list of genes and a concept set as input, calculates the matching score between these and finds the concept that contributes the most to the match. Author comments: The workflow is in Beta stage. It runs, but needs more testing with different parameter settings. This workflow can be used together with other workflows in this pack: http://www.myexperiment.org/packs/368 for functional gene annotation and knowledge discovery.

Created: 2013-02-06

Credits: Kristina Hettne Reinout van Schouwen Marco Roos BioSemantics

Attributions: SNPs to Concept Set through Concept Profile Matching v2

Match concept profiles with predefined set (2)

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Purpose of workflow: The workflow can be used to match a set of concept profiles with predefined set of concept profiles. Result: A list of concepts ordered by their match to the query concept profiles.

Created: 2013-02-05 | Last updated: 2014-07-14

Credits: Kristina Hettne Marco Roos Reinout van Schouwen BioSemantics

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Created: 2013-01-30 14:15:24

Credits: Stian Soiland-Reyes

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Trident (Package)

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The Hypothesis for the wf4ever Demo Pack 2013

Created: 2013-01-30 14:06:43 | Last updated: 2013-01-30 14:07:25

Credits: Marco Roos

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Plain text

Comments: 0 | Viewed: 52 times | Downloaded: 19 times

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