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
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 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
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

10. 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

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

12. 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

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. 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

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 …