kt_simul - Python model of chromosome mouvements during mitosis
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 :
- Sylvie Tournier (firstname.lastname@example.org) for all aspects related to the biology and for academical collaboration purposes.
- Guillaume Gay (email@example.com and http://damcb.org) for all aspects related to the physics and the code.
The underlying model is fully described in:
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.
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
This project is funded by the French National Research Agency as : ANR- BLAN 1206 01 Chromocatch, programme blanc 2010
This code is provided under the GPL compatible CeCILL licence (see LICENCE for full details).