Registry of Standard Biological Models/Presentation

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(Scope of the presentation (provisional))
(Registry of BioBrick Models)
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=== Registry of BioBrick Models===
=== Registry of BioBrick Models===
* Motivations
* Motivations
-
** ...
+
** to gain a '''deeper understanding''' of the function of BioBricks.
 +
** to promote the '''re-usability''' of BioBrick models.
 +
** to '''explore through simulations''' the properties of de-novo assemblies of parts.
 +
** to progress towards a '''faster/cheaper development process'''.
 +
** to complement the '''open-source spirit''' of Synthetic Biology and open-up a new form of '''''in Silico'' contributions'''.
* Standard Biological Model
* Standard Biological Model
** Modular design
** Modular design

Revision as of 16:49, 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
    • to gain a deeper understanding of the function of BioBricks.
    • to promote the re-usability of BioBrick models.
    • to explore through simulations the properties of de-novo assemblies of parts.
    • to progress towards a faster/cheaper development process.
    • to complement the open-source spirit of Synthetic Biology and open-up a new form of in Silico contributions.
  • 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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