Registry of Standard Biological Models/BioSysBio Abstract Draft: Difference between revisions
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==Introduction== | ==Introduction== | ||
One of the main | One of the main goals in Synthetic Biology is to assess the feasibility of building novel biological systems from interchangeable and standardized parts. In order to collect and share parts, a [http://parts.mit.edu/registry Registry of standardized DNA BioBricks] has been established at the MIT. [http://parts.mit.edu/registry/index.php/Help:An_Introduction_to_BioBricks BioBricks] can be [http://parts.mit.edu/registry/index.php/Help:BioBrick_Assembly assembled] to form devices and systems to operate in living cells. | ||
*[[User:Bcanton|BC]] 20:59, 27 September 2006 (EDT)What "the problem" refers to in the paragraph below isn't clear to me. Is it the feasibility of building novel systems or is it the specific system that one is trying to build? Possibly replace with the sentence below in red? | |||
<font color="red">Design of functioning devices and systems would benefit from accurate models of system function. To predict the function of systems built from many parts, we need to have accurate models for the parts and mechanisms to easily compose those part models into a system model.</font> | |||
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. | 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, | |||
Therefore, in parallel to increasing the number of parts available and [[Parts_characterization/Characterization_approaches | characterising them experimentally]], a logical extension to the Registry would be to build a Registry of BioBrick models to complement the physical parts. | |||
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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 | * to '''store''', '''search''' and '''curate''' models related to standardized DNA Biobricks. | ||
* to gain a '''deeper understanding''' | * to gain a '''deeper understanding''' of the function of BioBricks. | ||
* to promote the '''re- | * to promote the '''re-usability''' of BioBrick models. | ||
* to '''explore through simulations''' the properties of de-novo assemblies | * to '''explore through simulations''' the properties of de-novo assemblies of parts. | ||
* to | * to progress towards a '''faster/cheaper development process'''. | ||
* to complement the '''open-source spirit''' | * to complement the '''open-source spirit''' of Synthetic Biology and open-up a new form of '''"dry-work" contributions'''. | ||
|} | |} | ||
<br style="clear: both"> | |||
*[[User:Bcanton|BC]] 20:59, 27 September 2006 (EDT) replace "dry-work" with ''in silico''? | |||
A key aspect in this effort is the use of a description language able to describe and support the BioBrick concepts of modularity and abstraction. | |||
A key aspect in this effort is the use of a description language | |||
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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]] | |||
| | | | ||
* '''Human''' and '''machine readable'''. | * '''Human''' and '''machine readable'''. | ||
* Enable the | * Enable the description of '''qualitative and quantitative models''' of biochemical networks. | ||
* Enable the definition of '''modules''' (as biobricks have inputs/outputs). | * Enable the definition of '''modules''' (as biobricks have inputs/outputs). | ||
* Enable the definition of ''' | * Enable the definition of '''hierarchies 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/ | * Enable a minimum '''annotation scheme''' to comply with [http://www.nature.com/nbt/journal/v23/n12/full/nbt1156.html| MIRIAM]. | ||
*'''[[User:Bcanton|BC]] 22:01, 28 September 2006 (EDT):''' I replaced the Miriam link because the old one wasn't working for me. | |||
|} | |} | ||
==Results== | ==Results== | ||
In this article, | In this article, we demonstrate that such a '''Registry of BioBrick Models''' is achievable. A mock-up is provided based on the great flexibility and modularity offered by [http://www.cellml.org| '''CellML''']. | ||
Following the steps of already succesful model registries such as the [http://www.cellml.org/examples/repository/ CellML registry] or [http://www.ebi.ac.uk/biomodels/ BioModel registry], a BioBrick Model Registry will enable the curation of models. Using CellML and a MIRIAM annotation scheme will guarantee compliance with the previously cited registries. | |||
However, a strong emphasis is made on coupling the DNA BioBrick characterisation with their corresponding models. An iterative process between qualitative modelling and experimental characterization will insure consistency. | |||
The proposed framework could be the foundation of a future CAD environment for Synthetic Biology. | |||
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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]] | | [[Image:VBB_ActivatedPromoterRBS.png|right|200px|Activated Promoter/RBS Brick Architecture]] | ||
| First, we explore the definition of modular and re-usable 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 etc.). | |||
