Registry of Standard Biological Models/CellML Practical
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11 May 2024
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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]
