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 WebsiteUpload

Querying Display

alnitakStar3Star4Star5Star6Star7Star8

/GxData

GxDb SQL database

http://gx.igbmc.frWeb Services

Café des sciences QSub

Ordonnanceur

GxDb ressourcesLanguages 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

Tcl RPHP

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

The RadarGenerator PipeWork

Radar Generator

Radar Display

About Clustering

HtmlTable (PipeWork’s standard output)

DoOnList

DoOnList from ClusterComposition

StringInteractome output

StringInteractome WithAny.string

RMA gcRMA

Nb_clu Max Min Avg 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

Km_dpc 3 21656 1321 9137 3 20162 1762 9137

Mm_aic 157 484 27 174 160 400 1 171

Mm_bic 39 1337 38 702 40 1211 36 685

PLIER VSN

Km_dpc 2 19151 1419 10285 5 15586 23 4007

Mm_aic 137 327 2 150 140 301 2 143

Mm_bic 36 1152 13 571 32 1205 25 626

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

KUROVKolliger 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 …