Visualizing cells and their connectivity graphs for CompuCell3D

Developing models that simulate the behavior of different types of interacting biological cells can be a very time consuming and error prone task. CompuCell3D is an open source application that addresses this challenge. It provides interactive and customizable visualizations that help a user detect when a model is producing the desired behavior and when it is failing. It also allows for high quality image generation for publications and presentations. CompuCell3D uses the Python programming language which allows for easy extensions. Examples are provided for performing graph analyses of cell connectivity.

[1]  Glazier,et al.  Simulation of biological cell sorting using a two-dimensional extended Potts model. , 1992, Physical review letters.

[2]  John Wambaugh,et al.  Simulating Microdosimetry in a Virtual Hepatic Lobule , 2010, PLoS Comput. Biol..

[3]  Bülent Yener,et al.  Quantitative metric profiles capture three-dimensional temporospatial architecture to discriminate cellular functional states , 2011, BMC Medical Imaging.

[4]  John D. Hunter,et al.  Matplotlib: A 2D Graphics Environment , 2007, Computing in Science & Engineering.

[5]  James A Glazier,et al.  Multicell simulations of development and disease using the CompuCell3D simulation environment. , 2009, Methods in molecular biology.

[6]  J. Glazier,et al.  3D Multi-Cell Simulation of Tumor Growth and Angiogenesis , 2009, PloS one.

[7]  Jesús A. Izaguirre,et al.  COMPUCELL, a multi-model framework for simulation of morphogenesis , 2004, Bioinform..

[8]  D. Noble.  The music of life : biology beyond genes , 2008 .

[9]  Neil Gershenfeld,et al.  FAB: The Coming Revolution on Your Desktop--from Personal Computers to Personal Fabrication , 2005 .

[10]  François Graner,et al.  Growth laws and self-similar growth regimes of coarsening two-dimensional foams: transition from dry to wet limits. , 2012, Physical review letters.

[11]  James A. Glazier,et al.  Workflows for parameter studies of multi-cell modeling , 2010, SpringSim.

[12]  Aric Hagberg,et al.  Exploring Network Structure, Dynamics, and Function using NetworkX , 2008, Proceedings of the Python in Science Conference.