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MobyleNet - Mobyle Workshop - September 28, 2012

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MobyleNet - Mobyle Workshop - September 28, 2012

  1. 1. A brief introduction to MobyleNetJournée Mobyle 28 septembre 2012
  2. 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. 3. Seamless integration of remote servicesJournée Mobyle 28 septembre 2012
  4. 4. Chaîning cross platform servicesJournée Mobyle 28 septembre 2012
  5. 5. Integrated pipeline skills ... not limited to local services Remote services are seen “as local”Journée Mobyle 28 septembre 2012
  6. 6. Integrated pipeline skills ... up to workflowsJournée Mobyle 28 septembre 2012
  7. 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 acknowledgedJournée Mobyle 28 septembre 2012
  8. 8. “Configuring” MobyleNetExporting services: Config.py: EXPORTED_SERVICES = [ muscle, FAF-Drugs2, Frog2, T-Coffee, stride, HCA, plotSC, Yakusa ]Journée Mobyle 28 septembre 2012
  9. 9. “Configuring” MobyleNetImporting 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. 10. “Configuring” MobyleNetImporting services: effective deployment Mobdeploy -s ipmc -V deploy -j -p LEA3DJournée Mobyle 28 septembre 2012
  11. 11. “Configuring” MobyleNetImporting services: overloading remote menuconfigurationCategories.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. 12. “Configuring” MobyleNetImporting services: troubles - incompatible Mobyle versions across sites - incompatible datatypes - data persistence (bookmark!)Journée Mobyle 28 septembre 2012
  13. 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. 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. 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. 16. Assisting type compatibility checkMobylenet.rpbs.univ-paris-diderot.fr
  17. 17. Assisting type compatibility checkMobylenet.rpbs.univ-paris-diderot.fr
  18. 18. MobyleNet today
  19. 19. MobyleNet today New sites scheduled before end 2012: GDR Chemoinformatique Marseille (X. Morelli) Reims (JM Nuzillard) Strasbourg (D. Rognan) ...

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