A small modeling project for the 2014 Dresden Summer School in Systems Biology
The goal of this school's challenge was to develop a quantitative model for cell polarity establishment in a single-cell C. elegans embryo.
This phenomenon is often described using two population of proteins with antagonistic interactions, but (at first) we tried to make it simpler by modeling two populations of proteins without interactions but with different diffusion and advection coefficients.
We decided to focus on:
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Simplicity: The model is as simple as possible, without interactions between the two proteins. We want to see in what extent a diffusion and a differential advection are able to break symmetry. The implementation is also very simple (forward euler discretisation of an EDP).
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Pedagogy: The model is implemented step by step in an Ipython notebook, which means that all the code is visible and explained to the user. It can also be easily modified in order to test how it would behave. This is also why we choose to distribute it under a free-software license: you are welcome to copy and modify it !
You can download the ipython notebook to try our model interactively on your computer or visualize the non interactive version at http://nbviewer.ipython.org/github/geeklhem/polarikss/tree/master/
If you want to use it on your computer the dependencies are:
- Python libraries: numpy, scipy, pandas, matplotlib.
- Experimental results (for the verification and the flow speed input): as these are unpublished data, we cannot disclose them at the moment.
Copyright (C) 2014 - Dresden Summer School in Systems Biology Group 4
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.