Python model of chromosome movements during mitosis in Fission Yeast
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README.md

kt_simul - Python model of chromosome mouvements during mitosis

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Python model of chromosome mouvements during mitosis in Fission Yeast.

This python module provides the simulation of mitotic spindle elements, during cell division.

If you're interested in this work, please contact :

The underlying model is fully described in:

G. Gay, T.Courthéoux, C. Reyes, S. Tournier, Y. Gachet. A stochastic model of kinetochore–microtubule attachment accurately describes fission yeast chromosome segregation J. Cell Biol 2012

This article should be used for any citation of this work.

The 1D version has been used to describe chromosome congression in the following article : Mary, H., Fouchard, J., Gay, G., Reyes, C., Gauthier, T., Gruget, C., Pecreaux, J., Tournier, S. and Gachet, Y. (2015). Fission yeast kinesin-8 controls chromosome congression independently of oscillations. J. Cell Sci

The original version in 1D is available in the git branch simu_1D. The main branch master uses a new geometry system to simulate chromosomes in 3D.

Some code example and documentation con be found here : http://nbviewer.ipython.org/github/bnoi/kt_simul/tree/master/doc/notebooks/.

Mathematical documentation about the 1D model is available at doc/simu_spindle_1d.pdf.

Installation

The best way to install the dependencies is to use the Anaconda Python distribution. Then use the following command lines :

conda config --add channels conda-forge
conda install numpy scipy pandas matplotlib

To install the kt_simul model, do :

pip install -e git+https://github.com/bnoi/kt_simul.git#egg=master

Funding

This project is funded by the French National Research Agency as : ANR- BLAN 1206 01 Chromocatch, programme blanc 2010

Contributors

Licence

This code is provided under the GPL compatible CeCILL licence (see LICENCE for full details).