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== CompuCell3D - Based Simulations ==
[[links/index.php?id=35|Mathematical modeling of the capillary-like pattern generated by adrenomedullin-treated human vascular endothelial cells in vitro]] Diego Guidolin , Giovanna Albertin , Elisa Sorato , Barbara Oselladore , Alessandra Mascarin , Domenico Ribatti		 === CompuCell3D - Based Simulations ===
[[links/index.php?id=35|Mathematical modeling of the capillary-like pattern generated by adrenomedullin-treated human vascular endothelial cells in vitro]]  Diego Guidolin , Giovanna Albertin , Elisa Sorato , Barbara Oselladore , Alessandra Mascarin , Domenico Ribatti
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[[links/index.php?id=29|Simulation of Single-Species Bacterial-Biofilm Growth Using the Glazier-Graner-Hogeweg Model and the CompuCell3D Modeling Environment]] Nikodem J. Popawski, Abbas Shirinifard, Maciej Swat, and James A. Glazier, [[links/index.php?id=29|Simulation of Single-Species Bacterial-Biofilm Growth Using the Glazier-Graner-Hogeweg Model and the CompuCell3D Modeling Environment]]  Nikodem J. Popawski, Abbas Shirinifard, Maciej Swat, and James A. Glazier, ''Mathematical biosciences and engineering 5, 355-388 (2008)''
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''Mathematical biosciences and engineering 5, 355-388 (2008)'' [[links/index.php?id=30|Discovering Novel Cancer Therapies: A Computational Modeling and Search Approach]] Mahoney A. W., Smith B. G., Flann N. S., and Podgorski G. J., ''IEEE conference on Computational Intelligence in Bioinformatics and Bioengineering, (2008)''
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[[links/index.php?id=30|Discovering Novel Cancer Therapies: A Computational Modeling and Search Approach]] Mahoney A. W., Smith B. G., Flann N. S., and Podgorski G. J.,

''IEEE conference on Computational Intelligence in Bioinformatics and Bioengineering, (2008)''

[[links/index.php?id=28|Adhesion Between Cells, Diffusion of Growth Factors, and Elasticity of the AER Produce the Paddle Shape of the Chick Limb]] Nikodem J. PopÅ‚awski, Maciej Swat, J. Scott Gens and James A. Glazier,		 [[links/index.php?id=28|Adhesion Between Cells, Diffusion of Growth Factors, and Elasticity of the AER Produce the Paddle Shape of the Chick Limb]]  Nikodem J. PopÅ‚awski, Maciej Swat, J. Scott Gens and James A. Glazier,
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[[links/index.php?id=26|Dynamical Mechanisms For Skeletal Pattern Formation in the Vertebrate Limb]] H G E Hentschel, T Glimm, J A Glazier, S A Newman, ''Proc Biol Sci. 271, 1713–1722 (2004)'' [[links/index.php?id=26|Dynamical Mechanisms For Skeletal Pattern Formation in the Vertebrate Limb]]  H G E Hentschel, T Glimm, J A Glazier, S A Newman,  ''Proc Biol Sci. 271, 1713–1722 (2004)''
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[[links/index.php?id=27|A Hybrid Discrete-Continuum Model for 3D Skeletogenesis of the Vertebrate Limb]] R. Chaturvedi, C. Huang, J. A. Izaguirre, S. A. Newman, J. A. Glazier [[links/index.php?id=27|A Hybrid Discrete-Continuum Model for 3D Skeletogenesis of the Vertebrate Limb]]  R. Chaturvedi, C. Huang, J. A. Izaguirre, S. A. Newman, J. A. Glazier ''Lecture Notes in Computer Science 3305, 543-552 (2004)''
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''Lecture Notes in Computer Science 3305, 543-552 (2004)''

