Changes between Initial Version and Version 1 of application_pages/apps/java/geneDetection


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Timestamp:
10/26/15 09:33:34 (9 years ago)
Author:
trac
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  • application_pages/apps/java/geneDetection

    v1 v1  
     1[[PageOutline]] 
     2 
     3= Application Name = 
     4 
     5Gene Detection Service 
     6 
     7= Summary = 
     8 
     9* '''Name''': {{{Gene Detection Service}}} 
     10* '''Contact Person''': {{{support-compss@bsc.es}}} 
     11* '''Access Level''': {{{public}}} 
     12* '''License Agreement''': {{{Apache2}}} 
     13* '''Platform''': {{{COMPSs}}} 
     14* '''Repository''': [[https://compss.bsc.es/svn/bar/apps/java/geneDetection|Gene Detection Service]] 
     15 
     16 
     17== Description == 
     18The Gene Detection service offers the functionality to perform automatic functional analysis of the relevant genes of an aminoacid sequence using a combination of the Blast and Genewise Software and other bioinformatic services. More details about the algorithm can be found in [1]. 
     19Basically, the application is composed by 4 parts: Part A performs a format change of input data; Part B performs a search of similar aminoacid sequences; Part C performs the relevant gene search ; and finally, Part D perform the funtional analysis of the relevant genes.  
     20The number of parallel task varies depending on the number of similar sequences and the relevant genes found in every run and the number of concurrent runs invoqued in the service      
     21 
     22== Requirements == 
     23* Apache maven for building the software 
     24* Blast 2.2.15 
     25* Wise 2.2.0 
     26 
     27== Build instructions == 
     28 
     29mvn clean install -Dwise.location=//</path/to/wise/>// -Dblast.location=//</path/to/blast/>// 
     30 
     31== Execution instructions == 
     32 
     33This application is a webservice. To deploy it copy the following war files to an application server container 
     34 
     35${basedir}/target/GeneDetection-1.0-SNAPSHOT.war 
     36 
     37${basedir}/data/GeneDetectionGUI.war 
     38 
     39${basedir}/data/Monitor.war 
     40 
     41run the application server 
     42 
     43== References == 
     44 
     45 [1] R. Royo, J. Lopez, D. Torrents, and J. Gelpi, “A Bio Moby - based workflow for gene detection using sequence homology,” in //International Supercomputing Conference (ISC’08)//, Dresden (Germany), 2008. 
     46