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Revision as of 17:36, 13 October 2010 (view source) Liaochen (Talk | contribs) (→Simple demo with plac and lacI and IPTG) ← Older edit		Revision as of 17:37, 13 October 2010 (view source) Liaochen (Talk | contribs) (→The simplest example) Newer edit →
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	Using C-N Model we can model systems with great complexity		Using C-N Model we can model systems with great complexity
-	==The simplest example==	+	==The simplest example with only E.coli cell==
	===introduction===		===introduction===

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Revision as of 17:37, 13 October 2010

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

Contents 1 The simplest example with only E.coli cell 1.1 introduction 1.2 database construction 1.3 modelling and simulation 2 Basic example with pLac-LacI repression system 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

The simplest example with only E.coli cell

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 represent in the compartments definition. It ensures that the product and the modifier are the same, avoiding wrong mismatch of the product which is different with the modifier. Since number of E.coli cells will reach a stable level in a long time course, we use <math>k_{g}(1-C_{E.coli}/C_{max})C_{E.coli}V_{Flask}</math> as the reaction rate, where <math>k_{g}</math> is the growth rate of E.coli, <math>V_{Flask}</math> represents the size of E.coli, and <math>C_{E.coli}</math> and <math> C_{max}</math> are concentration of E.coli and its max concentration in the flask, respectively. The negative sign in the rate equation indicates self-repression of E.coli cells.

modelling and simulation

Model written in SBML format is available here. The dynamic curve of E.coli replication is plotted by time course simulation:

Basic example with pLac-LacI repression system

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