mwakok/mtdynamics

Simulation of microtubule growth dynamics in th presence and absence of physical obstacles

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

Reference / citation

You can read more about this simulation in:
Kok, Huber, Kalisch, Dogterom, 2021, bioRxiv, DOI: 10.1101/2021.12.07.471417

Please also cite this article if use the present code or results. Thanks!

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 can create an own environment for mtdynamics by 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.

Making a new release

To create release you need write permission on the repository.

1. Check author list in citation.cff file.
2. Update version in setup.py and CHANGELOG.md.
3. Update the CHANGELOG.md to include changes made.
4. Goto GitHub release page
5. Press draft a new release button
6. Fill version, title and description field
7. Press the Publish Release button

A GitHub action will run which will publish the new version to pypi.