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Journée Mobyle 28 septembre 2012
A brief introduction to MobyleNet
Journée Mobyle 28 septembre 2012
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.
Seamless integration of remote services
Journée Mobyle 28 septembre 2012
Chaîning cross platform services
Journée Mobyle 28 septembre 2012
Integrated pipeline skills ... not limited to local services
Remote services are seen “as local”
Journée Mobyle 28 septembre 2012
Integrated pipeline skills ... up to workflows
Journée Mobyle 28 septembre 2012
Remote services are executed remotely ...
Journée Mobyle 28 septembre 2012
Data is stored on remote server (input, output)
Mobyle has internal mechanisms to retrieve remote data
Cross site data persistence policy to be acknowledged
“Configuring” MobyleNet
Exporting services:
Journée Mobyle 28 septembre 2012
Config.py:
EXPORTED_SERVICES = [ 'muscle', 'FAF-Drugs2', 'Frog2', 'T-Coffee', 'stride', 'HCA', 'plotSC',
'Yakusa' ]
“Configuring” MobyleNet
Importing services:
Journée Mobyle 28 septembre 2012
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'] } } }
“Configuring” MobyleNet
Importing services: effective deployment
Journée Mobyle 28 septembre 2012
Mobdeploy -s ipmc -V deploy -j -p LEA3D
“Configuring” MobyleNet
Importing services: overloading remote menu configuration
Journée Mobyle 28 septembre 2012
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>
“Configuring” MobyleNet
Importing services: troubles
Journée Mobyle 28 septembre 2012
- incompatible Mobyle versions across sites
- incompatible datatypes
- data persistence (bookmark!)
Cross site service compatibility
Data typing is central for service compatibility. Type is composed of:
BioType (ADN, Protein, etc) DataType
− SuperClass− Class
DataFormat
Protein (Biotype) AbstractText (SuperClass) _3DStructure (Class) PDB (DataFormat)
Example
<type> <biotype>Protein</biotype> <datatype> <class>_3DStructure</class> <superclass>AbstractText</superclass> </datatype> <dataFormat>PDB</dataFormat> </type>
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
Assisting type compatibility checkMobylenet.rpbs.univ-paris-diderot.fr
Assisting type compatibility checkMobylenet.rpbs.univ-paris-diderot.fr
MobyleNet today
MobyleNet today
New sites scheduled before end 2012:
GDR Chemoinformatique
Marseille (X. Morelli)Reims (JM Nuzillard)Strasbourg (D. Rognan)...
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