Registry of Standard Biological Models/Presentation
Draft Presentation Notes
Problems to be addressed
- Modeling device/system behavior is difficult for researchers not trained in modeling.
- Characterization of parts/devices/systems needs guidance.
- Existing registries of models don't facilitate modular reuse.
- 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
- Links to related papers
- Addition of de novo part models
- Goal: Building novel biological systems from interchangeable and standardized biological parts.
- standardized interface
- 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
- 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.
- 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 ...