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Team:Exeter/Modelling
From 2013.igem.org
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== Introduction == | == Introduction == | ||
| - | We aim to produce | + | We aim to produce a model of system that predicts the optical properties of our bacteria (output) as a function of incident light (input). The purpose of this model is to numerically characterize our bio-bricks for future use. |
| - | The model will focus on the rates of the reactions in our pathways and how light interacts with both the sensors and pigments. The final model will predict what colour and tone a bacteria will be given light exposure. | + | <!-- The model will focus on the rates of the reactions in our pathways and how light interacts with both the sensors and pigments. The final model will predict what colour and tone a bacteria will be given light exposure. --> |
== The Team == | == The Team == | ||
| - | <gallery caption="We are Exeter iGEM's dry team. Together we are responsible for the creation and development of a working model of our system" perrow=6 widths=275 heights=300> | + | <gallery caption="We are Exeter iGEM's dry team. Together we are responsible for the creation and development of a working model of our system and other various tasks" perrow=6 widths=275 heights=300> |
Image:Exeter-angus-laurenson.jpg|<center>'''[[User:Angus|Angus Laurenson]]''' <br>Physics | Image:Exeter-angus-laurenson.jpg|<center>'''[[User:Angus|Angus Laurenson]]''' <br>Physics | ||
Image:Exeter-callum-vincent.jpg|<center>'''[[User:Cv235|Callum Vincent]]''' <br>Physics | Image:Exeter-callum-vincent.jpg|<center>'''[[User:Cv235|Callum Vincent]]''' <br>Physics | ||
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== The Model == | == The Model == | ||
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| + | The model is divided into three independant biological pathways. The chemistry of each is described by a set of rules whose rates are experimentally or theoretically determined. The three pathways are combined to form the final model. | ||
=== Assumptions === | === Assumptions === | ||
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* Only pathway specific species are rate limiting | * Only pathway specific species are rate limiting | ||
| - | === The Plan === | + | <!-- === The Plan === |
# The chemistry of our pathways are to be mapped out in detail. | # The chemistry of our pathways are to be mapped out in detail. | ||
# We will research what relevant models exist and make use of the most accurate. | # We will research what relevant models exist and make use of the most accurate. | ||
# We shall construct rudimentary equations for each step in our pathways. | # We shall construct rudimentary equations for each step in our pathways. | ||
| - | # Throughout the project our model will be updated either in light of experimental results or new ideas. | + | # Throughout the project our model will be updated either in light of experimental results or new ideas. --> |
=== Modelling Software === | === Modelling Software === | ||
Revision as of 10:39, 9 September 2013
Contents |
Introduction
We aim to produce a model of system that predicts the optical properties of our bacteria (output) as a function of incident light (input). The purpose of this model is to numerically characterize our bio-bricks for future use.
The Team
 Physics |
 Physics |
 Electrical Engineering |
The Model
The model is divided into three independant biological pathways. The chemistry of each is described by a set of rules whose rates are experimentally or theoretically determined. The three pathways are combined to form the final model.
Assumptions
Due to the complexity of biological systems our model will include but not be limited to the following assumptions:
- Classical elastic mechanics
- Bacteria contain a homogeneous mix of components
- All constituents move with brownian motion
- Bacteria are identical
- Bacteria evenly distributed across surface
- Bacteria do not interact
- Only pathway specific species are rate limiting
Modelling Software
The majority of our modelling efforts will be focused on creating a system of rules for the protein interaction programming language [http://www.kappalanguage.org/ Kappa]. Using Kappa we will be able to create a [http://en.wikipedia.org/wiki/Stochastic stochastic] model, which will take experimentally determined reaction rates and provide an accurate prediction of the bacteria's reaction to light exposure.
With many thanks to our sponsors:
