User:Jaroslaw Karcz/Modelling Sandbox: Difference between revisions
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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 | ||
|- | |||
| k<sub>2</sub> | |||
| | |||
| | |||
| | |||
|- | |||
| k<sub>3</sub> | |||
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|- | |- | ||
| | | k<sub>4</sub> | ||
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|- | |||
| k<sub>5</sub> | |||
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|- | |||
| 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 07:15, 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
[math]\displaystyle{ f_{obj}(k) = \sum_{i=1}^q (f_{obs}(i) - f_{per}(i,k))^2 }[/math]
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?) |
---|---|---|---|
k1 | x [units] | max. transcription rate of constitutive promoter (pTET) | Estimate |
k2 | |||
k3 | |||
k4 | |||
k5 | |||
k6 | x [units] | ||
[math]\displaystyle{ \delta_{GFP} }[/math] | 0.029 hrs -1 | degradation rate of GFP | Literature ~~ give reference |