Team:Exeter/Modelling

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Revision as of 14:01, 2 October 2013

Exeter iGEM 2013 · Paint by Coli

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 model uses two programs; [http://www.mathworks.co.uk/products/matlab/ MATLAB] and KaSiM combined using a batch file.

KaSiM is a [http://en.wikipedia.org/wiki/Stochastic stochastic] simulator that executes files written in [http://www.kappalanguage.org/ Kappa]. Kappa is a rule based modeling language for protein interaction networks.

MATLAB® is a high-level language and interactive environment for numerical computation, visualization, and programming. It can be used to analyze data, develop algorithms, and create models and applications.

Together they provide the necessary tools to create an accurate model of our bio-camera system.

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.

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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 == 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 model uses two programs; [http://www.mathworks.co.uk/products/matlab/ MATLAB] and KaSiM combined using a batch file.
+KaSiM is a [http://en.wikipedia.org/wiki/Stochastic stochastic] simulator that executes files written in [http://www.kappalanguage.org/ Kappa]. Kappa is a rule based modeling language for protein interaction networks.
+MATLAB® is a high-level language and interactive environment for numerical computation, visualization, and programming. It can be used to analyze data, develop algorithms, and create models and applications.
+Together they provide the necessary tools to create an accurate model of our bio-camera system.
 == The pathways ==