Treffer: Introduction to Computational Modeling of Multicellular Tissues.
Title:
Introduction to Computational Modeling of Multicellular Tissues.
Authors:
Dinh JL; Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington, UK., Godin C; Virtual Plants Project-Team, Inria, CIRAD, INRA, Montpellier, France.; Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, Inria, Lyon, France., Azpeitia E; Virtual Plants Project-Team, Inria, CIRAD, INRA, Montpellier, France. eazpeitia@matmor.unam.mx.; Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, Inria, Lyon, France. eazpeitia@matmor.unam.mx.; Centro de Ciencias Matemáticas, Universidad Nacional Autónoma de México, Morelia, Mexico. eazpeitia@matmor.unam.mx.
Source:
Methods in molecular biology (Clifton, N.J.) [Methods Mol Biol] 2022; Vol. 2395, pp. 107-145.
Publication Type:
Journal Article
Language:
English
Journal Info:
Publisher: Humana Press Country of Publication: United States NLM ID: 9214969 Publication Model: Print Cited Medium: Internet ISSN: 1940-6029 (Electronic) Linking ISSN: 10643745 NLM ISO Abbreviation: Methods Mol Biol Subsets: MEDLINE
Imprint Name(s):
Publication: Totowa, NJ : Humana Press
Original Publication: Clifton, N.J. : Humana Press,
Original Publication: Clifton, N.J. : Humana Press,
MeSH Terms:
References:
Dufour-Kowalski S, Pradal C, Dones N et al (2007) OpenAlea: an open-source platform for the integration of heterogeneous FSPM components. Presented at the FSPM07—5th international workshop on functional-structural plant models, November 4.
Pradal C, Dufour-Kowalski S, Boudon F et al (2008) OpenAlea: a visual programming and component-based software platform for plant modelling. Funct Plant Biol 35:751. (PMID: 10.1071/FP08084)
Cokelaer T, Pradal C, Fournier C (2009) Plant modelling with Python components in OpenAlea, presented at the EuroSciPy.
Merks RMH, Guravage M, Inzé D et al (2011) VirtualLeaf: an open-source framework for cell-based modeling of plant tissue growth and development. Plant Physiol 155:656–666. (PMID: 10.1104/pp.110.167619)
Merks RMH, Glazier JA (2005) A cell-centered approach to developmental biology. Phys Stat Mech Appl 352:113–130. (PMID: 10.1016/j.physa.2004.12.028)
Swat MH, Thomas GL, Belmonte JM et al (2012) Chapter 13—multi-scale modeling of tissues using CompuCell3D. In: Arkin A, Asthagiri AR (eds) Methods in cell biology. Academic, pp 325–366. (PMID: 10.1016/B978-0-12-388403-9.00013-8)
Dinh J-L jldinh/multicell: Python library to run biological simulations of 3D, multicellular tissues. https://github.com/jldinh/multicell/.
Pradal C, Boudon F, Nouguier C et al (2009) PlantGL: a python-based geometric library for 3D plant modelling at different scales. Graph Models 71:1–21. (PMID: 10.1016/j.gmod.2008.10.001)
Ciarletta P, Hillen T, Othmer H et al (2017) Mathematical models and methods for living systems: levico Terme, Italy 2014. Springer, New York, NY.
Cerutti G, Ali O, Godin C (2017) DRACO-STEM: an automatic tool to generate high-quality 3D meshes of meristem tissue at cell resolution. Front Plant Sci 8:353. (PMID: 10.3389/fpls.2017.00353)
(2016) Openalea-components: openalea components, openalea.
Hill AV (1910) The possible effects of the aggregation of the molecules of haemoglobin on its dissociation curves. J Physiol 40:iv–vii.
