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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 |
= Publications, Talks, and Links = |
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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, | === Recent Publications === |
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| ''Mathematical biosciences and engineering 5, 355-388 (2008)'' | [[http://www.sciencedirect.com/science/article/pii/B9780123884039000138|Multi-Scale Modeling of Tissues Using CompuCell3D]] - [[http://biocomplexity.indiana.edu/people/?p=staff|M.Swat]], [[http://www.if.ufrgs.br/pos/portugues/thomas.html|G.Thomas]], [[J.Belmonte|http://biocomplexity.indiana.edu/people/?p=students]], [[http://biocomplexity.indiana.edu/people/?p=staff|A.Shirinifard]], [[http://www.indiana.edu/~iubphys/faculty/mitja.shtml|D.Hmeljak]] and [[http://biocomplexity.indiana.edu/jglazier/|J.Glazier]]. "Computational Methods in Cell Biology, Methods in Cell Biology 110, 325-366" (2012) |
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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., | === 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) |
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| ''IEEE conference on Computational Intelligence in Bioinformatics and Bioengineering, (2008)'' | [[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 [[Models/BelmonteHesterSomite|model]] and a [[Models/BelmonteHesterSomite|movie]] are available] |
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| [[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, | [[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)'' |
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| ''Physica A: Statistical and Theoretical Physics 373, 521-532 (2007)'' | [[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 |
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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)'' | [[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)'' |
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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 | [[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)'' |
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| ''Lecture Notes in Computer Science 3305, 543-552 (2004)'' | [[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)'' |
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| == CompuCell3D Framework == [[links/index.php?id=18|From Genes to Organisms Via the Cell: A Problem-Solving Environment for Multicellular Development]] |
[[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)'' [[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)'' === 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]] |
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| [[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)'' |
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| 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)'' |
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| ''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)'' |
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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)'' | [[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)'' |
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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)'' | [[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)'' |
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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)'' | [[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)'' |
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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)'' | === Related Links === [[http://old.compucell3d.org/links/index.php?cat=talks|Recent Talks]] |
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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)'' | [[http://old.compucell3d.org/links/index.php?cat=biological|Biological Modeling]] |
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| == 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 ''' |
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| * Limb Development * Tumor and Cancer * Angiogenesis/Vasculogenesis * Biofilms |
[[http://old.compucell3d.org/links/index.php?cat=physical|Physical Modeling]] |
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| [[links/index.php?cat=physical|Physical Modeling]] * Soap Foams and Liquid Foams | * Soap Foams and Liquid Foams |
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| [[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]] |
Publications, Talks, and Links
Recent Publications
Multi-Scale Modeling of Tissues Using CompuCell3D - M.Swat, G.Thomas, http://biocomplexity.indiana.edu/people/?p=students, A.Shirinifard, D.Hmeljak and J.Glazier. "Computational Methods in Cell Biology, Methods in Cell Biology 110, 325-366" (2012)
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