Welcome to Simularium Models Util’s documentation!

!!! This repository is being actively developed and is not yet released, proceed with caution :)

Simularium repositories

This repository is part of the Simularium project (simularium.allencell.org), which includes repositories:

  • simulariumIO - Python package that converts simulation outputs to the format consumed by the Simularium viewer website

  • simularium-engine - C++ backend application that interfaces with biological simulation engines and serves simulation data to the front end website

  • simularium-viewer - NPM package to view Simularium trajectories in 3D

  • simularium-website - Front end website for the Simularium project, includes the Simularium viewer

Simularium Models Util

Build Status Documentation Code Coverage

Tools for building computational biology models and example models from the Simularium project.

Currently includes coarse-grained monomer ReaDDy models for actin, microtubules, and kinesin.

Quickstart

See examples/README.md to run example actin, microtubules, or kinesin models either locally or on AWS with Docker.

Installation

Stable Release: pip install simularium_models_util
 Development Head: pip install git+https://github.com/allen-cell-animated/simularium_models_util.git
 Local Editable Install pip install -e .[dev] (or pip install -e .\[dev\] on mac) from repo root directory

Documentation

For full package documentation please visit allen-cell-animated.github.io/simularium_models_util.

Development

See CONTRIBUTING.md for information related to developing the code.

Allen Institute Software License

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