gillespie: Python Gillespie Algorithm Simulation

This is an implementation of the Gillespie Algorithm in Python. The package by default performs simulation of the miRNA-TF-target protein FFL.

The reactions included are:

• TF transcription (at a constant rate $\alpha_T$)
• TF translation into protein at rate $\pi_T$ per TF mRNA
• decay of the TF mRNA at rate $\mu_T$
• decay of the TF protein at rate $\mu_Q$
• miRNA production at rate $\alpha_S(q) = \alpha_S \frac{q}{q+K_S}$
• miRNA decay at rate $\mu_S$
• target mRNA transcription at rate $\alpha_R(Q) = \alpha_R \frac{q}{q+K_R}$
• target mRNA decay at rate $\mu_R$
• target protein production at rate $\pi_R$ per mRNA
• target protein decay at rate $\mu_R$
• free target mRNA binds the miRNA at rate $\beta$ to make a mRNA-miRNA complex
• mRNA-miRNA complex falls apart at rate $\mu_C$, with the mRNA being lost and the miRNA recycled.

By default, we simulate a system with 1 TF, 1 miRNA, and 1 target protein. To simulate the system dynamically, we provide the GUI interface to set the parameters and visualize the simulation.

Key Features

1. Improved GUI
   • Simplified navigation and controls for setting up simulations.
   • Enhanced visualization tools to better represent data and results.
2. Core Features
   • Supports multiple simulation scenarios.
   • Dynamic updates to simulation parameters.

Installation

Recommanded pre-setup

Create a virtual environment and activate it before installing the package:

python -m venv venv
source venv/bin/activate

Installation via pip

Navigate to the root directory of this project, install the dependencies and then install this package

cd /<project-root>
pip install -r requirements.txt
pip install .

For development purpose, one can install it as an editable package via pip install -e .

(Potential) Additional dependencies for GUI

On Linux systems, the following additional dependencies are required to run the GUI (example for Ubuntu/Debian):

sudo apt install libxcb-xinerama0
sudo apt install '^libxcb.*-dev' libx11-xcb-dev libglu1-mesa-dev libxrender-dev libxi-dev libxkbcommon-dev libxkbcommon-x11-dev

Usage

Package usage

See examples/example.ipynb for a simple example of how to use the package.

Command Line Interface (CLI)

After installing it as an editable package, one can simply run the simulation via running the gillespie command:

gillespie --config <path-to-config-file> --output <output-dir> --plot-all-simulations --plot-all-species

Currently we support the configuration file in JSON format.

Graphical User Interface (GUI)

After installing the package, one can run the GUI via the following command:

gillespie-gui

When the application window appears:

• Use the interface to specify the parameters for your simulation.
• Click the appropriate button to start the simulation.

As the simulation runs:

• View results in real-time via the interactive plot.
• Adjust parameters dynamically if supported.

After the simulation:

• The defined parameters and the results are automatically saved for your convenience.
• Review the saved files for further analysis or reference.

Enjoy exploring and simulating complex scenarios with Gillispie Simulation!

If you encounter any issues or have suggestions for improvement, feel free to contribute or open an issue in this repository. Happy simulating!