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From 2010.igem.org

Using C-N Model we can model systems with great complexity

Contents 1 A simplest example with only E.coli 1.1 introduction 1.2 database construction 2 Simple demo with plac and lacI and IPTG 3 Demo of oscillator 4 Demo with reverse parts(Demo of toggle switch) 5 Demo with environmental conditions 6 Demo with substituent transfers 7 Demo with multi-compartment reactions 8 Demo with complex binding product

A simplest example with only E.coli

introduction

As the simplest example, a model of a flask with only E.coli cells inside will be shown. Only one reaction will be considered: the replication of E.coli. However, it is not trivial. MoDeL enables users to add such an auto-catalytic replication reaction easily and conveniently. The minimal database used for this model could be download here.

database construction

We only provide key points regarded with construction of this minimal database. To add the auto-catalytic reaction in the Reaction container, a species with only part E.coli is required. It has the simplest Chain-Node model format: only one chain with one part and no trees. The auto-catalytic reaction has one modifier and one product and they are both referred to E.coli defined in Species container. Since they are compartment-type species (species representing a compartment), attribute itself of compartmentLabel node in modifiers and products definitions should be set the same with label of the compartment they represented in the compartments definition. It ensures that the product and the modifier are the same, avoiding wrong mismatch of product to be different with the modifier. In our example, we use

Simple demo with plac and lacI and IPTG

Demo of oscillator

Demo with reverse parts(Demo of toggle switch)

Demo with environmental conditions

Demo with substituent transfers

Demo with multi-compartment reactions

Demo with complex binding product