Models For All Nicolas Le Novre Characterising dynamical behaviours - PowerPoint PPT Presentation

Models For All Nicolas Le Novère

Characterising dynamical behaviours Models Simulation Results Minimal requirements (SBRML) Data-models Ontologies

Is the matrix of standards complete? Models Simulation Results Minimal requirements (SBRML) Data-models Ontologies

Is the matrix of standards complete? Models Simulation Results Minimal requirements SBRML Data-models Ontologies

Disentangling the model life-cycle Model Model Simulation Numerical Parametrisation generation structure and analysis results ? ? SBRML

Disentangling the level of discourse Graphical representation BioPAX BioPAX Biological semantics Initial conditions (numbers) Model semantics (structure) SBML SBML SBML SBML

Many complementary modelling approaches State-Transitions, cable Neurobiology Physiology Approximation (PDE) Biochemistry Process Variable description Descriptions (ODE, PDE) (ODE, Monte-Carlo) Cell automata Multi-agents Developmental biology, plant biology PK/PD, statistical Pharmacometrics models

Parallel and redundant efforts Physiology Neurobiology Systems Biology FieldML BioPAX Developmental biology, plant biology Pharmacometrics

What if the world-wide web was built like this? leisure art and design business literacy natural sciences

The correct way to do it Personal info: vCard Presentation: CSS Semantics: RDF Graphics: SVG Display: HTML

Existing standards interoperability BioPAX

Overarching standardisation structure The “WorldWide Web consortium” of modelling in biology http://co.mbine.org/ HARMONY 2011 Standard Operating Procedures ● ● 18 to 22 April 2011, New-York Technical requirements ● ● http://www.biopax.org/harmony.php Governance ● ● COMBINE 2011 Single voice ● ● 3 to 7 September 2011, Heidelberg Discussions with Industry ● ● http://co.mbine.org/events/COMBINE_2011 Financial support ● ●

HARMONY Vs COMBINE annual meeting? COMBINE annual meeting: ● Presentation of results, tools, etc. ● General discussion ● Directed towards the general community, including end-users ● HARMONY ● Implementation of software support, development of specifications ● Technical discussions ● Directed towards developers, editors, ultra-geeks ● Both cost a lot of money!!! ● We need to demonstrate that they are productive ● Paper(s) will be submitted to SIGS after the meeting ●

Models For All Nicolas Le Novre Characterising dynamical behaviours - PowerPoint PPT Presentation

Models For All Nicolas Le Novre Characterising dynamical behaviours Models Simulation Results Minimal requirements (SBRML) Data-models Ontologies Is the matrix of standards complete? Models

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