Registry of Standard Biological Models/BioSysBio Abstract Draft: Difference between revisions

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| colspan="2" style="background:#efefef;" | '''Motivations behind a Registry of BioBrick Models'''
| colspan="2" style="background:#efefef;" | '''Motivations behind a Registry of BioBrick Models'''
|-
|-
| [[Image:VBB_RegistriesIcon.png|200px|DNA & Model registries]]
|   
|   
* to '''store''', '''search''' and '''curate''' models related to physical DNA Biobricks.
* to '''store''', '''search''' and '''curate''' models related to physical DNA Biobricks.
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* to go towards a '''faster/cheaper development process'''.
* to go towards a '''faster/cheaper development process'''.
* to complement the '''open-source spirit''' in Synthetic Biology and open-up a new form of '''"dry-work" contributions'''.
* to complement the '''open-source spirit''' in Synthetic Biology and open-up a new form of '''"dry-work" contributions'''.
| [[Image:VBB_RegistriesIcon.png|200px|DNA & Model registries]]
 
|}
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| colspan="2" style="background:#efefef;" | '''Properties needed for BioBrick description language'''
| colspan="2" style="background:#efefef;" | '''Properties needed for BioBrick description language'''
|-
|-
| [[Image:VBB_BioBrickLanguage.png|200px|DNA & Model registries]]
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* '''Human''' and '''machine readable'''.
* '''Human''' and '''machine readable'''.
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* Enable the definition of '''hierachies between modules''' (as a system will be composed of sub-systems or devices).
* Enable the definition of '''hierachies between modules''' (as a system will be composed of sub-systems or devices).
* Enable a '''annotation scheme''' to comply with [http://www.nature.com/nbt/journal/v23/n12/abs/nbt1156.html| MIRIAM], for example.
* Enable a '''annotation scheme''' to comply with [http://www.nature.com/nbt/journal/v23/n12/abs/nbt1156.html| MIRIAM], for example.
| [[Image:VBB_BioBrickLanguage.png|200px|DNA & Model registries]]
 
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| colspan="2" style="background:#efefef;" |'''Generic CellML architecture for BioBricks'''
| colspan="2" style="background:#efefef;" |'''Generic CellML architecture for BioBricks'''
|-
|-
| [[Image:VBB_ActivatedPromoterRBS.png|right|200px|Activated Promoter/RBS Brick Architecture]]
| First, we explore the definition of modular and re-useable models to represent the available DNA BioBricks. A series of  [[Registry_of_Standard_Biological_Models/Basic_Component_Models|'''generic model architectures''']] in CellML is defined for most of the types of parts encountered in the DNA registry (plasmid, promoter, RBS, proteins, riboswitch ...).  
| First, we explore the definition of modular and re-useable models to represent the available DNA BioBricks. A series of  [[Registry_of_Standard_Biological_Models/Basic_Component_Models|'''generic model architectures''']] in CellML is defined for most of the types of parts encountered in the DNA registry (plasmid, promoter, RBS, proteins, riboswitch ...).  
| [[Image:VBB_ActivatedPromoterRBS.png|right|200px|Activated Promoter/RBS Brick Architecture]]
 
|-
|-
| colspan="2" style="background:#efefef;" |'''Catalog of quantitative BioBrick models'''
| colspan="2" style="background:#efefef;" |'''Catalog of quantitative BioBrick models'''
|-
|-
| [[Image:VirtualBioBrickModelCatalogIcon.png|right|200px|BioBrick Model Catalog]]
| Second, a [[Registry_of_Standard_Biological_Models/Model_Catalog|'''catalog of quantitative models''']] based on already characterized parts is presented.
| Second, a [[Registry_of_Standard_Biological_Models/Model_Catalog|'''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.
An ongoing effort to characterized experimentaly BioBricks is providing us data to move from a qualitative description to a more quantitative one.
| [[Image:VirtualBioBrickModelCatalogIcon.png|right|200px|BioBrick Model Catalog]]
 
|-
|-
| colspan="2" style="background:#efefef;" |'''Building simulations from modular BioBrick models'''
| colspan="2" style="background:#efefef;" |'''Building simulations from modular BioBrick models'''
|-
|-
| [[Image:VBB_Inverter.png|right|200px|Inverter Brick Architecture]]
| To conclude, the versatility of the approach is demonstrated by simulating different sytems from a set of pre-defined models [to be defined].  
| To conclude, the versatility of the approach is demonstrated by simulating different sytems from a set of pre-defined models [to be defined].  
| [[Image:VBB_Inverter.png|right|200px|Inverter Brick Architecture]]
|}
|}
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Revision as of 09:58, 27 September 2006

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.

Motivations behind a Registry of BioBrick Models
DNA & Model registries
  • to store, search and curate models related to physical DNA Biobricks.
  • to gain a deeper understanding in the way BioBricks work.
  • to promote the re-useability of BioBrick models.
  • to explore through simulations the properties of de-novo assemblies between parts.
  • to go towards a faster/cheaper development process.
  • to complement the open-source spirit in Synthetic Biology and open-up a new form of "dry-work" contributions.


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
DNA & Model registries
  • Human and machine readable.
  • Enable the describtion of qualitative and quantitative models of biochemical networks.
  • Enable the definition of modules (as biobricks have inputs/outputs).
  • Enable the definition of hierachies between modules (as a system will be composed of sub-systems or devices).
  • Enable a annotation scheme to comply with MIRIAM, for example.

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
Activated Promoter/RBS Brick Architecture
Activated Promoter/RBS Brick Architecture
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
BioBrick Model Catalog
BioBrick Model Catalog
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.

Building simulations from modular BioBrick models
Inverter Brick Architecture
Inverter Brick Architecture
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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