Difference between revisions of "Registry of Standard Biological Models/Presentation"

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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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=Presentation=
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[[:Image:RoSBM Final.ppt|'''View our presentation (.ppt)''']]
  
==Scope of the presentation (provisional)==
+
 
 +
==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
 +
 
 +
==Ontology==
 +
 
 +
==Services that could be provided==
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*Store, search, and annotate models
 +
*Interface
 +
*Links to related papers
 +
*Addition of  ''de novo'' part models
  
 
=== Biological Engineering===
 
=== Biological Engineering===
* building novel biological systems from interchangeable and standardized parts.
+
* Goal: Building novel biological systems from interchangeable and standardized biological parts.
* Biobricks  
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* 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 modelling in engineering and life science.
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* Use of modeling in engineering and life science.
* Current Practices
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* Current Practices:
* Current Issues
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** models: quantitative, kinetic.
 +
** Description languages: SBML, CellML, MML, Matlab, R ...
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** 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
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** to gain a '''deeper understanding''' of the function of BioBricks.
 
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** to promote the '''re-usability''' of BioBrick models.
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** to '''explore through simulations''' the properties of de-novo assemblies of parts.
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** to progress towards a '''faster/cheaper development process'''.
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** 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
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** 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==

Latest revision as of 14:05, 14 November 2007

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

Ontology

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 ...