Interactive web tools Raymond Ripp 9 mars 2010

Batch Processing and Web Interaction  GxDb GxUpload GxAnalysis GxQuerying GxDisplay  ImAnno Annotation Analysis Querying Display RR Normalisation Signal Intensity Ratio Quality control  Cluspack  StringInteractome  Go  GPS  … lists of genes

GxDb

GxDb Upload procedure

Resume an existing session

GxDb Website Upload Querying Display alnitak Star3 Star4 Star5 Star6 Star7 Star8 /GxData GxDb SQL database Web Services Café des sciences QSub Ordonnanceur GxDb ressources Languages 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 TclRPHP TclCluspack 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

RMAgcRMA Nb_cluMaxMinAvgNb_cluMaxMinAvg Km_dpc Mm_aic Mm_bic MAS5.0dChip Km_dpc Mm_aic Mm_bic PLIERVSN Km_dpc Mm_aic Mm_bic 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

KUROV Kolliger 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  …