|- | |- | ||
| 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 | An ongoing effort to characterize BioBricks experimentally is providing us data to move from a qualitative description to a more quantitative one. | ||
|- | |- | ||
| 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]] | | [[Image:VBB_Inverter.png|right|200px|Inverter Brick Architecture]] | ||
| To conclude, the versatility of the approach is demonstrated by simulating different systems from a set of pre-defined models: | |||
*[[Registry_of_Standard_Biological_Models/Model_Catalog/BBa_I5610_Model|Elowitz's Repressilator.]] | |||
*[[Registry_of_Standard_Biological_Models/Model_Catalog/BBa_20100_Model|Band Detector from Basu and Weiss.]] | |||
|} | |} | ||
<br><br> | <br><br> | ||
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==Conclusion== | ==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- | 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-usable. | ||
With the increase of available physical DNA parts in the MIT Registry, as well as the | With the increase of available physical DNA parts in the MIT Registry, as well as the characterisation of these parts, such a repository will help to provide a deeper understanding of the BioBrick properties and speed up the process of building new devices and systems. But more importantly, it will help to federate the growing number of contributions from the modeling community and build on the experimental characterization of BioBricks. | ||
==References== | ==References== |
Latest revision as of 19:02, 28 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 goals in Synthetic Biology is to assess the feasibility of building novel biological systems from interchangeable and standardized parts. In order to collect and share parts, a Registry of standardized DNA BioBricks has been established at the MIT. BioBricks can be assembled to form devices and systems to operate in living cells.
- BC 20:59, 27 September 2006 (EDT)What "the problem" refers to in the paragraph below isn't clear to me. Is it the feasibility of building novel systems or is it the specific system that one is trying to build? Possibly replace with the sentence below in red?
Design of functioning devices and systems would benefit from accurate models of system function. To predict the function of systems built from many parts, we need to have accurate models for the parts and mechanisms to easily compose those part models into a system model.
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, in parallel to increasing the number of parts available and characterising them experimentally, a logical extension to the Registry would be to build a Registry of BioBrick models to complement the physical parts.
- BC 20:59, 27 September 2006 (EDT) replace "dry-work" with in silico?
A key aspect in this effort is the use of a description language able to describe and support the BioBrick concepts of modularity and abstraction.
Properties needed for BioBrick description language | |
|
Results
In this article, we demonstrate that such a Registry of BioBrick Models is achievable. A mock-up is provided based on the great flexibility and modularity offered by CellML.
Following the steps of already succesful model registries such as the CellML registry or BioModel registry, a BioBrick Model Registry will enable the curation of models. Using CellML and a MIRIAM annotation scheme will guarantee compliance with the previously cited registries. However, a strong emphasis is made on coupling the DNA BioBrick characterisation with their corresponding models. An iterative process between qualitative modelling and experimental characterization will insure consistency. The proposed framework could be the foundation of a future CAD environment for Synthetic Biology.
Generic CellML architecture for BioBricks | |
First, we explore the definition of modular and re-usable 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 etc.). | |
Catalog of quantitative BioBrick models | |
Second, a catalog of quantitative models based on already characterized parts is presented.
An ongoing effort to characterize BioBricks experimentally is providing us data to move from a qualitative description to a more quantitative one. | |
Building simulations from modular BioBrick models | |
To conclude, the versatility of the approach is demonstrated by simulating different systems from a set of pre-defined models: |
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-usable. With the increase of available physical DNA parts in the MIT Registry, as well as the characterisation of these parts, such a repository will help to provide a deeper understanding of the BioBrick properties and speed up the process of building new devices and systems. But more importantly, it will help to federate the growing number of contributions from the modeling community and build on the experimental characterization of BioBricks.
References
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