== CompuCell3D Framework ==		 === CompuCell3D Framework ===
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[[links/index.php?id=20|A Framework For Three-Dimensional Simulation of Morphogenesis]]
Trevor M. Cickovski, Chengbang Huang, Rajiv Chaturvedi, Tilmann Glimm, H. George E. Hentschel, Mark S. Alber, James A. Glazier, Stuart A. Newman, Jesus A. Izaguirre,
''IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), 2, 273-288 (2005)''		 [[links/index.php?id=20|A Framework For Three-Dimensional Simulation of Morphogenesis]] Trevor M. Cickovski, Chengbang Huang, Rajiv Chaturvedi, Tilmann Glimm, H. George E. Hentschel, Mark S. Alber, James A. Glazier, Stuart A. Newman, Jesus A. Izaguirre, ''IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), 2, 273-288 (2005)''
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[[links/index.php?id=22|On Multiscale Approaches to Three-Dimensional Modeling of Morphogenesis]]
R. Chaturvedi, C. Huang, B. Kazmierczak, T. Schneider, J. A. Izaguirre, T. Glimm, H. G. E. Hentschel, S. A. Newman, J. A. Glazier, M. Alber,
''Journal of The Royal Society Interface 2, 237-253 (2005)'' 		 [[links/index.php?id=22|On Multiscale Approaches to Three-Dimensional Modeling of Morphogenesis]]  R. Chaturvedi, C. Huang, B. Kazmierczak, T. Schneider, J. A. Izaguirre, T. Glimm, H. G. E. Hentschel, S. A. Newman, J. A. Glazier, M. Alber,  ''Journal of The Royal Society Interface 2, 237-253 (2005)''
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[[links/index.php?id=23|A Cell-Centered Approach to Developmental Biology]]
Roeland M.H. Merks, and James A. Glazier,
''Physica A: Statistical Mechanics and its Applications 352, 113-130 (2005)'' 		 [[links/index.php?id=23|A Cell-Centered Approach to Developmental Biology]] Roeland M.H. Merks, and James A. Glazier,  ''Physica A: Statistical Mechanics and its Applications 352, 113-130 (2005)''
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[[links/index.php?id=25|Empirical Evaluation of Design Patterns in Scientific Application]]
Kedar Aras, ''Master's Thesis, Dept. of Computer Science & Eng., Univ. of Notre Dame (2005)''		 [[links/index.php?id=25|Empirical Evaluation of Design Patterns in Scientific Application]]  Kedar Aras, ''Master's Thesis, Dept. of Computer Science & Eng., Univ. of Notre Dame (2005)''
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[[links/index.php?id=21|CompuCell, a Multi-Model Framework For Simulation of Morphogenesis]]
J. A. Izaguirre, R. Chaturvedi, C. Huang, T. Cickovski, J. Coffland, G. Thomas, G. Forgacs, M. Alber, G. Hentschel, S. A. Newman, and J. A. Glazier,
''Bioinformatics 20, 1129-1137 (2004)''		 [[links/index.php?id=21|CompuCell, a Multi-Model Framework For Simulation of Morphogenesis]]  J. A. Izaguirre, R. Chaturvedi, C. Huang, T. Cickovski, J. Coffland, G. Thomas, G. Forgacs, M. Alber, G. Hentschel, S. A. Newman, and J. A. Glazier,  ''Bioinformatics 20, 1129-1137 (2004)''
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[[links/index.php?id=24|BIOLOGO: A Domain-Specific Language For Morphogenesis]]
Trevor M. Cickovski,
''Master’s Thesis, Dept. of Computer Science & Eng., Univ. of Notre Dame (2004)''		 [[links/index.php?id=24|BIOLOGO: A Domain-Specific Language For Morphogenesis]] Trevor M. Cickovski,  ''Master’s Thesis, Dept. of Computer Science & Eng., Univ. of Notre Dame (2004)''
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[[links/index.php?cat=talks|Recent Talks]][[links/index.php?cat=biological|Biological Modeling]]  [[links/index.php?cat=talks|Recent Talks]][[links/index.php?cat=biological|Biological Modeling]]
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[[links/index.php?cat=physical|Physical Modeling]] 
[[links/index.php?cat=physical|Physical Modeling]]
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CompuCell3D - Based Simulations

