Team:Evry/Programming

From 2013.igem.org

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where N is the number of equations in the system.<br/>
where N is the number of equations in the system.<br/>
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On implémente ainsi les système en python. L’accès au code source de la résolutions numériques nous permet d'introduire des domaines de définitions pour les variables d'états. Ce qui permet d'avoir plus de stabilité dans la résolutions numériques.
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This is how we implemented the equation systems in Python. The fact that we didn't use ODE-solving libraries allowed us to introduce definition domains for some variables, which improved the overall stability in numerical resolutions.<br/>
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Le tout est encapsulé dans une classe python pour une utilisation plus simple.
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For a simpler and quicker use of repetitive tasks, we also encapsulated everything in a class scheme.
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<h2>Display</h2>
<h2>Display</h2>

Revision as of 23:23, 4 October 2013

Iron coli project

Programming methods

This part exposes our technical and algorithmical choices, the implementation and the numerical resolution of our models.

Models implementation

All our models are using the Python language. Python has several major perks:

  • Very good floating numbers management
  • High level programming
  • Object-oriented
  • Not an exclusively numerical tool, which allows much more options than Scilab or Matlab

Numerical resolution of ODEs

We chose not to use the resolution functions included in Scipy to have more coding liberties.
To solve our ODEs, we used a simple Euler method. Here is an example:
Let the following be a Cauchy problem:

Considering the following Taylor expansion:

On défini la suite tel que et
et ainsi on définie tel que et
Thus, we can define the Euler method:

Which, standardized, becomes .

In the end, all our differential equation systems are implemented like so:

where N is the number of equations in the system.

This is how we implemented the equation systems in Python. The fact that we didn't use ODE-solving libraries allowed us to introduce definition domains for some variables, which improved the overall stability in numerical resolutions.
For a simpler and quicker use of repetitive tasks, we also encapsulated everything in a class scheme.

Display

We used the Matplot library to display 2D and 3D curves.