cytoskeleton-analyser 1.6.5

Examines simulated cell microtubules

cytoskeleton-analyser is a postprocessor for extraction, analysis and human-friendly presentation of the raw binary results generated by Explicit-Microtubules.

Explicit-Microtubules Explicit-Microtubules is a C++ simulator of the whole-cell microtubule system. It reconstructs computationally the microtubule geometry and real-time dynamics in 3d space and time using stochastic algorithms. In the course of the simulation based on a multitude of bioogical information, it outputs detailed histories of microtubule dynamics along with three-dimensional snapshots of microtubules. However, designed to be focuced on versatile generation procedures, Explicit-Microtubules only includes basic data analysis.

Complementing the simulator, cytoskeleton-analyser is designed to extract, analyse and visualize various characteristics of the stochastically reconstructed microtubule system.

##Requirements

Cytoskeleton Analyser requires python 3.9 or later.

When installing by pip, the following dependencies are installed automatically:

• NumPy
• SciPy
• Matplotlib
• meshio
• SQLAlchemy

##Installation

Provided that python is present, in the simplest case the Cytoskeleton Analyser may be installed globallly using pip:

pip install cytoskeleton-analyser

However, the recommended way is installing the package into a python virtual environment, which adds only a few commans:

1. Create a project directory (here named ‘myproject’) and cd to it.

2. Create a python virtual environment (here named ‘venv3.9’).

3. Activate the virtual environment.

4. Install as above.

mkdir myproject && cd myproject
python3 -m venv venv3.9
source venv3.9/bin/activate
pip install cytoskeleton-analyser

Alternatively, if you want to install the python package straight from the GitHub repository, replace the last line above with

pip install git+git://github.com/vsukhor/cytoskeleton-analyser

Getting Started

A more complete introduction, use examples and API are available in the documentation.`

License

cytoskeleton-analyser is available under the terms of the BSD 3 Clause license. See LICENSE.txt for more information.