Registry of Standard Biological Models/CellML Practical

Scope of the abstract

 * Demonstrate the use of CellML 1.1 to describe BioBricks (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. 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: BBa_I13522
 * It might be better to use BBa_I7101 as this has been characterized quite extensively by Caitlin Conboy and Jennifer Braff (westerns, northerns etc.).
 * the concept of PoPS 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 BBa_Q04121 )
 * 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: BBa_I5610
 * 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
 * CellML
 * SBML
 * MML


 * Databases of models
 * CellML repository
 * BioModels [www.ebi.ac.uk/biomodels]


 * Previous CAD system
 * BioJADE
 * BioSPICE


 * BioBricks
 * Part registry