Santillán M, Mackey MC (2008) A proposed mechanism for the interaction of the segmentation clock and the determination front in somitogenesis. PLoS One 3:e1561. (PMID: 10.1371/journal.pone.0001561)
Alon U (2006) An introduction to systems biology: design principles of biological circuits. CRC Press. (PMID: 10.1201/9781420011432)
Lander AD (2011) Pattern, growth, and control. Cell 144:955–969. (PMID: 10.1016/j.cell.2011.03.009)
Murray JD (2011) Mathematical biology: I. An introduction. Springer Science & Business Media.
Jönsson H, Heisler MG, Shapiro BE et al (2006) An auxin-driven polarized transport model for phyllotaxis. Proc Natl Acad Sci U S A 103:1633–1638. (PMID: 10.1073/pnas.0509839103)
Zažímalová E, Petrasek J, and Benková E (2014) Auxin and its role in plant development, Springer.
Turing AM (1952) The chemical basis of morphogenesis. Royal Society.
Gierer A, Meinhardt H (1972) A theory of biological pattern formation. Kybernetik 12:30–39. (PMID: 10.1007/BF00289234)
Meinhardt H, Gierer A (1974) Applications of a theory of biological pattern formation based on lateral inhibition. J Cell Sci 15:321–346. (PMID: 10.1242/jcs.15.2.321)
Meinhardt H (1982) Models of biological pattern formation. Academic Press.
Kondo S, Miura T (2010) Reaction-diffusion model as a framework for understanding biological pattern formation. Science 329:1616–1620. (PMID: 10.1126/science.1179047)
Garikipati K (2009) The kinematics of biological growth. Appl Mech Rev 62:030801. (PMID: 10.1115/1.3090829)
Konstankiewicz K, Zdunek A (2001) Influence of turgor and cell size on the cracking of potato tissue. Int Agrophysics 15:27–30.
Errera L (1886) Sur une condition fondamentale d’équilibre des cellules vivantes. Comptes Rendus Hebd Séances Académie Sci 103:822–824.
Eissing T, Kuepfer L, Becker C et al (2011) A computational systems biology software platform for multiscale modeling and simulation: integrating whole-body physiology, disease biology, and molecular reaction networks. Front Physiol 2:4. (PMID: 10.3389/fphys.2011.00004)
Meier-Schellersheim M, Mack G (1999) SIMMUNE, a tool for simulating and analyzing immune system behavior.
Meier-Schellersheim M, Xu X, Angermann B et al (2006) Key role of local regulation in chemosensing revealed by a new molecular interaction-based modeling method. PLoS Comput Biol:2, e82.
Meier-Schellersheim M, Fraser IDC, Klauschen F (2009) Multi-scale modeling in cell biology. Wiley Interdiscip Rev Syst Biol Med 1:4–14. (PMID: 10.1002/wsbm.33)
Walpole J, Papin JA, Peirce SM (2013) Multiscale computational models of complex biological systems. Annu Rev Biomed Eng 15:137–154. (PMID: 10.1146/annurev-bioeng-071811-150104)
https://www.wiley.com/en-ai/Introduction+to+Stochastic+Differential+Equations+with+Applications+to+Modelling+in+Biology+and+Finance-p-9781119166061.
Kauffman SA (1969) Metabolic stability and epigenesis in randomly constructed genetic nets. J Theor Biol 22:437–467. (PMID: 10.1016/0022-5193(69)90015-0)
Ingalls BP (2012) Mathematical modelling in systems biology: an introduction. The MIT Press.
https://www.taylorfrancis.com/books/mono/10.1201/9780429283321/introduction-systems-biology-uri-alon.
https://pubmed.ncbi.nlm.nih.gov/11911796/.
Sun J, Garibaldi JM, Hodgman C (2012) Parameter estimation using meta-heuristics in systems biology: a comprehensive review. IEEE/ACM Trans Comput Biol Bioinform 9:185–202. (PMID: 10.1109/TCBB.2011.67)
https://iopscience.iop.org/article/10.1088/0266-5611/25/12/123014/meta.
https://pubmed.ncbi.nlm.nih.gov/29119503/.
