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Detrprok (4)

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In the case study of stranded and prokaryotic RNAseq data, the Det'Rprok workflow detects candidates of 3 kinds of non coding RNA: 5'UTRs, antisense RNAs, and small RNAs.Inputs: i) an mapping file (bam format) containing one valid alignment by read, ii) a feature file (gff format) annotating the genomic sequences used for the mapping. Dependencies (from the Galaxy toolshed): "s_mart", "detrprok_scripts"

Created: 2013-05-20 | Last updated: 2015-11-03

Microbial Metagenomic Trait Statistical An... (9)

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This workflow retrieves the following microbial metagenomic traits from the Microbial Metagenomic Trait Database: -GC content -Variance of GC content -Dinucleotides -Number of rRNA -Codon usage -Amino acid composition -Acidic to basic amino acids ratio -% of Transcriptional factors -% of classified reads -Functional content -Functional diversity -Taxonomic content -Taxonomic diversity After the retrieval performs the ecological analyses described in Barberan et al. 2012 (http://dx.doi.or...

Created: 2012-12-19 | Last updated: 2014-11-12

Credits: Antonio Fernandez-Guerra Renzo Peliny BioVeL

Executes Python script (4)

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Snippet showing how to use Taverna Tool in Service template folder for executing a Python script. This workflow needs Python to be installed on the local system, and declared in the PATH enviromental variable, so any python script could be executed from a terminal.

Created: 2011-07-14 | Last updated: 2013-04-22

Credits: Jose Enrique Ruiz

NCBI BLAST (SOAP) (1)

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Perform a BLAST search using the EMBL-EBI’s NCBI BLAST (SOAP) service (see http://www.ebi.ac.uk/Tools/webservices/services/sss/ncbi_blast_soap). The query sequence, database to search and BLAST program to use are inputs, the other parameters for the search are allowed to default.

Created: 2010-11-29 | Last updated: 2013-03-28

Attributions: EBI_NCBI_BLAST NCBI BLAST (SOAP)

List all algorithms and descriptors an Ope... (2)

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 Uses the OpenTox API 1.1 to discover all the available algorithms and descriptors for a given service.

Created: 2010-04-01 | Last updated: 2010-11-13

Credits: Egon Willighagen

Open PDB entries in Jmol for hits found fo... (3)

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Queries Bio2RDF for proteins of which the title contains 'HIV', downloads them using the EMBL webservices and opens them in Bioclipse for visualization with Jmol.

Created: 2010-03-14 | Last updated: 2010-06-23

Credits: Egon Willighagen

Triplify search results from all KEGG data... (3)

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Search all KEGG databases using bfind SOAP service and merge results into a bmuri list and a ntriples string. 

Created: 2009-11-30 | Last updated: 2009-11-30

Credits: Francois Belleau

workflow1 (1)

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blast dando o ID de uma proteinablast dando o ID de uma proteina ex: database is ‘SWISS’, for program, ‘blastp’, and for ID ‘1220173blast dando o ID de uma proteina with interpro scan ex: database is SWISS’, for program, blastp, and for ID 1220173blast dando o ID de uma proteina ex: database is SWISS’, for program, blastp, and for ID 1220173

Created: 2009-11-16

Credits: Jorgep

Attributions: EBI_InterProScan for Taverna 2

Ex (1)

Ex of exercise

Created: 2009-11-16

Credits: Mventosa

Attributions: EBI_InterProScan for Taverna 2

What is [query] from NCBI, EBI, UniProt an... (2)

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test values: query = paget disease query = pdb4 query = hk1 query = h1n1 This rdfiser query those four federated search services EB-Eye, KEGG LinkDB, NCBI Entrez and UniProt knowledgebase. RDF triples are returned for search statistics with Bio2RDF normalised URIs. This workflow should be used responsibly because it can generate high load at the provider resources. test values: query = paget disease query = pdb4 query = hk1 query = h1n1 query = paget disease query = pdb4 query = hk1 que...

Created: 2009-11-03 | Last updated: 2009-11-03

Credits: Francois Belleau

Lists all Taverna 2 workflows (1)

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Uses Bioclipse and the MyExperiment SPARQL end point.

Created: 2009-08-21 | Last updated: 2009-08-22

Credits: Egon Willighagen

Split text/string into its lines and filte... (2)

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When retrieving a URL or soemthing alike, one can often identify the region of interest as a single line. Besides the expected output, also some interim values, like the lines split are forwarded, to allow some straight-forward cascading of filters with reduced redundancy.

Created: 2009-08-19

Credits: Steffen Möller

Extract Scientific Terms (1)

This workflow takes in a document containg text and removes any non-ascii characters. The cleaned text is then sent to a service in Dresden, to extract all scientific terms. These terms represent a concept profile for the input concpet. Any null values are also removed.

Created: 2009-08-10 | Last updated: 2009-08-10

Credits: Paul Fisher

Term Extraction with NaCTeM's TerMine Tool (2)

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Pass in text and retrieve a list of terms discovered ranked by their importance within the text.

Created: 2009-07-23

Credits: Brian Rea National Centre for Text Mining (NaCTeM)

Arabidopsis thaliana QTL Analysis (1)

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This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in Arabidopsis thaliana. The workflow requires an input of: a chromosome name or number; a QTL start base pair position; QTL end base pair position. Data is then extracted from BioMart to annotate each of the genes found in this region. The UniProt identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to searcg for pathways in the KEGG pathway database. ...

Created: 2009-07-08 | Last updated: 2009-12-14

Credits: Paul Fisher

Retrieve sequence in EMBL format (1)

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This workflow retrieves a sequence associated with its features in embl format

Created: 2009-07-03

Credits: Stian Soiland-Reyes

Attributions: Retrieve sequence in EMBL format

Demonstration of configurable iteration (1)

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This workflow shows the use of the iteration strategy editor to ensure that only relevant combinations of inputs are used during an implicit iteration.

Created: 2009-07-03 | Last updated: 2009-07-03

Credits: Stian Soiland-Reyes Tomoinn

Attributions: Demonstration of configurable iteration

Execute GWorkflowDL workflow using Taverna... (1)

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This workflow makes use of the "Grid Workflow Execution Service" (GWES) in order to exececute a GWorkflowDL workflow by means of the Taverna Workbench 2. As the GWES is deployed as a regular SOAP service, the WSDL can be imported as a normal service into the Taverna Workbench. This workflow contains all the input parameters as string constants, so it can be started right away without user inputs.

Created: 2009-06-30

Credits: Andreas Hoheisel

Attributions: Execute GWorkflowDL workflow using Taverna 2

Execute GWorkflowDL workflow using Taverna 2 (1)

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This workflow makes use of the "Grid Workflow Execution Service" (GWES) in order to exececute a GWorkflowDL workflow by means of the Taverna Workbench 2. As the GWES is deployed as a regular SOAP service, the WSDL can be imported as a normal service into the Taverna Workbench.

Created: 2009-06-30 | Last updated: 2009-06-30

Credits: Andreas Hoheisel