CompuCell3D|
Size: 4298
Comment:
|
Size: 5705
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 === [[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0024999|Computer Simulations of Cell Sorting Due to Differential Adhesion]] Ying Zhang, Gilberto L. Thomas, Maciej Swat, Abbas Shirinifard, James A. Glazier. ''PLoS One'' (2011) |
| Line 4: | Line 4: |
| [[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, | [[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002155|A Multi-cell, Multi-scale Model of Vertebrate Segmentation and Somite Formation]] Susan D. Hester, Julio M. Belmonte, J. Scott Gens, Sherry G. Clendenon, James A. Glazier. ''PLoS Computational Biology'' (2011) [The model and a [[Models/BelmonteHesterSomite|movie]] are available] |
| Line 6: | Line 6: |
| ''Mathematical biosciences and engineering 5, 355-388 (2008)'' | [[Cc3dPaper0|Evolution and morphogenesis of differentiated multicellular organisms: autonomously generated diffusion gradients for positional information.]] Knabe, J.F., Nehaniv, C.L., Schilstra, M.J. ''Artificial Life XI: Proceedings of the Eleventh International Conference on the Simulation and Synthesis of Living Systems, pp. 321–328. MIT Press, Cambridge (2008)'' |
| Line 8: | Line 8: |
| [[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., | [[http://old.compucell3d.org/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 10: | Line 10: |
| ''IEEE conference on Computational Intelligence in Bioinformatics and Bioengineering, (2008)'' | [[http://old.compucell3d.org/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 12: | Line 12: |
| [[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, | [[http://old.compucell3d.org/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 14: | Line 14: |
| ''Physica A: Statistical and Theoretical Physics 373, 521-532 (2007)'' | [[http://old.compucell3d.org/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, ''Physica A: Statistical and Theoretical Physics 373, 521-532 (2007)'' |
| Line 16: | Line 16: |
| [[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)'' | [[http://old.compucell3d.org/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 18: |
| [[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 | [[http://old.compucell3d.org/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 20: | Line 20: |
| ''Lecture Notes in Computer Science 3305, 543-552 (2004)'' == CompuCell3D Framework == [[links/index.php?id=18|From Genes to Organisms Via the Cell: A Problem-Solving Environment for Multicellular Development]] |
=== CompuCell3D Framework === [[http://old.compucell3d.org/links/index.php?id=18|From Genes to Organisms Via the Cell: A Problem-Solving Environment for Multicellular Development]] |
| Line 29: | Line 27: |
| [[links/index.php?id=20|A Framework For Three-Dimensional Simulation of Morphogenesis]] | [[http://old.compucell3d.org/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 29: |
| 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, | [[http://old.compucell3d.org/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 31: |
| ''IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), 2, 273-288 (2005'''')'' | [[http://old.compucell3d.org/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 33: |
| [[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)'' | [[http://old.compucell3d.org/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 35: |
| [[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)'' | [[http://old.compucell3d.org/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 37: |
| '' ''[[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)'' | [[http://old.compucell3d.org/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 41: | Line 39: |
| [[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)'' | === Related Links === [[http://old.compucell3d.org/links/index.php?cat=talks|Recent Talks]] |
| Line 43: | Line 42: |
| [[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)'' | [[http://old.compucell3d.org/links/index.php?cat=biological|Biological Modeling]] |
| Line 45: | Line 44: |
| == Related Links == [[links/index.php?cat=talks|Recent Talks]][[links/index.php?cat=biological|Biological Modeling]] * Differential Adhesion and Cell Sorting |
* Differential Adhesion and Cell Sorting * '''Limb Development ''' * '''Tumor and Cancer ''' * '''Angiogenesis/Vasculogenesis ''' * '''Biofilms ''' |
| Line 48: | Line 50: |
| * Limb Development * Tumor and Cancer * Angiogenesis/Vasculogenesis * Biofilms |
[[http://old.compucell3d.org/links/index.php?cat=physical|Physical Modeling]] |
| Line 53: | Line 52: |
| [[links/index.php?cat=physical|Physical Modeling]] * Soap Foams and Liquid Foams | * Soap Foams and Liquid Foams |
| Line 55: | Line 54: |
| [[links/index.php?cat=simulations|Simulations Using GGH/CPM Approach]][[links/index.php?cat=background|General Background on Biophysical Modeling and Development]] | [[http://old.compucell3d.org/links/index.php?cat=simulations|Simulations Using GGH/CPM Approach]] [[http://old.compucell3d.org/links/index.php?cat=background|General Background on Biophysical Modeling and Development]] |
CompuCell3D - Based Simulations
Computer Simulations of Cell Sorting Due to Differential Adhesion Ying Zhang, Gilberto L. Thomas, Maciej Swat, Abbas Shirinifard, James A. Glazier. PLoS One (2011)
A Multi-cell, Multi-scale Model of Vertebrate Segmentation and Somite Formation Susan D. Hester, Julio M. Belmonte, J. Scott Gens, Sherry G. Clendenon, James A. Glazier. PLoS Computational Biology (2011) [The model and a movie are available]
Evolution and morphogenesis of differentiated multicellular organisms: autonomously generated diffusion gradients for positional information. Knabe, J.F., Nehaniv, C.L., Schilstra, M.J. Artificial Life XI: Proceedings of the Eleventh International Conference on the Simulation and Synthesis of Living Systems, pp. 321–328. MIT Press, Cambridge (2008)
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
- Differential Adhesion and Cell Sorting
Limb Development
Tumor and Cancer
Angiogenesis/Vasculogenesis
Biofilms
- Soap Foams and Liquid Foams