biobridge 0.2.0

A library for simulating all biology related things, analyzing them and visualizing them.

Biobridge

Biobridge is a Python library for simulating biological processes and systems also analyzing them, visualising them, and interacting with them.

Installation

Firstly you need to install pyrosetta

Then install biobridge

pip install biobridge

Usage

To use Biobridge in your project, import it for example:

from biobridge import *
# Create two proteins
protein1 = Protein("Protein A", "ACDEFGHIKLMNPQRSTVWY")
protein2 = Protein("Protein B", "YVWTSRQPNMLKIHGFEDCA")

# Define bindings for the proteins
protein1.add_binding("Site 1", "High")
protein2.add_binding("Site 3", "Medium")

# Create a cell with specific properties
cell1 = Cell(
    name="Cell X",
    cell_type="Epithelial Cell",
)

organelle = Mitochondrion(0.5, 100)

# Add organelles to the cell
cell1.add_organelle(organelle, quantity=10)
cell1.add_organelle(Organelle("Nucleus", 1), quantity=1)
cell1.add_organelle(Organelle("Ribosome", 100), quantity=100)
cell1.add_chromosome(Chromosome(DNA("ATCG" * 1000), "Chromosome 1"))

# Print cell details
print("Cell X Description:")
print(cell1)

The notable functions are:

from biobridge import *

Cell()
DNA()
RNA()
Protein()
Chromosome()
Environment()
Tissue()
System()
ImageAnalyzer()
Orchestrator()
Virus()
Infection()
SQLDNAEncoder()
SurgicalSimulator()

To build do

hatch build

To see more examples how to use biobridge see the test files, biobridge works well with jupyter notebooks.

You can setup a config for biobridge to do this download the create_config.py file.

If you want to use something else than vscode you can use my editor built for this library.