Boudon F, Chopard J, Ali O et al (2015) A computational framework for 3D mechanical modeling of plant morphogenesis with cellular resolution. PLoS Comput Biol 11:e1003950. (PMID: 10.1371/journal.pcbi.1003950)
Berthold G (1886) Studien über protoplasmamechanik. A Felix.
Thompson DW (1942) On growth and form. Cambridge University Press.
Pradal C, Dufour-Kowalski S, Boudon F et al (2008) OpenAlea: a visual programming and component-based software platform for plant modelling. Funct Plant Biol 35:751. (PMID: 10.1071/FP08084)
Cokelaer T, Pradal C, Fournier C (2009) Plant modelling with Python components in OpenAlea, presented at the EuroSciPy.
Merks RMH, Guravage M, Inzé D et al (2011) VirtualLeaf: an open-source framework for cell-based modeling of plant tissue growth and development. Plant Physiol 155:656–666. (PMID: 10.1104/pp.110.167619)
Merks RMH, Glazier JA (2005) A cell-centered approach to developmental biology. Phys Stat Mech Appl 352:113–130. (PMID: 10.1016/j.physa.2004.12.028)
Swat MH, Thomas GL, Belmonte JM et al (2012) Chapter 13—multi-scale modeling of tissues using CompuCell3D. In: Arkin A, Asthagiri AR (eds) Methods in cell biology. Academic, pp 325–366. (PMID: 10.1016/B978-0-12-388403-9.00013-8)
Dinh J-L jldinh/multicell: Python library to run biological simulations of 3D, multicellular tissues. https://github.com/jldinh/multicell/.
Pradal C, Boudon F, Nouguier C et al (2009) PlantGL: a python-based geometric library for 3D plant modelling at different scales. Graph Models 71:1–21. (PMID: 10.1016/j.gmod.2008.10.001)
Ciarletta P, Hillen T, Othmer H et al (2017) Mathematical models and methods for living systems: levico Terme, Italy 2014. Springer, New York, NY.
Cerutti G, Ali O, Godin C (2017) DRACO-STEM: an automatic tool to generate high-quality 3D meshes of meristem tissue at cell resolution. Front Plant Sci 8:353. (PMID: 10.3389/fpls.2017.00353)
(2016) Openalea-components: openalea components, openalea.
Hill AV (1910) The possible effects of the aggregation of the molecules of haemoglobin on its dissociation curves. J Physiol 40:iv–vii.
Santillán M, Mackey MC (2008) A proposed mechanism for the interaction of the segmentation clock and the determination front in somitogenesis. PLoS One 3:e1561. (PMID: 10.1371/journal.pone.0001561)
Alon U (2006) An introduction to systems biology: design principles of biological circuits. CRC Press. (PMID: 10.1201/9781420011432)
Lander AD (2011) Pattern, growth, and control. Cell 144:955–969. (PMID: 10.1016/j.cell.2011.03.009)
Murray JD (2011) Mathematical biology: I. An introduction. Springer Science & Business Media.
Jönsson H, Heisler MG, Shapiro BE et al (2006) An auxin-driven polarized transport model for phyllotaxis. Proc Natl Acad Sci U S A 103:1633–1638. (PMID: 10.1073/pnas.0509839103)
Zažímalová E, Petrasek J, and Benková E (2014) Auxin and its role in plant development, Springer.
Turing AM (1952) The chemical basis of morphogenesis. Royal Society.
Gierer A, Meinhardt H (1972) A theory of biological pattern formation. Kybernetik 12:30–39. (PMID: 10.1007/BF00289234)
Meinhardt H, Gierer A (1974) Applications of a theory of biological pattern formation based on lateral inhibition. J Cell Sci 15:321–346. (PMID: 10.1242/jcs.15.2.321)
Meinhardt H (1982) Models of biological pattern formation. Academic Press.
