By Anwar Shaikh

Indiana University Bloomington

An open-source simulation environment for multi-cell, single-cell-based modeling of tissues, organs and organisms. Uses Cellular Potts Model to model cell behavior.

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Version 3.7.7 - published on 16 May 2018

doi:10.4231/D3XP6V584 cite this

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CompuCell3D is a flexible scriptable modeling environment, which allows the rapid construction of sharable Virtual Tissue in-silico simulations of a wide variety of multi-scale, multi-cellular problems including angiogenesis, bacterial colonies, cancer, developmental biology, evolution, the immune system, tissue engineering, toxicology and even non-cellular soft materials. CompuCell3D models have been used to solve basic biological problems, to develop medical therapies, to assess modes of action of toxicants and to design engineered tissues. CompuCell3D intuitive and make Virtual Tissue modeling accessible to users without extensive software development or programming experience. It uses Cellular Potts Model to model cell behavior.


Compucell3D is led by Anwar Shaikh (IU), Maciej Swat (IU) and James Glazier (IU) in collabration with Dr. David Umulis (PU) and team.

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This project is currently funded by generous support from the U.S. National Science Foundation (NSF) and National Institutes of Health (NIH). Grants: NSF- 1720625, “Network for Computational Nanotechnology - Engineered nanoBIO Node” and NIH- R01 GM122424, “Competitive Renewal of Development and Improvement of the Tissue Simulation Toolkit”.

Cite this work

Researchers should cite this work as follows:

  • Anwar Shaikh (2018), "CompuCell3D," (DOI: 10.4231/D3XP6V584).

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