MT dynamics simulation
Project description
Microtubule dynamics simulation
Simulation of microtubule growth dynamics in the presence and absence of physical obstacles.
Work done by:
- Simulation code: Florian Huber and Maurits Kok
- Experiments run by: Maurits Kok and Svenja-Marei Kalisch
- Marileen Dogterom
Simulation code
The full simulation code used to produce the results as published in [coming soon] is provided.\ in this repository.
The code consits of the main simulation code (simulation_main.py and simulation_functions.py). Simulation parameters are specified in simulation_parameters.py. Functions for plotting the results are provided in plotting_functions.py.
Requirements
Python version 3.6 or higher.
Installation
If you work with Anaconda you choose to create an own environment for mtdynamics
bu running the following commands:
# install mtdynamics in a new virtual environment to avoid dependency clashes
conda create --name mtdynamics python=3.7
conda activate mtdynamics
pip install mtdynamics
pip install jupyter # Optional, if you want to run jupyter notebooks from this environment
conda install -c anaconda pywin32 # Optional, if you run into win32api error (e.g. when using Python 3.8)
Or simply install mtdynamics in your already existing environment:
pip install mtdynamics
Runing the simulation
Jupyter notebook(s) are provided to illustrate how to run the simlation. They can be found in the folder \notebooks
.
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