1. A brief introduction to MobyleNet
Journée Mobyle 28 septembre 2012

2. Goals:
Federate communities by establishing cross site dialog
Not limited to exchange of expertise about software implementation
Instead, take advantage of complementary skills and go for trusted
interoperability, avoiding local implementation of all software
“Each site has its own expertise, and the skills to maintain,
update, evolve the corresponding tools”, for the benefit of all.
Journée Mobyle 28 septembre 2012

3. Seamless integration of remote services
Journée Mobyle 28 septembre 2012

4. Chaîning cross platform services
Journée Mobyle 28 septembre 2012

5. Integrated pipeline skills ... not limited to local services
Remote services are seen
“as local”
Journée Mobyle 28 septembre 2012

6. Integrated pipeline skills ... up to workflows
Journée Mobyle 28 septembre 2012

7. Remote services are executed remotely ...
Data is stored on remote server (input, output)
Mobyle has internal mechanisms to retrieve remote data
Cross site data persistence policy to be acknowledged
Journée Mobyle 28 septembre 2012

8. “Configuring” MobyleNet
Exporting services:
Config.py:
EXPORTED_SERVICES = [ 'muscle', 'FAF-Drugs2', 'Frog2', 'T-Coffee',
'stride', 'HCA', 'plotSC',
'Yakusa' ]
Journée Mobyle 28 septembre 2012

9. “Configuring” MobyleNet
Importing services:
Config.py:
PORTALS={
'ipmc': {
'url': 'http://mobyle.ipmc.cnrs.fr/cgi-bin/',
'help' : 'dominique.douguet@ipmc.cnrs.fr',
'repository': 'http://mobyle.ipmc.cnrs.fr/',
'services': { 'programs' :['XLogP', 'PLANTS', 'LEA3D']
}
}
}
Journée Mobyle 28 septembre 2012

10. “Configuring” MobyleNet
Importing services: effective deployment
Mobdeploy -s ipmc -V deploy -j -p LEA3D
Journée Mobyle 28 septembre 2012

11. “Configuring” MobyleNet
Importing services: overloading remote menu
configuration
Categories.xml:
<categories>
<category name="sompak" class="program">Drugs:SOM:creation</category>
<category name="molconvert" class="program">Drugs:Tools</category>
<category name="cons" class="program">Sequence:Alignment:consensus</category>
<category name="SeqLogo" class="program">Sequence:Analysis</category>
<category name="iANTPatScan" class="program">Sequence:Analysis</category>
<category name="iANTMultalinNucleic" class="program">Sequence:Comparison</category>
<category name="iANTMultalinProteic" class="program">Sequence:Comparison</category>
<category name="InterproAnnotation" class="program">Sequence:Annotation</category>
<category name="HeliageneGetSequence" class="program">Sequence:Retrieval</category>
<category name="Atome2" class="program">Structure:Prediction:3D_structure</category>
</categories>
Journée Mobyle 28 septembre 2012

12. “Configuring” MobyleNet
Importing services: troubles
- incompatible Mobyle versions across sites
- incompatible datatypes
- data persistence (bookmark!)
Journée Mobyle 28 septembre 2012

13. Cross site service compatibility

Data typing is central for service compatibility.

Type is composed of:

BioType (ADN, Protein, etc)

DataType
− SuperClass
− Class

DataFormat

14. Example

Protein (Biotype)

AbstractText (SuperClass)

_3DStructure (Class)

PDB (DataFormat)
<type>
<biotype>Protein</biotype>
<datatype>
<class>_3DStructure</class>
<superclass>AbstractText</superclass>
</datatype>
<dataFormat>PDB</dataFormat>
</type>

15. Compatibility rules for chaining

Output biotype compatible with input biotype

DataType: “specific to general” rule

E.g.: Nucleic Sequence Alignment → Sequence
Alignment

DataFormat: identicals or require format
converter

16. Assisting type compatibility check
Mobylenet.rpbs.univ-paris-diderot.fr

17. Assisting type compatibility check
Mobylenet.rpbs.univ-paris-diderot.fr

18. MobyleNet today

19. MobyleNet today
New sites scheduled
before end 2012:
GDR Chemoinformatique
Marseille (X. Morelli)
Reims (JM Nuzillard)
Strasbourg (D. Rognan)
...