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 ressources /GxData GxDb SQL database http://gx.igbmc.fr 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 GxDb requires many ressources that are summarized here. Here, it’s the user who access the website GxDb First case, he queries the database. The question is sended to web server (alnitak) which interrogates the database. The answer comes back to alnitak then to the user. Second case, he upload his .cel file. The data are sended to alnitak which tranfers data to database or disk. Third case, he launch the automatic protocol, this information is always sended to alnitak and through cafe des sciences, it launch the program on a star. Qsub is a command of the Sun Grid Engine which is able indeed to identify the least charged machine and submit your job to it. The ordonnanceur is a scheduler which waits the creation of files before launch the continuation of programs Here, you have all languages used 9

Ordonnanceur 1/3 Upload … up to 30’ Normalisation … 2 hours then run Normalisation … 2 hours then load into the sql database and run the Clustering … several hours “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

Ordonnanceur 3/3 To create your Todo … : All is logged Get the status 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

Cluspack Clusters of congRD1 RMA gcRMA 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 21656 1321 9137 20162 1762 157 484 27 174 160 400 171 39 1337 38 702 40 1211 36 685 PLIER VSN 19151 1419 10285 5 15586 23 4007 137 327 301 143 1152 13 571 32 1205 25 626

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 …