CompuCell3D|
Size: 4298
Comment:
|
Size: 4214
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 1: | Line 1: |
| == 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 |
| Line 4: | Line 3: |
| [[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=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 |
| Line 6: | Line 5: |
| ''Mathematical biosciences and engineering 5, 355-388 (2008)'' | [[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)'' |
| Line 8: | Line 7: |
| [[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., | [[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)'' |
| Line 10: | Line 9: |
| ''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. Popławski, 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. Popławski, Maciej Swat, J. Scott Gens and James A. Glazier, |
| Line 16: | Line 13: |
| [[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)'' |
| Line 18: | Line 15: |
| [[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)'' |
[[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)'' |
| Line 29: | Line 24: |
| [[links/index.php?id=20|A Framework For Three-Dimensional Simulation of Morphogenesis]] | [[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)'' |
| Line 31: | Line 26: |
| 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, | [[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)'' |
| Line 33: | Line 28: |
| ''IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), 2, 273-288 (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)'' |
| Line 35: | Line 30: |
| [[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=25|Empirical Evaluation of Design Patterns in Scientific Application]] Kedar Aras, ''Master's Thesis, Dept. of Computer Science & Eng., Univ. of Notre Dame (2005)'' |
| Line 37: | Line 32: |
| [[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=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)'' |
| Line 39: | Line 34: |
| '' ''[[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=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=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)'' |
| Line 46: | Line 37: |
| [[links/index.php?cat=talks|Recent Talks]][[links/index.php?cat=biological|Biological Modeling]] * Differential Adhesion and Cell Sorting | [[links/index.php?cat=talks|Recent Talks]][[links/index.php?cat=biological|Biological Modeling]] |
| Line 48: | Line 39: |
| * Limb Development * Tumor and Cancer * Angiogenesis/Vasculogenesis * Biofilms |
* Differential Adhesion and Cell Sorting * '''Limb Development ''' * '''Tumor and Cancer ''' * '''Angiogenesis/Vasculogenesis ''' * '''Biofilms ''' |
| Line 53: | Line 45: |
| [[links/index.php?cat=physical|Physical Modeling]] * Soap Foams and Liquid Foams | [[links/index.php?cat=physical|Physical Modeling]] * Soap Foams and Liquid Foams |
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)
Related Links
Recent TalksBiological Modeling
- Differential Adhesion and Cell Sorting
Limb Development
Tumor and Cancer
Angiogenesis/Vasculogenesis
Biofilms
- Soap Foams and Liquid Foams
Simulations Using GGH/CPM ApproachGeneral Background on Biophysical Modeling and Development