Registry of Standard Biological Models/Presentation

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View our presentation (.ppt)

Draft Presentation Notes

Problems to be addressed

  1. Modeling device/system behavior is difficult for researchers not trained in modeling.
  2. Characterization of parts/devices/systems needs guidance.
  3. Existing registries of models don't facilitate modular reuse.
  4. Difficult for modelers to contribute to the BioBrick effort.

A solution to some of the above

  • The Registry of Standard Biological Models

An example of a model entry in the RoSBM

Definition of a model

  • Kinetic ODE model
  • Defined inputs/outputs (and units)
  • Reusable and modular
  • Compliant with MIRIAM schema


Services that could be provided

  • Store, search, and annotate models
  • Interface
  • Links to related papers
  • Addition of de novo part models

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 ...