1. Interactive web tools Raymond Ripp 9 mars 2010

2. 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

3. GxDb

4. GxDb Upload procedure

7. Resume an existing session

9. GxDb Website Upload Querying Display alnitak Star3 Star4 Star5 Star6 Star7 Star8 /GxData GxDb SQL database http://gx.igbmc.fr 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

10. 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

11. 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

12. 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

13. 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

16. The RadarGenerator PipeWork

17. Radar Generator

21. Radar Display

22. About Clustering

23. HtmlTable (PipeWork’s standard output)

24. DoOnList

25. DoOnList from ClusterComposition

27. StringInteractome output

28. StringInteractome WithAny.string

29. RMAgcRMA Nb_cluMaxMinAvgNb_cluMaxMinAvg Km_dpc2202831081106826249491390 Mm_aic14034131521503568161 Mm_bic331182296474492719549 MAS5.0dChip Km_dpc3216561321913732016217629137 Mm_aic157484271741604001171 Mm_bic3913373870240121136685 PLIERVSN Km_dpc219151141910285515586234007 Mm_aic13732721501403012143 Mm_bic3611521357132120525626 Cluspack Clusters of congRD1

30. ImAnno ISH images annotation Cst3

33. ImAnno ISH images annotation

34. ImAnno Sieves

35. ImAnno DoOnList

38. ImAnno Cluspack Display

40. Run StringInteractome from DoOnList

42. Back to existing StringInteractome

44. ImAnno ISH images annotation

45. KUROV Kolliger Utriculus Retina Olfactif Vibriss

46. All possible KUROV combinations

49. 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  …