Team:Exeter/Modelling

From 2013.igem.org

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== Introduction ==
== Introduction ==
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We aim to produce a model that predicts how the optical properties of our bacteria change in response to incident light. The model is composed of a red, green and a blue light activated pathway. The chemistry of each pathway is described by a set of rules. The rates of which are experimentally or theoretically determined. The purpose of the model is to numerically characterize our bio-bricks for future use and to help us create the first colour coliroid.
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We aim to produce a model that predicts how the optical properties of our bacteria change in response to incident light. The purpose of the model is to numerically characterize our bio-bricks for future use and to help us create the first colour coliroid.
<!-- 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. -->
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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. KaSiM, a stochastic simulator will be used to run the code that we write in Kappa and produce our results. We wil plot our results using GNU plot.
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. KaSiM, a stochastic simulator will be used to run the code that we write in Kappa and produce our results. We wil plot our results using GNU plot.
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== The pathways ==
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The model is composed of a red, green and a blue light activated pathway. The chemistry of each pathway is described by a set of rules. The rates of which are experimentally or theoretically determined.
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<gallery caption="Pathway block diagrams" perrow=6 widths=275 heights=300>
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Image:PathwayBlockDiagram.png|<center>
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</gallery>
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== Assumptions ==
== Assumptions ==

Revision as of 13:23, 9 September 2013

Exeter iGEM 2013 · Paint by Coli

Contents

Introduction

We aim to produce a model that predicts how the optical properties of our bacteria change in response to incident light. The purpose of the model is to numerically characterize our bio-bricks for future use and to help us create the first colour coliroid.


The Team

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
Angus Laurenson
Physics
Callum Vincent
Physics
Henri Laakso
Electrical Engineering


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. KaSiM, a stochastic simulator will be used to run the code that we write in Kappa and produce our results. We wil plot our results using GNU plot.

The pathways

The model is composed of a red, green and a blue light activated pathway. The chemistry of each pathway is described by a set of rules. The rates of which are experimentally or theoretically determined.

Pathway block diagrams



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


Exeter iGEM 2013 · Paint by Coli
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