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Interactive web tools

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Interactive web tools

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  1. Interactive web tools Raymond Ripp 9 mars 2010

  2. 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

  3. GxDb

  4. GxDb Upload procedure

  5. Resume an existing session

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. The RadarGenerator PipeWork

  12. Radar Generator

  13. Radar Display

  14. About Clustering

  15. HtmlTable (PipeWork’s standard output)

  16. DoOnList

  17. DoOnList from ClusterComposition

  18. StringInteractome output

  19. StringInteractome WithAny.string

  20. Cluspack Clusters of congRD1

  21. ImAnno ISH images annotation Cst3

  22. ImAnno ISH images annotation

  23. ImAnno Sieves

  24. ImAnno DoOnList

  25. ImAnno Cluspack Display

  26. Run StringInteractome from DoOnList

  27. Back to existing StringInteractome

  28. ImAnno ISH images annotation

  29. KUROVKolliger Utriculus Retina Olfactif Vibriss

  30. All possible KUROV combinations

  31. 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 • …