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Team:Edinburgh/Modelling/Genomic
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| - | <p> | + | <p>The genomic BRIDGE model, focused as it is on interactions the BRIDGE protocol, requires only one basic agent - the DNA agent presented previously in the <a href="https://2010.igem.org/Team:Edinburgh/Modelling/Kappa">introduction to Kappa</a>. This basic agent, chained together as shown in Figure 1, can then be used to construct larger composite agents that represent different sequences in the BRIDGE protocol - for example, the <i>cat-sacB</i> construct or the insert.</p> |
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| + | <p><b>Figure 1:</b> Three Kappa agents, representing DNA, bound together at their respective upstream and downstream sites.</p><br><br></center> | ||
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Revision as of 13:06, 18 August 2010
Overview: Modelling genomic BRIDGEs
Unlike the modelling of genetic regulation networks or metabolic pathways, modelling a generic protocol does not achieve much in light of the ultimate goal of being able to understand and answer questions regarding biological processes. On the other hand, we did wish to have a model corresponding to the BRIDGE protocol, and such a model would be useful to demonstrate an ability of Kappa that has not been touched upon yet: perturbations. These are described in further detail below, but in short allow for certain effects (such as activation or inhibition of rules) to be enacted at certain times within simulation of the model.
The sections below describe, in turn: the agents and rules that are present in the model, the perturbations that govern time-dependent behaviour, the results of running the simulation, and analysis of the results obtained.
The Model
The genomic BRIDGE model, focused as it is on interactions the BRIDGE protocol, requires only one basic agent - the DNA agent presented previously in the introduction to Kappa. This basic agent, chained together as shown in Figure 1, can then be used to construct larger composite agents that represent different sequences in the BRIDGE protocol - for example, the cat-sacB construct or the insert.
Figure 1: Three Kappa agents, representing DNA, bound together at their respective upstream and downstream sites.
