Visualizing cells and their connectivity graphs for CompuCell3D

Author

Heiland, R. ; Shirinifard, A. ; Swat, M. ; Thomas, Gordon L. ; Sluka, J. ; Lumsdaine, A. ; Zaitlen, B. ; Glazier, J.A.

fYear

2012

fDate

14-15 Oct. 2012

Firstpage

85

Lastpage

90

Abstract

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.

Keywords

biology computing; computer graphics; graph theory; high level languages; CompuCell3D; Python programming language; biological cells; cells visualisation; connectivity graphs; customizable visualizations; Biological system modeling; Cells (biology); Data visualization; Educational institutions; Graphical user interfaces; Solid modeling; Sorting; D.3.2 [Programming Languages]: Language Classifications — Very high-level languages; J.3 [Computer Applications]: Life and Medical Sciences — Biology and Genetics;

fLanguage

English

Publisher

ieee

Conference_Titel

Biological Data Visualization (BioVis), 2012 IEEE Symposium on

Conference_Location

Seattle, WA

Print_ISBN

978-1-4673-4729-7

Type

conf

DOI

10.1109/BioVis.2012.6378597

Filename

6378597