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Tools

CompuCell3d 

This app provides a graphical front end that allows users to perform single-cell and multi-cell modeling of tissues in an open-source simulation environment based on the CompuCell3d Framework.

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cc3d nanoHUB Tool Setup

This script generates GitHub repositories to facilitate the deployment of CompuCell3D tools. Run the script found herego to nanoHUB's tool creation page follow the instructions, and deploy your app!

Tellurium

A Python Environment for Reproducible Dynamical Modeling of Biological Networks

Tellurium provides the interfacial code to convert between standard formats and utilize powerful libraries without requiring technical expertise, allowing you to focus on what’s important: building better models. Tellurium also provides first-class support for exchangeability via COMBINE archives, allowing you to share your models and simulations with other tools.

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PhysiCell-Jupyter-GUI

This repository facilitates the deployment of a PhysiCell model in a Jupyter notebook GUI. Follow the README instructions and deploy your app!

Running a single Python script in the repository auto-generates a Jupyter notebook GUI that will allow easy editing of model parameters and visualization of output files. The directory structure and content of the repository matches a template required for a nanoHUB tool installation. However, creating an actual nanoHUB tool is optional; the GUI created here should also work (with fewer bells & whistles, perhaps) on your personal computer, assuming you have the required Python modules and are able to run a Jupyter notebook server.