Team:Exeter/Modelling

From 2013.igem.org

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== Introduction ==
== Introduction ==
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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.
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We aim to produce a model that predicts the optical properties of our bacteria (output) as a function of incident light (input). It is divided into three independant biological pathways. One for each light sensor; Red, Green and Blue. The chemistry of each pathway is described by a set of rules whose rates are experimentally or theoretically determined. The three pathways are combined to form the final model. 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. -->
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<!-- Pose and model for the images, feathers, glitter, leathers -->
<!-- Pose and model for the images, feathers, glitter, leathers -->
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== The Model ==
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== Modelling Software ==
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The model is divided into three independant biological pathways. One for each light sensor; Red, Green and Blue. 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.
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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.
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=== Assumptions ===
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== Assumptions ==
Due to the complexity of biological systems our model will include but not be limited to the following assumptions:
Due to the complexity of biological systems our model will include but not be limited to the following assumptions:
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* Only pathway specific species are rate limiting
* Only pathway specific species are rate limiting
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# The chemistry of our pathways are to be mapped out in detail.
# The chemistry of our pathways are to be mapped out in detail.
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# 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. -->
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=== Modelling Software ===
 
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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.
 
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Revision as of 10:45, 9 September 2013

Exeter iGEM 2013 · Paint by Coli

Contents

Introduction

We aim to produce a model that predicts the optical properties of our bacteria (output) as a function of incident light (input). It is divided into three independant biological pathways. One for each light sensor; Red, Green and Blue. The chemistry of each pathway is described by a set of rules whose rates are experimentally or theoretically determined. The three pathways are combined to form the final model. The purpose of this model is to numerically characterize our bio-bricks for future use.


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.

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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