# User:Jaroslaw Karcz/Modelling Sandbox

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! Parameter | ! Parameter | ||

- | ! | + | ! Value |

- | ! | + | ! Description |

- | ! Comment | + | ! Comment (literature, derived?) |

|- | |- | ||

- | | | + | | k<sub>1</sub> |

- | | | + | | x [units] |

- | | max. transcription rate of constitutive promoter ( | + | | max. transcription rate of constitutive promoter (pTET) |

- | + | ||

- | + | ||

- | + | ||

- | + | ||

- | + | ||

| Estimate | | Estimate | ||

+ | |- | ||

+ | | k<sub>2</sub> | ||

+ | | | ||

+ | | | ||

+ | | | ||

+ | |- | ||

+ | | k<sub>3</sub> | ||

+ | | | ||

+ | | | ||

+ | | | ||

+ | |- | ||

+ | | k<sub>4</sub> | ||

+ | | | ||

+ | | | ||

+ | | | ||

+ | |- | ||

+ | | k<sub>5</sub> | ||

+ | | | ||

+ | | | ||

+ | | | ||

+ | |- | ||

+ | | k<sub>6</sub> | ||

+ | | x [units] | ||

+ | | | ||

+ | | | ||

+ | |- | ||

+ | | <math> \delta_{GFP} </math> | ||

+ | | 0.029 hrs <sup>-1</sup> | ||

+ | | degradation rate of GFP | ||

+ | | Literature <font color = red> ~~ give reference </font> | ||

|} | |} | ||

<br> | <br> |

## Revision as of 10:15, 20 October 2007

## Model Development

The process of modelling consists of a number of layers; the following is a description of the modelling workflow:

**Definition of the problem****Verification of information available****Selection of model structure****Establishing a simple model****Sensitivity analysis****Experimental tests of the model predictions****Stating the agreements and divergences between experimental and modelling results, including any emergent behaviour****Iterative refinement of model**

## Introduction

The real world is dominated by complexity, especially biological systems

Mathematical modelling and computer simulations provide a means of understanding the innate funtioning of system - dynamics, and to arrive at well-founded predictions about their future development and the effect of interactions with the environment.
So what is a model? A model is an abstract representation of objects and processes that explain the features/nature of these objects or processes. We present the model of our construct, as a system of differential equations to describe the dynamics of that network.

## Model Parameters

Parameter | Value | Description | Comment (literature, derived?) |
---|---|---|---|

k_{1}
| x [units] | max. transcription rate of constitutive promoter (pTET) | Estimate |

k_{2}
| |||

k_{3}
| |||

k_{4}
| |||

k_{5}
| |||

k_{6}
| x [units] | ||

δ_{GFP}
| 0.029 hrs ^{-1}
| degradation rate of GFP | Literature ~~ give reference |