Registry of Standard Biological Models

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Registry of Standard Biological Models

• Barry Canton (MIT)
• Vincent Rouilly (Imperial College)
• Registry Workshop
• November 2007,Boston

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Biological Systems Need Models!
Michigan iGEM Team 07
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Challenges

• Modeling takes time, expertize
• Weak adoption of standards for model construction
• Models hard to share, reuse

(Sound familiar?)
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Challenges

• Building takes time, expertize
• Weak adoption of standards for system
  construction
• Parts hard to share, reuse

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Registry of Standard Biological Parts
http//parts.mit.edu
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Registry of Standard Biological Models
http//openwetare.org/wiki/RoSBM
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Modeling the Parts Registry
Parts
Project 5 -models-
Project 1 -models-
Project 2 -models-
Project 3 -models-
Project 4 -models-
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Modeling with Parts Models Registries
Project 5 -models-
Project 1 -models-
Project 2 -models-
Project 3 -models-
Project 4 -models-
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Open data sharing
Model Predictions
Experimental Data
Project 5 -models-
Project 1 -models-
Project 2 -models-
Project 3 -models-
Project 4 -models-
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CellML Database
http//www.cellml.org/models
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Biomodels Database
http//www.ebi.ac.uk/biomodels/
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Asmparts software
http//soft.synth-bio.org/asmparts.html
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MIRIAM initiative
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RoSBM Motivations / Mission

• 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.

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What Do We Want the RoSBM to Do?

• Store, Search, Annotate, and Curate models of
  standardized biological parts.
• Provide a one-to-many match between DNA
  biological parts and models.
• Interface with CAD tools.

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BioBrick Characterization
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BioBrick Characterization
Experiments
Modeling
Early experiments to estimate dynamic range of
AHL and general response
Define Model
Fit Model on Data
More experiments to improve estimation Of
parameters
Predict next best experimental points
Fit model on new data
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One part, many models?
GFP(t) f(AHL,LuxR,t)
BBa_T9002
GFP f(AHL)
GFP(t) f(AHL,mRNALuxR, PLuxR, mRNAGFP, PLuxR,
RNAp, Ribosomes, t)
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(No Transcript)
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Proof of Concept
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desired relationships
Part category
Model category
Models Including This one
Bio DB
Part
Model
Similar Models
Models Included in this one
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Data Connectivity
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Data Connectivity
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Data Connectivity
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Data Connectivity
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Thank you!
bcanton_at_mit.edu vincent.rouilly_at_gmail.com http//o
penwetware.org/wiki/RoSBM
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ideas

• Level of abstraction
• controlled vocabularies
• Description language
• MIAGE standard

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Model Curation

• Machine readable
• Conform to a description standard
• Make sure the model works
• Referencing author, publications, contact
• Pointing to biological databases
• MIRIAM standard

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SBML / CellML Overview
Compartments
Species
SBML model
Rules

Reactions
Events
Components
CellML model
Variables name, init_value, interface, units

Math
Units
Imports
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What is a Biological Part Model?

• What we mean by Biological Model
• Abstraction of a biological process using a
  formal mathematical description
• Focus on kinetic models
• Focus on Ordinary Differential Equations System

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Content

• Advantages offered by modelling
• Problems to be addressed
• A solution to some of the above (Motivations)
• An example of a model entry in the RoSBM
  (Scenarii of use)
• What is a Standard Biological Model ?
• Simple Model repository or reusable modeling
  component.
• Open issues (level of abstraction, description
  language, )

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Current Practices

• More and more projects explore their project with
  modelling
• Matlab, C/C, Proprietary platform, SBML

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Unused Images