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Visualizing cells and their connectivity graphs for CompuCell3D

Mitja Hmeljak
Chris Mueller
Alex Dementsov
Dr. Mark Alber
Dr. Jesus Izaguirre
Joseph Coffland

CompuCell3D (CC3D; is a software application that simulates the behaviors of generalized cells. The visualization of those cells also illustrates their connectivity with each other. CompuCell3D is primarily used to develop models for multi-cellular biology, however, it is also used for non-biological models.

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Project development

Institution: Biocomplexity Institute, Indiana University, Instituto de Fisica Universidade Federal do Rio Grande do Sul, Department of Physics, Biocomplexity Institute Indiana University, CREST, Pervasive Technology Institute Indiana University

This project received support from the National Institutes of Health, National Institute of General Medical Sciences grants R01 GM077138 and R01 GM076692, the Environmental Protection Agency grant R835001, the Lilly Endowment Inc. and the Biocomplexity Institute at Indiana University. Indiana Universitys Research Technologies (RT/UITS), provided time and assistance with BigRed and Quarry clusters for simulations. The Advanced Visualization Lab in RT helped generate the tumor model on their 3D printer. Early versions of CompuCell3D were developed at the University of Notre Dame by JAG, Dr. Mark Alber, Dr. Jesus Izaguirre, Joseph Coffland, and collaborators with the support of National Science Foundation, Division of Integrative Biology, grant IBN-00836563. Other developers (current and past) from Indiana University include Mitja Hmeljak, Chris Mueller and Alex Dementsov. The following source software communities have provided a foundation for CC3D: Python, numpy, IPython, VTK, NetworkX and matplotlib.