Registry of Standard Biological Models/CellML Practical

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Current revision (19:16, 30 October 2007) (view source)
 
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*Databases of models
*Databases of models
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**CellML repository [http://www.cellml.org/examples/repository/]
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**CellML repository [http://www.cellml.org/models/]
**BioModels [www.ebi.ac.uk/biomodels]
**BioModels [www.ebi.ac.uk/biomodels]

Current revision

Scope of the abstract

  • Demonstrate the use of CellML 1.1 to describe BioBricks [1](encapsulated and hierarchical assemblies)
    • building a modular Repressilator (see practicals)
  • Define requested features of a Virtual BioBrick Repository
    • review on existing model repository
    • specific requirements for a virtual biobrick repository
    • toward a Synthetic Biology CAD system

Practical with CellML to describe BioBricks

List of models defining a CellML structure : Registry_of_Standard_Biological_Models/Basic_Component_Models

CellML 1.1 looks very flexible and could provide all the desired features that we are looking for in order to describe a BioBrick [2]. Some testing has to be done on real examples to see how far we can incorporate BioBrick concepts into CellML description capabilities.

  • Practical 1: Describe a simple genetic assembly (promoter + RBS + protein coding region + stop codon) from the description of each sub-component.
    • example of such a part: <bbpart>BBa_I13522</bbpart>
      • It might be better to use <bbpart>BBa_I7101</bbpart> as this has been characterized quite extensively by Caitlin Conboy and Jennifer Braff (westerns, northerns etc.).
    • the concept of PoPS [3] could be used as a connection mechanism from a dynamical perspective
    • Each part could be represented as a CellML 'component' and then a group could be created to produce the final assembly
  • Practical 2: Describe a standardized inverter as a CellML module (example found here <bbpart>BBa_Q04121</bbpart> )
    • NB: this is a non functional assembly as there is no promoter to the coding region
    • Define clear inputs and outputs to allow future assembly with counter parts (i.e. LacI protein with LacI promoter)
  • Practical 3: From 3 standardized inverter build the Elowitz repressilator
    • part found here: <bbpart>BBa_I5610</bbpart>
    • demonstrate modularity and re-use offered by CellML
    • An abstraction could be created to encapsulate everything and define an oscillator device (use of group concept in CellML).

General aim

In this article, we are investigating the creation of a virtual equivalent to the DNA parts registry using CellML. Each physical DNA part would have one or multiple models to describe their properties. A model registry could be the core of a CAD system for synthetic biology where new assemblies of parts would be simulated and tested before starting the wetlab.

This problem has 2 main required features: a standardized description language and a structured repository for the created models

  • Wish list for a BioBrick description language
    • standardized
    • machine and human readable
    • quantitative and/or qualitative description
    • modular
    • hierarchical

Wish list for a BioBrick model repository

    • store, curate and search models
    • reference DNA part registry
    • drag and drop mechanism to assemble new systems

Background and References

  • Description language for bio-models
  • Databases of models
    • CellML repository [6]
    • BioModels [www.ebi.ac.uk/biomodels]
  • Previous CAD system
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