Mobyle @ RPBS A web portal for structural bioinformatics and chemoinformatics Julien Maupetit, Pierre Tufféry. RPBS Université Paris Diderot Paris 7 Bâtiment Lamarck 36, rue Hélène Brion 75013 Paris, France 2009/11/30
RPBS - MTi
Outline
The RPBS Plateform
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The Mobyle Project
RPBS Mobyle Portal
The RPBS Plateform
RPBS - MTi
Outline
The RPBS Plateform
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The RPBS Plateform
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The Mobyle Project
The Mobyle Project
RPBS Mobyle Portal
RPBS - MTi
Outline
The RPBS Plateform
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The RPBS Plateform
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The Mobyle Project
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RPBS Mobyle Portal
The Mobyle Project
RPBS Mobyle Portal
RPBS - MTi
Outline
The RPBS Plateform
The Mobyle Project
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The RPBS Plateform RPBS Project Location & computing resources
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The Mobyle Project
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RPBS Mobyle Portal
RPBS Mobyle Portal
RPBS - MTi
Outline
The RPBS Plateform
The Mobyle Project
RPBS Mobyle Portal
RPBS Project Ressource Parisienne en Bioinformatique Structurale Collaborative research in the field of structural bioinformatics Services related to protein structure Research groups implicated 1
MTi - INSERM U973 - Université Paris 7
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DSIMB - INSERM U665 - Université Paris 7
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ABI - Université Paris 6
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IMPMC - CNRS UMR 7590 - Université Paris 6 et 7
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IBBMC-MIP - CNRS UMR 8619 - Université Paris-sud 11
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CNAM-STIC - Conservatoire National des Arts et Métiers, Paris
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MAP5 - CNRS UMR 8145 - University Paris Descartes
Who ? Project coordination : Dr Pierre Tufféry Technical director : Dr Julien Maupetit
RPBS - MTi
Outline
The RPBS Plateform
The Mobyle Project
RPBS Mobyle Portal
Location & computing resources Where ? → Paris Rive Gauche : Lamarck 5th floor
What ? Programs : more than 200 on-line programs available Storage : 8To + 15To (2010) Computing : 84 CPU cores (64/32bits : 66/18) + 160 CPU Cores (2010) Services : structural bioinformatics, 3D printing (new in 2010 !)
RPBS - MTi
Outline
The RPBS Plateform
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The RPBS Plateform
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The Mobyle Project Motivation Participative design Functionalities Architecture overview XML program description XML program description Quick tour : workspace Quick tour : form submission Quick tour : results Incoming features Related projects
The Mobyle Project
RPBS Mobyle Portal
RPBS - MTi
Outline
The RPBS Plateform
The Mobyle Project
RPBS Mobyle Portal
Motivation Key problem Ease the acces to bio/chemo-informatics tools, for scientists. Bioinformatics tools are often command-line tools Command line-tools → steep learning curve Providing a web interface, which biologists are more familiar with Developing custom cgis is both a time consuming and error-prone approach. Based on former projects → PISE system (1999, C. Letondal) and P-Serveur (2004, P. Tufféry et al.)
RPBS - MTi
Outline
The RPBS Plateform
The Mobyle Project
RPBS Mobyle Portal
Participative design
User interviews, participatory workshops Need for a stable and integrated set of tools Synthetic view of results and analysis Re-usability features User-defined and ready-to-use "pipelines" → Skepticism towards complex products
RPBS - MTi
Outline
The RPBS Plateform
The Mobyle Project
RPBS Mobyle Portal
Functionalities Users Service search/discovery Service usage and documentation Data and services integration Workspace navigation Admins Users assistance Job management, tracability Developers Easy integration for new tools RPBS - MTi
Outline
The RPBS Plateform
The Mobyle Project
RPBS Mobyle Portal
Architecture overview
Web server Web Portal
Core Server
⚙ Jobs management
(user interface)
⚙ Users management Network Remote Access
Administration ⚙ Tools
XML
User accounts XML
Submission System (e.g., SGE, Torque)
Bio-Programs
Programs publication ⚙
Jobs
Execution environment
(e.g., BLAST, EMBOSS, Phylip)
Program definitions XML
Bio-Banks (e.g., SWISSPROT, PDB)
RPBS - MTi
Outline
The RPBS Plateform
The Mobyle Project
RPBS Mobyle Portal
XML program description
Information in Mobyle stored in XML format (program definition, job status) What is a mobyle program description ? a network service definition a program wrapper a UI (User Interface) definition a "semantic" description
The main goal of this practical is to introduce you the essential tools for homology ... The sequence file unknown.seq (in the sequences directory) contains the ... .fr/cgi-bin/npsa_automat.pl?page=/NPSA/npsa_clustalw.html (Note that you are.
Nov 30, 2009 - Search for a 3D template. Select templates of interest. Query/template sequence alignment. Preparing modeller input. Perform the 3D modeling.
Greedy Algorithm and a Coarse-Grained Force Field to solve ... quence, still remains a challenge in computational biology. We are developing a .... cRMSd (α carbons Root Mean Square Deviation) criterion was first used to drive the greedy al- gorithm
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Abstract--A structural model for the geometry of Fe(III) octahe-dra near the surface of finely divided ... XANES, suggested that 20 to 30% of surface Fe atoms.
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and structured documents [39]. Document image interpretation is an artificial intelligence problem based on three entities: a control system, a pattern recognition ...
Feb 25, 2009 - An agent-based paradigm for the simulation of complex systems is based on the modelling of ..... We recall that the ideal gas law is pV = nRT ,.
2000), inventory management (Minner, 2003) and scheduling .... 2006), that is based on immune system and also devoted to ...... ing - A Fusion of Foundations .
