Registry of Standard Biological Models/Presentation

View our presentation (.ppt)

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

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 ...