Installation¶

Requirements¶

Python 3.11 or later

Install from PyPI¶

pip install pyvcell

Install with Poetry (for development)¶

git clone https://github.com/virtualcell/pyvcell.git
cd pyvcell
poetry install

Verify the installation¶

import pyvcell.vcml as vc
print("pyvcell imported successfully")

Workspace directory¶

pyvcell stores simulation output in a workspace directory. By default this is ./workspace relative to your current working directory. You can change it:

import pyvcell.vcml as vc

# Check the current workspace
print(vc.get_workspace_dir())

# Set a custom workspace
vc.set_workspace_dir("/path/to/my/workspace")

The workspace directory is created automatically if it doesn't exist.

Included visualization libraries¶

pyvcell bundles several visualization libraries, all installed automatically:

Matplotlib — 2D plots and concentration time series
VTK / PyVista — 3D volume rendering and mesh visualization
Trame — Interactive browser-based 3D widgets (for Jupyter notebooks)

Next steps¶

Quick Start — Load a model, simulate, and plot results