All content

DNA sequence analysis pilot (Blat) (2)

• Download

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

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

• Download

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

DNA sequence analysis pilot (1)

• Download

  http://amc-app1.amc.sara.nl/twiki/bin/view/         Workflow-based  DNA sequence analysis on the Dutch Life Science Grid, presented as Application Showcase at the NBIC Conference 2009, Lunteren, The Netherlands, 17 & 18 March 2009. http://www.biomedgrid.it/programme may 15th 2009. Hands on workflow: grid-enabled medical imaging  (Johan Montagnat – Tristan Glatard)  

Created: 2009-07-10 | Last updated: 2009-11-30

Credits: Angela Luijf Glatard

GATE Monte-Carlo simulations (3)

• Download

Application description is found in the following papers: Jan S et al, GATE: a simulation toolkit for PET and SPECT. Phys. Med. Biol. 49 (2004) 4543-4561 Sarrut D. and Guigues L. Region-oriented CT image representation for reducing computing time of Monte Carlo simulations. Med Phys. 35(4):1452-1463. 2008 Two components (fgate and merge, merge being disabled in experiments conducted for the heteropar and JGC papers) are run on the EGEE grid. A quite elaborated workflow is ma...

Created: 2009-05-23 | Last updated: 2009-08-13

Credits: Glatard

X!Tandem and PeptideProphet on the Grid (1)

• Download

The workflow performs the execution of X!Tandem and PeptideProphet from the TPP toolbox on the Grid. The execution is performed by the UNICORE Plugin for Taverna. mzXMLDecomposer/Composer is used to run the execution of X!Tandem in parallel. extract_values extract relevant information from thetandem.interact.pep.xml File. The file can then remain on the remote storage.

Created: 2013-08-13 | Last updated: 2013-09-04

Credits: Sonja Holl Yassene Magnus Palmblad

Attributions: de Bruin et al. Workflow 1 Cloud Parallel Processing of Tandem Mass Spectrometry Based Proteomics Data: X!Tandem

Sff2Fasta_Blast_Blat_ParseBlast (1)

• Download

Blast and Blat Roche 454 sequences against a reference database on the Dutch Life Science Grid Conversion of Roche 454 sequences to fasta Blat sequences against a database Blast sequences against a database Parse Blast results http://www.bioinformaticslaboratory.nl/  

Created: 2010-09-22 | Last updated: 2010-09-22

Credits: Barbera van Schaik Antoine van Kampen Angela Luijf Silvia Olabarriaga

Sff2Fasta_Blat (1)

• Download

Blat Roche 454 sequences against a reference database on the Dutch Life Science Grid Conversion of Roche 454 sequences to fasta Blat sequences against a database http://www.bioinformaticslaboratory.nl/  

Created: 2010-09-22 | Last updated: 2010-09-22

Credits: Barbera van Schaik Antoine van Kampen Angela Luijf Silvia Olabarriaga

Sff2Fasta_Blast_ParseBlast (1)

• Download

Blast Roche 454 sequences against a reference database on the Dutch Life Science Grid Conversion of Roche 454 sequences to fasta Blast sequences against a database Parse Blast results http://www.bioinformaticslaboratory.nl/      

Created: 2010-09-22 | Last updated: 2010-09-22

Credits: Barbera van Schaik Antoine van Kampen Angela Luijf Silvia Olabarriaga