Kondo S, Miura T (2010) Reaction-diffusion model as a framework for understanding biological pattern formation. Science 329:1616–1620. (PMID: 10.1126/science.1179047)
Garikipati K (2009) The kinematics of biological growth. Appl Mech Rev 62:030801. (PMID: 10.1115/1.3090829)
Konstankiewicz K, Zdunek A (2001) Influence of turgor and cell size on the cracking of potato tissue. Int Agrophysics 15:27–30.
Errera L (1886) Sur une condition fondamentale d’équilibre des cellules vivantes. Comptes Rendus Hebd Séances Académie Sci 103:822–824.
Eissing T, Kuepfer L, Becker C et al (2011) A computational systems biology software platform for multiscale modeling and simulation: integrating whole-body physiology, disease biology, and molecular reaction networks. Front Physiol 2:4. (PMID: 10.3389/fphys.2011.00004)
Meier-Schellersheim M, Mack G (1999) SIMMUNE, a tool for simulating and analyzing immune system behavior.
Meier-Schellersheim M, Xu X, Angermann B et al (2006) Key role of local regulation in chemosensing revealed by a new molecular interaction-based modeling method. PLoS Comput Biol:2, e82.
Meier-Schellersheim M, Fraser IDC, Klauschen F (2009) Multi-scale modeling in cell biology. Wiley Interdiscip Rev Syst Biol Med 1:4–14. (PMID: 10.1002/wsbm.33)
Walpole J, Papin JA, Peirce SM (2013) Multiscale computational models of complex biological systems. Annu Rev Biomed Eng 15:137–154. (PMID: 10.1146/annurev-bioeng-071811-150104)
https://www.wiley.com/en-ai/Introduction+to+Stochastic+Differential+Equations+with+Applications+to+Modelling+in+Biology+and+Finance-p-9781119166061.
Kauffman SA (1969) Metabolic stability and epigenesis in randomly constructed genetic nets. J Theor Biol 22:437–467. (PMID: 10.1016/0022-5193(69)90015-0)
Ingalls BP (2012) Mathematical modelling in systems biology: an introduction. The MIT Press.
https://www.taylorfrancis.com/books/mono/10.1201/9780429283321/introduction-systems-biology-uri-alon.
https://pubmed.ncbi.nlm.nih.gov/11911796/.
Sun J, Garibaldi JM, Hodgman C (2012) Parameter estimation using meta-heuristics in systems biology: a comprehensive review. IEEE/ACM Trans Comput Biol Bioinform 9:185–202. (PMID: 10.1109/TCBB.2011.67)
https://iopscience.iop.org/article/10.1088/0266-5611/25/12/123014/meta.
https://pubmed.ncbi.nlm.nih.gov/29119503/.
Boudon F, Chopard J, Ali O et al (2015) A computational framework for 3D mechanical modeling of plant morphogenesis with cellular resolution. PLoS Comput Biol 11:e1003950. (PMID: 10.1371/journal.pcbi.1003950)
Berthold G (1886) Studien über protoplasmamechanik. A Felix.
Thompson DW (1942) On growth and form. Cambridge University Press.
Contributed Indexing:
Keywords: Computational biology; Gene networks; Multiscale models; Pattern formation; Tissue modeling
Entry Date(s):
Date Created: 20211125 Date Completed: 20220121 Latest Revision: 20220121
Update Code:
20250114
DOI:
10.1007/978-1-0716-1816-5_7
PMID:
34822152
Database:
MEDLINE
Weitere Informationen
The study of biological tissues is extremely complicated, as they comprise mechanisms and properties at many different temporal and spatial scales. For this reason, modeling is becoming one of the most active and important research fields for the analysis and understanding of tissues. However, this is not a simple task, as it requires mathematical and computational skills, as well as the development of software tools for its implementation. Here, we provide an introduction covering some of the most important and basic issues for modeling tissues. In particular, we focus on both the chemical and cellular properties of a tissue. We explain how to represent and couple these properties within a virtual tissue. All our examples were done using Multicell, a Python library that simplifies their reproducibility, even by readers with little experience in biological modeling.
(© 2022. Springer Science+Business Media, LLC, part of Springer Nature.)