Python model of chromosome mouvements during mitosis in Fission Yeast (http://mitotic-machine.org).

This python module provides the simulation of mitotic spindle elements (for now, the kinetochore and the spindle pole bodies), during cell division in fission yeast. For more details see online documentation.

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

• Sylvie Tournier (sylvie.tournier-gachet@univ-tlse3.fr) for all aspects related to the biology and for academical collaboration purposes.
• Guillaume Gay (gllm.gay@gmail.com) for all aspects related to the code

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 (link to article).

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

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

• Guillaume Gay gllm.gay@gmail.com : main author
• Hadrien Mary hadrien.mary@gmail.com : contributor

kt_simul is part of the BNOI Project https://github.com/bnoi.

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

• Python 2.7 and Python 3
• numpy >= 1.7
• scipy >= 0.12
• cython >= 0.19
• pandas >= 0.12
• matplotlib (optional) >= 1.2
• PyQt4 (optional)

You can directly clone this repo, then install with setuptools:

git clone https://github.com/bnoi/kt_simul.git
cd kt_simul/
python setup.py build
python setup.py install

Or you can install kt_simul via pip (dependencies will be automatically installed):

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

You will need a C compiler for the cython part.

from kt_simul.io.xml_handler import ParamTree
from kt_simul.core.simul_spindle import Metaphase
from kt_simul.io.simuio import SimuIO
from kt_simul.core import parameters

PARAMFILE = parameters.PARAMFILE
MEASUREFILE = parameters.MEASUREFILE

# Change some parameters
paramtree = ParamTree(PARAMFILE)
paramtree.change_dic('dt', 10)
paramtree.change_dic('span', 2000)
paramtree.change_dic('t_A', 1750)

measuretree = ParamTree(MEASUREFILE, adimentionalized=False)

# Init simu
meta = Metaphase(verbose=True, paramtree=paramtree, measuretree=measuretree, initial_plug='random')

# Launch simu
meta.simul()

# Save results
SimuIO(meta).save("simu.h5")

# Show trajectories (matplotlib needed)
meta.show()

Simulation can be "played" with Qt based GUI:

from kt_simul.gui.animation import Animator

anim = Animator(meta)
anim.play()