Registry of Standard Biological Models/Presentation: Difference between revisions
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New page: =Presentation= ==Scope of the presentation (provisional)== === Biological Engineering=== * building novel biological systems from interchangeable and standardized parts. * Biobricks * T... |
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=== Biological Engineering=== | === Biological Engineering=== | ||
* | * Goal: Building novel biological systems from interchangeable and standardized biological parts. | ||
* Biobricks | * Biobricks | ||
** modularity | |||
** standardized interface | |||
** characterization | |||
* The Registry of Standardized Biological Parts. | * The Registry of Standardized Biological Parts. | ||
** ... | |||
=== Modelling Biological Systems === | === Modelling Biological Systems === | ||
* Use of | * Use of modeling in engineering and life science. | ||
* Current Practices | * Current Practices: | ||
* Current Issues | ** 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=== | === Registry of BioBrick Models=== | ||
* Motivations | * Motivations | ||
* Expected Services from the Registry | ** ... | ||
* 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== | ==Open issues== | ||
Revision as of 20:39, 16 September 2007
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
- ...
- 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 ...