Mathematical modeling of the capillary-like pattern generated by adrenomedullin-treated human vascular endothelial cells in vitro Diego Guidolin , Giovanna Albertin , Elisa Sorato , Barbara Oselladore , Alessandra Mascarin , Domenico Ribatti

Simulation of Single-Species Bacterial-Biofilm Growth Using the Glazier-Graner-Hogeweg Model and the CompuCell3D Modeling Environment Nikodem J. Popawski, Abbas Shirinifard, Maciej Swat, and James A. Glazier, Mathematical biosciences and engineering 5, 355-388 (2008)

Discovering Novel Cancer Therapies: A Computational Modeling and Search Approach Mahoney A. W., Smith B. G., Flann N. S., and Podgorski G. J., IEEE conference on Computational Intelligence in Bioinformatics and Bioengineering, (2008)

Adhesion Between Cells, Diffusion of Growth Factors, and Elasticity of the AER Produce the Paddle Shape of the Chick Limb Nikodem J. Popławski, Maciej Swat, J. Scott Gens and James A. Glazier,

Physica A: Statistical and Theoretical Physics 373, 521-532 (2007)

Dynamical Mechanisms For Skeletal Pattern Formation in the Vertebrate Limb H G E Hentschel, T Glimm, J A Glazier, S A Newman, Proc Biol Sci. 271, 1713–1722 (2004)

A Hybrid Discrete-Continuum Model for 3D Skeletogenesis of the Vertebrate Limb R. Chaturvedi, C. Huang, J. A. Izaguirre, S. A. Newman, J. A. Glazier Lecture Notes in Computer Science 3305, 543-552 (2004)

CompuCell3D Framework

From Genes to Organisms Via the Cell: A Problem-Solving Environment for Multicellular Development

Trevor Cickovski, Kedar Aras, Maciej Swat, Roeland M. H. Merks, Tilmann Glimm, H. George E. Hentschel, Mark S. Alber, James A. Glazier, Stuart A. Newman, Jes A. Izaguirre

Computing in Science and Engineering, 9, 50-60 (2007)

A Framework For Three-Dimensional Simulation of Morphogenesis Trevor M. Cickovski, Chengbang Huang, Rajiv Chaturvedi, Tilmann Glimm, H. George E. Hentschel, Mark S. Alber, James A. Glazier, Stuart A. Newman, Jesus A. Izaguirre, IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), 2, 273-288 (2005)

On Multiscale Approaches to Three-Dimensional Modeling of Morphogenesis R. Chaturvedi, C. Huang, B. Kazmierczak, T. Schneider, J. A. Izaguirre, T. Glimm, H. G. E. Hentschel, S. A. Newman, J. A. Glazier, M. Alber, Journal of The Royal Society Interface 2, 237-253 (2005)

A Cell-Centered Approach to Developmental Biology Roeland M.H. Merks, and James A. Glazier, Physica A: Statistical Mechanics and its Applications 352, 113-130 (2005)

Empirical Evaluation of Design Patterns in Scientific Application Kedar Aras, Master's Thesis, Dept. of Computer Science & Eng., Univ. of Notre Dame (2005)

CompuCell, a Multi-Model Framework For Simulation of Morphogenesis J. A. Izaguirre, R. Chaturvedi, C. Huang, T. Cickovski, J. Coffland, G. Thomas, G. Forgacs, M. Alber, G. Hentschel, S. A. Newman, and J. A. Glazier, Bioinformatics 20, 1129-1137 (2004)

BIOLOGO: A Domain-Specific Language For Morphogenesis Trevor M. Cickovski, Master’s Thesis, Dept. of Computer Science & Eng., Univ. of Notre Dame (2004)

Recent TalksBiological Modeling

  • Differential Adhesion and Cell Sorting

  • Limb Development

  • Tumor and Cancer

  • Angiogenesis/Vasculogenesis

  • Biofilms

Physical Modeling

  • Soap Foams and Liquid Foams

Simulations Using GGH/CPM ApproachGeneral Background on Biophysical Modeling and Development

CompuCell3D: Publications (last edited 2026-06-08 16:40:39 by jpSluka)