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Taverna 2.3 starter pack

Created: 2011-06-21 14:16:18 | Last updated: 2012-04-05 13:55:40

26 items in this pack

Comments: 0 | Viewed: 162 times | Downloaded: 66 times

DNA sequence analysis pilot (Blat) (2)

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http://amc-app1.amc.sara.nl/twiki/bin/view/  Workflow-based  DNA sequence analysis on the Dutch Life Science Grid. This workflow is  based on http://www.myexperiment.org/workflows/840 , the last component (Blast analysis) is replaced by Blat analysis    

Created: 2009-11-20 | Last updated: 2009-11-30

Credits: Angela Luijf Barbera van Schaik Glatard

Attributions: DNA sequence analysis pilot

NCBI Gi to Kegg Pathways (1)

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This workflow converts a list of NCBI gi numbers and  converts them to a list of KEGG genes. Those KEGG gene ids are subsequently turned into KEGG pathway identifiers and descriptions. It also removes any null values from a list of strings. Example input for this workflow is as follows (new line separated): gi:215422388 gi:120407068

Created: 2009-06-08 | Last updated: 2009-12-14

Credits: Paul Fisher

BioAID_EnirchBioModelWithProteinsFromText (7)

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This workflow is for demonstration purposes only. Please contact the authors if you wish to try it. We will gladly collaborate with you. Summary This workflow extracts proteins and protein relations from Medline. Extracted protein names (symbols of at least 3 characters) are validated against mouse, rat, and human UniProt symbols, so the results are limited to these species. This workflow follows the following basic steps: it retrieves documents relevant for the query string i...

Created: 2009-05-16 | Last updated: 2009-05-16

Credits: Marco Roos Sophia katrenko Andrew Gibson M. Scott Marshall Willem van Hage Edgar Martijn Schuemie AID

Pathways and Gene annotations for Arabidop... (2)

This workflow searches for genes obtained from affy_ath1 affymetrix probeset identifiers. The Entrez and 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: 2009-03-06 | Last updated: 2009-12-03

Credits: Paul Fisher Peter Li

Attributions: Pathways and Gene annotations for QTL region

What is Paget's disease sparql query example (3)

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SELECT distinct ?s1 FROM <http://atlas.bio2rdf.org/sparql> WHERE {   ?s1 ?p1 ?o1 .   ?o1 bif:contains "paget" .   FILTER( regex(?s1, "omim")   OR regex(?s1, "geneid") OR regex(?s1, "uniprot")) }   followed by SELECT ?type1, count(*) FROM <http://localhost:8890/sparql> WHERE {   ?s1 ?p1 ?o1 .   ?o1 bif:contains "paget" .   ?s1  

Created: 2009-01-20

Credits: Francois Belleau

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Trident Example Workflows

Created: 2008-10-08 13:33:38 | Last updated: 2008-10-22 12:45:31

9 items in this pack

Comments: 0 | Viewed: 264 times | Downloaded: 68 times

mustang provides structural alignment of t... (3)

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This workflow experiments with the partial execution of jobs on a computational grid. The workflow elements "mustang" and "boxshade" are executed on grid nodes. Access to these resources is orchestrated with the plugin available on http://grid.inb.uni-luebeck.de. Please contact the author of this workflow for access permissions.

Created: 2008-08-20 | Last updated: 2008-08-25

Credits: Steffen Möller

Attributions: Fetch PDB flatfile from RCSB server

EBI_ClustalW_alignment_tree (2)

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Given a set of sequences perform an multiple sequence alignment and from the multiple alignment derive a phylogenetic tree. The popular ClustalW program (see http://www.clustal.org/), as implemented in the EBI's WSClustalW2 service (see http://www.ebi.ac.uk/Tools/webservices/services/clustalw2) is used to perform both tasks.

Created: 2008-05-31 | Last updated: 2010-12-03

Credits: Hamish McWilliam

Attributions: EBI_ClustalW2 EBI_ClustalW2_phylogentic_tree