Registry of Standard Biological Models/Presentation

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(New page: =Presentation= ==Scope of the presentation (provisional)== === Biological Engineering=== * building novel biological systems from interchangeable and standardized parts. * Biobricks * T...)
(Scope of the presentation (provisional))
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=== Biological Engineering===
=== Biological Engineering===
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* building novel biological systems from interchangeable and standardized parts.
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* Goal: Building novel biological systems from interchangeable and standardized biological parts.
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* Biobricks  
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* Biobricks
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** modularity
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** standardized interface
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** characterization
* The Registry of Standardized Biological Parts.
* The Registry of Standardized Biological Parts.
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** ...
=== Modelling Biological Systems ===
=== Modelling Biological Systems ===
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* Use of modelling in engineering and life science.
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* Use of modeling in engineering and life science.
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* Current Practices
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* Current Practices:
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* Current Issues
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** models: quantitative, kinetic.
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** Description languages: SBML, CellML, MML, Matlab, R ...
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** Registries of models: SBML, CellML, Biomodels.
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* Current Issues:
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** some implementations are platform dependent (e.g. Matlab)
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** difficult to share and re-use models.
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** validation against experimental data.
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** ...
=== Registry of BioBrick Models===
=== Registry of BioBrick Models===
* Motivations
* Motivations
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* Expected Services from the Registry
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** ...
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* Standard Biological Model
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** Modular design
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** Standardized Interface
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** Characterization (Parameters, Transfer functions, Sensitivity analysis, ...)
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* Expected Services from the Registry of Models
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** Provide a one-to-many match between DNA biological parts and models.
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** Store, Search, Annotate, and Curate models of standadized biological parts.
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** Interface with CAD tools.
==Open issues==
==Open issues==

Revision as of 16:39, 16 September 2007

Contents

Presentation

Scope of the presentation (provisional)

Biological Engineering

  • Goal: Building novel biological systems from interchangeable and standardized biological parts.
  • Biobricks
    • modularity
    • standardized interface
    • characterization
  • The Registry of Standardized Biological Parts.
    • ...

Modelling Biological Systems

  • Use of modeling in engineering and life science.
  • Current Practices:
    • models: quantitative, kinetic.
    • Description languages: SBML, CellML, MML, Matlab, R ...
    • Registries of models: SBML, CellML, Biomodels.
  • Current Issues:
    • some implementations are platform dependent (e.g. Matlab)
    • difficult to share and re-use models.
    • validation against experimental data.
    • ...

Registry of BioBrick Models

  • Motivations
    • ...
  • Standard Biological Model
    • Modular design
    • Standardized Interface
    • Characterization (Parameters, Transfer functions, Sensitivity analysis, ...)
  • Expected Services from the Registry of Models
    • Provide a one-to-many match between DNA biological parts and models.
    • Store, Search, Annotate, and Curate models of standadized biological parts.
    • Interface with CAD tools.

Open issues

  • What type of models should be targeted (kinetic description, qualitative description ...) ?
  • What is a standardized model ? What is the right level of abstraction of a model ?
  • Link with the existing biological description languages (SBML, CellML, ...) ?
  • Link with the existing model repositories (SBML, CellML, Biomodels) ?
  • Minimal information needed to describe a SBM (see MIRIAM initiative), Annotation and curation ?
  • Type of services expected from the RoSBM ?
  • Connectivity with the other registries (Parts registry and others in the future) ?
  • Tools which could benefit from such a model registry ?
  • Project management: private implementation, open source project, release of a standard, guidelines ...
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