Cited By
View all- Glazier J(2012)Visualizing cells and their connectivity graphs for CompuCell3DProceedings of the 2012 IEEE Symposium on Biological Data Visualization (BioVis)10.1109/BioVis.2012.6378597(85-90)Online publication date: 14-Oct-2012
Workflows for parameter studies of multi-cell modeling
Authors: 
Randy Heiland, Maciek Swat, Benjamin Zaitlen, James Glazier, and Andrew LumsdaineAuthors Info & Claims
Randy Heiland, Maciek Swat, Benjamin Zaitlen, James Glazier, and Andrew LumsdaineAuthors Info & ClaimsApril 2010
Article No.: 94, Pages 1 - 6
Abstract
Running simulations for multi-cell tissue models can involve numerous parameters and consume considerable computing resources. This paper presents an overview and use case of two open source projects - CompuCell3D, a multi-cell modeling framework, and VisTrails, a workflow system for parameter exploration and data management.
References
[1]
Dubois, P. F. 2007. Python for Scientific Computing, Computing in Science & Engineering, vol. 9, no. 3, May/June 2007.
[2]
Cickovski, T., Aras, K., Swat, M., Merks, R. M. H., Glimm, T., Hentschel, H. G. E., Alber, M. S., Glazier, J. A., Newman, S. A., and Izaguirre, J. A. 2007. From Genes to Organisms Via the Cell: A Problem-Solving Environment for Multicellular Development. Computing in Science and Engineering, 9: 50--60 (2007).
[3]
Glazier, J. A., Balter, A., and Poplawski, N. J. 2007. Magnetization to Morphogenesis: A Brief History of the Glazier-Graner-Hogeweg Model. In Single-Cell-Based Models in Biology and Medicine, A. R. A. Anderson, M. A. J. Chaplain, and K. A. Rejniak, Ed. Birkhäuser, Basel, Boston and Berlin, 79--106.
[4]
Swat, M. H., Hester, S. D., Balter, A. I., Heiland, R. W., Zaitlen, B. L., and Glazier, J. A. 2009. Multicell simulations of development and disease using the CompuCell3D simulation environment. In Systems Biology, I. V. Maly, Ed. volume 500 of Methods in Molecular Biology, pages 361--428. Humana Press, Clifton, N.J.
[5]
Graner, F. and Glazier, J. A. 1992. Simulation of Biological Cell Sorting Using a Two-Dimensional Extended Potts Model. Physical Review Letters 69, 2013--2016 (1992).
[6]
Callahan, S. P., Freire, J., Santos, E., Scheidegger, C. E., Silva, C. T., and Vo, H. T. 2006. VisTrails: visualization meets data management. In Proceedings of the 2006 ACM SIGMOD international Conference on Management of Data (Chicago, IL, USA, June 27--29, 2006). SIGMOD '06. ACM, New York, NY, 745--747. DOI= http://doi.acm.org/10.1145/1142473.1142574
[7]
Heiland R., Mooney, S. D., Boverhof, J., Jackson, K., Swat, M., Balter, A., Christie, M., and Insley, J. 2007. Python for Scientific Gateways Development. In Proceedings of the International Workshop on Grid Computing Environments, Reno, NV, November 2007.
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Information
Published In
April 2010
1726 pages
ISBN:9781450300698
- General Chairs:
- Robert McGraw,
- Eric Imsand,
- Program Chair:
- Michael J. Chinni
Sponsors
- SCS: Society for Modeling and Simulation International
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Publisher
Society for Computer Simulation International
San Diego, CA, United States
Publication History
Published: 11 April 2010
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Cited By
View all- Glazier J(2012)Visualizing cells and their connectivity graphs for CompuCell3DProceedings of the 2012 IEEE Symposium on Biological Data Visualization (BioVis)10.1109/BioVis.2012.6378597(85-90)Online publication date: 14-Oct-2012
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