Registry of Standard Biological Models/CellML Practical: Difference between revisions
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==Scope of the abstract== | |||
*Demonstrate the use of CellML 1.1 to describe BioBricks [http://parts.mit.edu/registry/index.php/Help:Contents](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== | |||
<font color=red> List of models defining a CellML structure : [[Registry_of_Standard_Biological_Models/Basic_Component_Models]] </font> | |||
CellML 1.1 looks very flexible and could provide all the desired features that we are looking for in order to describe a BioBrick [http://parts.mit.edu/registry/index.php/Help:Contents]. | |||
Some testing has to be done on real examples to see how far we can incorporate BioBrick concepts into CellML description capabilities. | |||
*<font color=green>Practical 1: </font> 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 [http://openwetware.org/wiki/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 | |||
*<font color=green>Practical 2: </font>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) | |||
*<font color=green>Practical 3: </font>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 [http://parts.mit.edu 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 | This problem has 2 main required features: a standardized description language and a structured repository for the created models | ||
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**store, curate and search models | **store, curate and search models | ||
**reference DNA part registry | **reference DNA part registry | ||
**drag and drop to | **drag and drop mechanism to assemble new systems | ||
==Background and References== | ==Background and References== | ||
*Description language for bio-models | *Description language for bio-models | ||
**CellML | **CellML [http://www.cellml.org] | ||
**SBML | **SBML [http://sbml.org] | ||
**MML | **MML | ||
*Databases of models | *Databases of models | ||
**CellML repository | **CellML repository [http://www.cellml.org/models/] | ||
**BioModels [www.ebi.ac.uk/biomodels] | |||
**BioModels | |||
*Previous CAD system | *Previous CAD system | ||
**BioJADE | **BioJADE [https://hpds1.mit.edu/handle/1721.1/28408] | ||
**BioSPICE | **BioSPICE [http://biospice.lbl.gov/] | ||
*BioBricks | *BioBricks [http://parts.mit.edu/registry/index.php/Help:Contents] | ||
*Part registry | *Part registry[http://parts.mit.edu/registry] |
Latest revision as of 16:16, 30 October 2007
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
- example of such a part: <bbpart>BBa_I13522</bbpart>
- 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
- Databases of models
- CellML repository [6]
- BioModels [www.ebi.ac.uk/biomodels]