Registry of Standard Biological Models/BioSysBio Abstract Draft
Registry of BioBricks Models using CellML
Author(s): Vincent Rouilly1, Barry Canton2, Poul Nielsen3, Richard Kitney1
Affiliations: 1Imperial College London, 2MIT, 3The University of Auckland
Contact:email: vincent.rouilly@ic.ac.uk
Keywords: 'synthetic biology' 'biobrick' 'cellML' 'model database'
Introduction
One of the main goal in Synthetic Biology is to assess the possibility of building biological systems from interchangeable and standardized parts. In order to provide building blocks, a Registry of physical DNA BioBricks has been established at the MIT. BioBricks can then be assembled to form devices or more complicated systems in living cells.
As in most engineering fields, the challenge begins with a comprehensive description and understanding of the problem. This involves qualitative and quantitative analysis: clear physical interpretation of the problem followed by an adequate mathematical description. Therefore, alongside the effort of characterizing experimentaly the BioBricks , a logical extension to the Registry would be to build a Registry of Biobrick Models to complement the wetlab work.
A key aspect in this effort is the use of a description language being able to describe and support the BioBrick concepts.
Properties needed for BioBrick description language | |
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Results
In this article, is demonstrated that such Registry of BioBrick Models is achievable. A mock-up is provided based on the great flexibility and modularity offered by CellML.
Generic CellML architecture for BioBricks | |
First, we explore the definition of modular and re-useable models to represent the available DNA BioBricks. A series of generic model architectures in CellML is defined for most of the types of parts encountered in the DNA registry (plasmid, promoter, RBS, proteins, riboswitch ...). | |
Catalog of quantitative BioBrick models | |
Second, a catalog of quantitative models based on already characterized parts is presented.
An ongoing effort to characterized experimentaly BioBricks is providing us data to move from a qualitative description to a more quantitative one. |
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Building simulations from modular BioBrick models | |
To conclude, the versatility of the approach is demonstrated by simulating different sytems from a set of pre-defined models [to be defined]. |
Conclusion
The concept of a Registry of BioBrick models based on CellML has been demonstrated. It takes advantage of CellML flexibility and modularity to provide a catalog of quantitative models which are standardized, modular and re-useable. With the increase of available physical DNA parts in the MIT Registry, as well as the characterization of these parts, such a repository will help to gain a deeper understanding of the BioBrick properties and speeding up the process of building-up new devices and systems. But more importantly, it will help to federate the growing number of contributions from the modeling community.
Stuff that we might want to include too
- synergy between the definition of a biobrick model and the way its characterization is done (validation scheme between simulation and experiment)
- future work: CAD system with drag and drop of biobricks and use of 'CellML units' to validate connections between modules,
- elaborate on MIRIAM compliance + touch on linking model with gene and protein databases.
- conclusion is not great ...
References
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