8.1 Main configuration XML file

<Parameter key="min:memory" value="200"/> : minimum size for a standard use (a message is displayed if the user memory is below this threshold)
<Proxy host='www-cache' port='1234'/> : proxy address for the URL

<TranscriptomeURLTemplate>
file:///C:/VAMP/data/xml/trs/#ProjectId#/#NumHisto#/chr/chr#ChrAlias#.xml
</TranscriptomeURLTemplate>
Used for locating the transcriptome data from a CGH array (#variables# are set from the XML CGH array data files)

<LOHURLTemplate>
file:///C:/VAMP/data/xml/microsat/#ProjectId#/#NumHisto#/chr/chr#ChrAlias#.xml
</LOHURLTemplate>
	Used for locating the LOH data from a CGH array (#variables# are set from the XML CGH array data files)

 Parameterization of the contextual menu of an object of Clone type: how to add an hypertext link:
 <PropertyElementMenu object='DataElement' type='Clone'>
  <MenuItem type='separator'/>
  <MenuItem type='menu' title='External Links'>
       <MenuItem
            type='url'
            title='NCBI Clone Viewer' 
	url='http://www.ncbi.nlm.nih.gov/genome/clone/clname.cgi?stype=Name&amp;list=#Name#'
            target='_blank'/>
       <MenuItem
            type='url'
            title='NCBI Map Viewer'
	url='http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?ORG=hum&amp;query=#Name#&amp;MAPS=cntg-r,clone,sts,genes,comp&amp;CHR=#Chr#&amp;ABS_ZOOM=6M'
            target='_blank'/>
       <MenuItem
            type='url'
            title='Working Draft (UCSC)' 
	    url='@data'
            target='_blank'>
<token>
http://www.genome.ucsc.edu/cgi-bin/hgTracks?position=chr#Chr#:</token>
<sub>
<property>Position</property>
<token>150000</token>
</sub>
<token>-</token>
<add>
<property>Position</property>
<token>150000</token>
</add>
       </MenuItem>
       <MenuItem
            type='url'
            title='Ensembl ContigView'
	    url='@data'
            target='_blank'>
<token>
http://www.ensembl.org/Homo_sapiens/contigview?chr=#Chr#&amp;vc_start=</token>
<sub>
<property>Position</property>
<token>150000</token>
</sub>
<token>&amp;vc_end=</token>
<add>
<property>Position</property>
<token>150000</token>
</add>
       </MenuItem>
       <MenuItem
            type='url'
            title='Ensembl CytoView'
	    url='@data'
            target='_blank'>
<token>
http://www.ensembl.org/Homo_sapiens/cytoview?chr=#Chr#&amp;vc_start=</token>
<sub>
<property>Position</property>
<token>150000</token>
</sub>
<token>&amp;vc_end=</token>
<add>
<property>Position</property>
<token>150000</token>
</add>
       </MenuItem>
   </MenuItem>
 </PropertyElementMenu>

 
 Parameterization of the contextual menu of an object of ProbeSet type: how to add an hypertext link:
  <PropertyElementMenu object='DataElement' type='ProbeSet'>
  <MenuItem type='separator'/>
  <MenuItem type='menu' title='External Links'>
       <MenuItem
            type='url'
            title='Genecards Viewer' 
	    url='http://genecards.curie.fr/cgi-genecards/cardsearch.pl?search=#SourceID#'     
            target='_blank'/>
  </MenuItem>
 </PropertyElementMenu>


 Parameterization of the contextual menu of the "Minimap: how to add an hypertext link:
<PropertyElementMenu object='MiniMapChr'>
   <MenuItem type='menu' title='External Links'>
       <MenuItem
            type='url'
            title='NCBI Map Viewer' 
	    url='http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?ORG=human&amp;MAPS=cntg-r,clone,sts,genes,comp&amp;CHR=#Name#'
            target='_blank'/>
   </MenuItem>
 </PropertyElementMenu>

 <PropertyElementMenu object='MiniMapBand'>

   <MenuItem type='menu' title='External Links'>
       <MenuItem
            type='url'
            title='NCBI Cancer Chromosomes'
            url='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=cancerchromosomes&amp;term=%2B#Chr##Arm##Name#&amp;cmd=Search'
            target='_blank'/>
   </MenuItem>
 </PropertyElementMenu>

 <UserDocumentation url='...'/> : indicates the physical localization of the user's guide

several examples of how to call a cgi (does not function locally) :
<Parameter key="eXcel:URL" value="http://bioinfo.curie.fr/cgi-bin/cghaia/export.pl?format=xl"/>
<Parameter key="eXcelChrAvg:URL" value="http://bioinfo.curie.fr/cgi-bin/cghaia/average_chr.pl?format=xl"/>
<Parameter key="cluster:URL" value="http://bioinfo.curie.fr/cgi-bin/cghaia/vamp_plugin.pl?action=clust"/>

root of the physical localization of the data xml files :
<Parameter key="importData:baseURL" value="file:///C:/VAMP/data/xml/cgh/"/>


indicates the physical localization of the image file which are used by the applet :
<Parameter key="applet_home_img:URL" value="file:///C:/VAMP/images/applet_home.png"/>
<Parameter key="cytoband:URL" value="file:///C:/VAMP/data/xml/cytoband/human"/>
<GraphElementIcon type="CGH Array" url="file:///C:/VAMP/images/vamp_cgh.jpg"/>
<GraphElementIcon type="CGH Chromosome Merge" url="file:///C:/VAMP/images/vamp_cgh.jpg"/> 
<GraphElementIcon type="CGH Array Merge" url="file:///C:/VAMP/images/vamp_cgh.jpg"/>
<GraphElementIcon type="CGH Average" url="file:///C:/VAMP/images/vamp_cgh.jpg"/>
<GraphElementIcon type="Transcriptome" url="file:///C:/VAMP/images/trs.jpg"/>
<GraphElementIcon type="Transcriptome Average" url="file:///C:/VAMP/images/trs.jpg"/>
<GraphElementIcon type="Transcriptome Relative" url="file:///C:/VAMP/images/trs.jpg"/>
<GraphElementIcon type="Transcriptome Merge Relative" url="file:///C:/VAMP/images/trs.jpg"/>
<GraphElementIcon type="LOH" url="VAMP/images/LOH.jpg"/>

indicates the physical localization of cytogenetics descriptions :
<Cytoband organism="Human"
          url="file:///C:/VAMP/data/xml/cytoband/human/mai_2004"
          resolutions="400:550:850"
          default_resolution="400"/>
<Cytoband organism="Mouse"
          url="file:///C:/VAMP/data/xml/cytoband/mouse"
          resolutions="400"/>

indicates the physical localization of a file used for customized printing of a reporting :
<PrintPageTemplate url="file:///C:/VAMP/configuration/xml/print-report.xml"/>