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

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

Oct 22, 2022 244 likes •408 views

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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Models For All

Nicolas Le Novère

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Minimal requirements Data-models Ontologies Models Simulation Results

(SBRML)

Characterising dynamical behaviours

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Minimal requirements Data-models Ontologies Models Simulation Results

(SBRML)

Is the matrix of standards complete?

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Minimal requirements Data-models Ontologies Models Simulation Results

SBRML

Is the matrix of standards complete?

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Model generation

SBRML

Model structure Parametrisation Simulation and analysis Numerical results

? ? Disentangling the model life-cycle

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Model semantics (structure) Initial conditions (numbers)

SBML SBML

Disentangling the level of discourse

Biological semantics Graphical representation

BioPAX BioPAX

SBML SBML

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Many complementary modelling approaches

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

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Parallel and redundant efforts

Physiology Neurobiology Developmental biology, plant biology Pharmacometrics

BioPAX

Systems Biology FieldML

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What if the world-wide web was built like this?

leisure art and design business literacy natural sciences

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The correct way to do it

Personal info: vCard Presentation: CSS Semantics: RDF Graphics: SVG Display: HTML

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Existing standards interoperability BioPAX

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Overarching standardisation structure

The “WorldWide Web consortium” of modelling in biology http://co.mbine.org/

  • HARMONY 2011
  • 18 to 22 April 2011, New-York
  • http://www.biopax.org/harmony.php
  • COMBINE 2011
  • 3 to 7 September 2011, Heidelberg
  • http://co.mbine.org/events/COMBINE_2011
  • Standard Operating Procedures
  • Technical requirements
  • Governance
  • Single voice
  • Discussions with Industry
  • Financial support
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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
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