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Goal

The project is an ambitious task to create a model of a whole yeast cell in the course of about a week. Naturally we will have to sacrifice accuracy and detail to speed and efficiency. Don't let that creep into your daily routine when doing science!

The basic structure of the project is already prepared for you in the folder Project. It contains a few modules that give you a first codebase to work on.

The goal is to learn to work in a team on a program that is longer than a few lines of code and to create something together.

You should form groups of two to three students to work on subtasks and implement new modules for the model.

Structure

The model is inspired by the structure of a model published by Karr et al. 2014 and has a three main classes:

1. Model: The model object contains the simulation routine and manages the simulation process. It registers molecules and processes to simulate a whole model and lets them communicate.
2. Biomolecule: Specific molecules are of the type Biomolecule or can get additional attributes by inheriting from this class.
3. Process: Processes that happen in the cell modify Biomolecules. The class Process provides the basic attributes and methods needed for this. The specific processes should be derived from this class.