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CompuCell3D (CC3D) is an open-source software framework for building and executing multi-cell biological virtual-tissue models. It represents cells using the Glazier–Graner–Hogeweg model, also known as Cellular Potts model. The primary CC3D application consists of two separate tools, a smart model editor (Twedit++) and a tool for model execution, visualization and steering (Player). The CompuCell3D version 4.x release introduces support for Jupyter Notebooks, aninteractive computational environment, which brings the benefits ofreproducibility, portability, and self-documentation.Since model specifications in CC3D are written in Python and CC3DML and Jupyter supports Python and other languages, Jupyter can naturally act as an integrated development environment (IDE) for CC3D users as well as a live document with embedded text and simulations.This update follows thetrend in software to move away from monolithic freestanding applications to the distribution of methodologies in the form of libraries that can be used in conjunction with other libraries and packages.Withthese benefits, CC3D deployed inJupyter Notebookis a more natural and efficient platform for scientific publishing and education using CC3D. |
