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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.
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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 Batch Processing and Web Interaction
GxDbressources Languages used: PHP (HTML) - Upload - PipeWork - RadarGenerator - Fed R - Treatment and analysis protocol - RReportGenerator SQL Tcl - Gx (~ Gscope) - Probeset loading C - Cluspack /GxData GxDb SQL database alnitak http://gx.igbmc.fr Web Services Café des sciences QSub Ordonnanceur Star3 Star4 Star5 Star6 Star7 Star8 • GxDb Website • Upload • Querying • Display
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 PHP Tcl R 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
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 • …