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 ...