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Interactive web tools. Raymond Ripp 9 mars 2010. GxDb GxUpload GxAnalysis GxQuerying GxDisplay ImAnno Annotation Analysis Querying Display. R Normalisation Signal Intensity Ratio Quality control Cluspack StringInteractome Go GPS … lists of genes. - PowerPoint PPT Presentation
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Interactive web tools
Raymond Ripp
9 mars 2010
Batch Processing and Web Interaction
GxDb GxUpload GxAnalysis GxQuerying GxDisplay
ImAnno Annotation Analysis Querying Display
R Normalisation Signal Intensity Ratio Quality control
Cluspack StringInteractome Go GPS … lists of genes
GxDb
GxDb Upload procedure
Resume an existing session
GxDb WebsiteUpload
Querying Display
alnitakStar3Star4Star5Star6Star7Star8
/GxData
GxDb SQL database
http://gx.igbmc.frWeb Services
Café des sciences QSub
Ordonnanceur
GxDb ressourcesLanguages used:
PHP (HTML) - Upload - PipeWork - RadarGenerator - Fed
R - Treatment and analysis protocol - RReportGenerator
SQL
Tcl - Gx (~ Gscope) - Probeset loading
C - Cluspack
Ordonnanceur 1/3
Upload … up to 30’
then run Normalisation … 2 hours
then load into the sql database and run the
Clustering … several hours
then load into the sql database “Hello !!! All is done ! ”
PHP
Tcl RPHP
PHP
PHP Tcl Cluspack
PHP
PHP
Ordonnanceur 2/3
Suppose you create /genomics/link/Ordonnanceur/myscript.tcl_todo.txt
Every minute, the Ordonnanceur : If there is no …_inprogess.txt
Copies it into myscript.tcl_inprogess.txt Copies it into myscript.tcl Runs myscript.tcl
If myscript.tcl wants to wait (1’) for something exec Ordonnanceur DeleteInProgress MySelf exec Ordonnanceur DeleteScript MySelf exit
If myscript.tcl has finished its task exec Ordonnanceur DeleteAll MySelf exit
Ordonnanceur 3/3
To create your Todo … : Ordonnanceur CreateToDo MyScript.tcl … and you get a unique name
All is logged …/Ordonnanceur/MyScript.log …/Ordonnanceur/log/Ordonnanceur.log
Get the status Ordonnanceur GetToDo Ordonnanceur GetInProgess Ordonnanceur GetLog Ordonnanceur GetDone
Querying, Display, Lists of Genes
GxDb managing What is available
Probesets, Genes Experiments, Arraytypes Analysis software, Clustering software Samples, Organisms, Individuals, etc. RealExps
Signal Intensities RadarGenerator
Clustering Cluster context, Cluster composition Clusters of a gene, Groups of genes
String Interactome GO, GSEA Meta-Analysis
The RadarGenerator PipeWork
Radar Generator
Radar Display
About Clustering
HtmlTable (PipeWork’s standard output)
DoOnList
DoOnList from ClusterComposition
StringInteractome output
StringInteractome WithAny.string
RMA gcRMA
Nb_clu Max Min Avg Nb_clu Max Min Avg
Km_dpc 2 20283 1081 10682 62 4949 1 390
Mm_aic 140 341 3 152 150 356 8 161
Mm_bic 33 1182 29 647 44 927 19 549
MAS5.0 dChip
Km_dpc 3 21656 1321 9137 3 20162 1762 9137
Mm_aic 157 484 27 174 160 400 1 171
Mm_bic 39 1337 38 702 40 1211 36 685
PLIER VSN
Km_dpc 2 19151 1419 10285 5 15586 23 4007
Mm_aic 137 327 2 150 140 301 2 143
Mm_bic 36 1152 13 571 32 1205 25 626
Cluspack Clusters of congRD1
ImAnno ISH images annotation
Cst3
ImAnno ISH images annotation
ImAnno Sieves
ImAnno DoOnList
ImAnno Cluspack Display
Run StringInteractome from DoOnList
Back to existing StringInteractome
ImAnno ISH images annotation
KUROVKolliger Utriculus Retina Olfactif Vibriss
All possible KUROV combinations
Conclusions … and To Do
It works … The user can create his own lists and run several analysis tools We have to add more and more tools. Test it.
Nice colors … Some technical problems (multi sessions) Perfomance Add new functionalities …