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Team:Edinburgh/Modelling/Bacterial
From 2010.igem.org
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<a name="Repressilator" id="Repressilator"></a><h2>The Repressilator</h2> | <a name="Repressilator" id="Repressilator"></a><h2>The Repressilator</h2> | ||
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| + | <p>The core of the model is formed by the Elowitz repressilator designed by Ty Thomson in 2009 (available to view <a href="http://www.cellucidate.com/showcase_books/182350-Rule-Based-Modeling-of-BioBrick-Parts">here</a>). This was one of the first to incorporate the concept of standardised biological parts (i.e. BioBricks) into a modelling context, attempting to "introduce a modular framework for modelling BioBrick parts and systems using rule-based modelling". The idea was to model at the level of individual parts, such that systems could be constructed using different components by paying a cost upfront with the construction of models of the parts, and thus making modular construction of specific models practically effort free - similar, in fact, to the idea of characterised and composable BioBricks used in the design and construction of synthetic circuits.</p> | ||
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<p><b>Figure 1:</b> A composite agent with four DNA agents joined together at their upstream and downstream sites, representing the <i>cat-sacB</i> construct and surrounding DNA.</p><br><br></center> | <p><b>Figure 1:</b> A composite agent with four DNA agents joined together at their upstream and downstream sites, representing the <i>cat-sacB</i> construct and surrounding DNA.</p><br><br></center> | ||
| - | Credit Ty | + | Credit Ty Thomson for original base model. |
Results thereof. | Results thereof. | ||
Revision as of 11:06, 24 August 2010
Overview: Modelling bacterial BRIDGEs
The second Kappa model created for the project attempted to realise the original vision we held for the system: a composite device based on the tried and tested Elowitz repressilator, combined with three different light-producing and light-sensing pathways. The primary objective of the modelling would then be to confirm that the three systems interacted with one another in roughly the manner we expect, without undue interference or trouble. We would also try to use the model to analyse the structure of the system and possibly to compare different proposed subsystems against one another, to analyse which one would work better.
The following sections describe, in turn: the repressilator model that forms the core of the system, the red light production and signal transduction pathways, the blue light production and signal transduction pathways, the green light production and signal transduction pathways, the results obtained by running the simulation, and finally the analysis of the results obtained.
The Repressilator
The core of the model is formed by the Elowitz repressilator designed by Ty Thomson in 2009 (available to view here). This was one of the first to incorporate the concept of standardised biological parts (i.e. BioBricks) into a modelling context, attempting to "introduce a modular framework for modelling BioBrick parts and systems using rule-based modelling". The idea was to model at the level of individual parts, such that systems could be constructed using different components by paying a cost upfront with the construction of models of the parts, and thus making modular construction of specific models practically effort free - similar, in fact, to the idea of characterised and composable BioBricks used in the design and construction of synthetic circuits.
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