pyvcell
This is the python wrapper for vcell modeling and simulation for
- local scripting of spatial modeling, simulation, data analysis and visualization workflows using Virtual Cell technology
- access to Virtual Cell remote APIs - with public access or as an authenticated Virtual Cell user.
Local simulation, analysis and visualization with pyvcell
download or create new spatial models
- load/save VCML (Virtual Cell’s native format - import/export to VCell UI)
- load/save SBML (Systems Biology Markup Language)
- load from Antimony (friendly textual language for SBML)
- create/edit any VCML object (e.g. species, model, geometry) programmatically
local editing with Python objects
- edit parameters. add/remove/edit species, compartments, reactions, initial conditions, diffusion coefficients
- create/edit geometry objects, create/edit vcell applications and simulations
run local simulations
- run local spatial simulations (for reactions, diffusion, and advection) stored in local workspace.
analyze local simulation result:
- Time-series summary statistics available as NumPy arrays.
- spatiotemporal arrays stored as Zarr datastores and available as NumPy arrays.
- 3D mesh data using VTK unstructured grids, analyzed with VTK
local visualization
- built-in plotting and 3D visualization via Matplotlib and VTK/PyVista
- make your own plots or 3D renderings.
installation
The easiest way to install pyvcell is by using the Python Package Index and pip. We highly recommend setting up a virtual environment for dependency management. Run the following command to install pyvcell from PyPI
pip install pyvcell
Usage
import pyvcell.vcml as vc
biomodel = vc.load_vcml_file('path/to/your/model.vcml')
results = vc.simulate(biomodel, "sim1")
results.plotter.plot_concentrations()
Documentation
Full documentation is available at https://virtualcell.github.io/pyvcell/
Examples:
Antimony example
Parameters example
Geometry import example
1 maintainer
Metadata
1 maintainer
Release files for pyvcell 0.5.1
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Source distribution (sdist)
| File | Size | Uploaded | Provenance | |
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| pyvcell-0.5.1.tar.gz | 219.6 kB | Without provenance | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| pyvcell-0.5.1-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 676.2 kB
Release files / pyvcell-0.5.1.tar.gz
| Download URL | pyvcell-0.5.1.tar.gz |
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| Size | 219.6 kB |
| Tags | Source |
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Release files / pyvcell-0.5.1-py3-none-any.whl
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| Size | 456.6 kB |
| Tags | Python 3 |
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