Pyology

Pyology is a object-oriented model of a biological cell, implemented as a Python library. It provides a framework for simulating cellular processes and metabolic pathways.

Features

• Simulates various cellular components and organelles
• Models metabolic pathways such as glycolysis and the Krebs cycle
• Implements energy production mechanisms (ATP synthesis)
• Provides a flexible and extensible architecture for cellular simulations

Installation

To install Pyology, you can use pip:

pip install pyology

Usage

Here's a basic example of how to use Pyology:

from pyology.cell import Cell
from pyology.simulation import Reporter, SimulationController

# Create a cell and simulation components
cell = Cell()
reporter = Reporter()
sim_controller = SimulationController(cell, reporter)

# Run a simulation with a specific amount of glucose
glucose_amount = 4
results = sim_controller.run_simulation(glucose_amount)

# Access and analyze the results
print(f"Final ATP: {results['final_cytoplasm_atp'] + results['final_mitochondrion_atp']:.2f}")

For more detailed examples and usage instructions, please refer to the documentation.

Components

Pyology includes the following main components:

• Cell
• Mitochondrion
• Cytoplasm
• Krebs Cycle
• Endoplasmic Reticulum
• Golgi Apparatus
• Cell Membrane

Each component is modeled to represent its biological counterpart and interact with other components in the simulation.

Contributing

Contributions to Pyology are welcome! Please refer to the CONTRIBUTING.md file for guidelines on how to contribute to this project.

License

Pyology is released under the MIT License. See the LICENSE file for more details.

Contact

For questions, issues, or suggestions, please open an issue on the GitHub repository.