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 0.4.2
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | Provenance | |
|---|---|---|---|---|
| pyvcell-0.4.2.tar.gz | 197.4 kB | Without provenance | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| pyvcell-0.4.2-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 645.6 kB
Release files / pyvcell-0.4.2.tar.gz
| Download URL | pyvcell-0.4.2.tar.gz |
|---|---|
| Size | 197.4 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
f522d75e36efcf29b7c35f30f720e77da1599988f723c58fafe5d6342ef24590
|
|
BLAKE2b-256 checksum How to use checksums |
47c201954bfa0e87acfa749591c707d25365e4cc92ec4dd984e97a82e786bedb
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
uv/0.12.23 {"installer":{"name":"uv","version":"0.12.23","subcommand":["publish"]},"python":null,"implementation":{"name":null,"version":null},"distro":{"name":"Ubuntu","version":"24.04","id":"noble","libc":null},"system":{"name":null,"release":null},"cpu":null,"openssl_version":null,"setuptools_version":null,"rustc_version":null,"ci":true}
|
Release files / pyvcell-0.4.2-py3-none-any.whl
| Download URL | pyvcell-0.4.2-py3-none-any.whl |
|---|---|
| Size | 448.2 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
878a79d07a43141e4921bcf476526b896ad50a232188f1bdd435e38b4dd8f475
|
|
BLAKE2b-256 checksum How to use checksums |
5ccf3fab2953f1818d038d50ff76920acec569849a22010161090c0034bc4f38
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
uv/0.12.23 {"installer":{"name":"uv","version":"0.12.23","subcommand":["publish"]},"python":null,"implementation":{"name":null,"version":null},"distro":{"name":"Ubuntu","version":"24.04","id":"noble","libc":null},"system":{"name":null,"release":null},"cpu":null,"openssl_version":null,"setuptools_version":null,"rustc_version":null,"ci":true}
|
Security for pyvcell 0.4.2
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
No provenance found
None of the files in this release were uploaded with provenance metadata.
A note on package security
PyPI is a repository for distributing packages, not a service for auditing them. While third-party security researchers and our staff do their best to detect and remove malicious packages, PyPI cannot guarantee the quality, security or suitability of any given package.
To learn more about protecting yourself from malicious actors, visit our package security documentation.
