From Genes to Organisms Via the Cell: A Problem-Solving Environment for Multicellular Development
Trevor Cickovski,Kedar Aras,M. Swat,Roeland M. H. Merks,Tilmann Glimm,H. George E. Hentschel,Mark Alber,James A. Glazier,Stuart A. Newman,Jesús A. Izaguirre +9 more
TLDR
CompuCell3D is presented, a multitiered, flexible, and scalable problem-solving environment for morphogenesis simulations that's written in C++ using object-oriented design patterns.Abstract:
To gain performance, developers often build scientific applications in procedural languages, such as C or Fortran, which unfortunately reduces flexibility. To address this imbalance, the authors present CompuCell3D, a multitiered, flexible, and scalable problem-solving environment for morphogenesis simulations that's written in C++ using object-oriented design patterns.read more
Citations
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Journal ArticleDOI
Chaste: an open source C++ library for computational physiology and biology.
Gary R. Mirams,Christopher J. Arthurs,Miguel O. Bernabeu,Rafel Bordas,Jonathan Cooper,Alberto Corrias,Yohan Davit,Sara-Jane Dunn,Alexander G. Fletcher,Daniel G. Harvey,Megan E. Marsh,James M. Osborne,Pras Pathmanathan,Pras Pathmanathan,Joe Pitt-Francis,James Southern,Nejib Zemzemi,David J. Gavaghan +17 more
TL;DR: Chaste as mentioned in this paper is an open source C++ library for the computational simulation of mathematical models developed for physiology and biology, such as cardiac electrophysiology and cancer development, which can be used to solve a wide range of problems.
Book ChapterDOI
Multi-Scale Modeling of Tissues Using CompuCell3D
Maciej Swat,Gilberto L. Thomas,Gilberto L. Thomas,Julio M. Belmonte,Abbas Shirinifard,Dimitrij Hmeljak,James A. Glazier +6 more
TL;DR: This tutorial introduces the lattice-based Glazier-Graner-Hogeweg (GGH) Monte Carlo multi-cell modeling and the open-source GGH-based CompuCell3D simulation environment that allows rapid and intuitive modeling and simulation of cellular and multi- cellular behaviors in the context of tissue formation and subsequent dynamics.
Journal ArticleDOI
A multiscale model of thrombus development.
TL;DR: Simulation results demonstrate the development of an inhomogeneous internal structure of the thrombus, which is confirmed by the preliminary experimental data and makes predictions about different stages inThrombus development, which can be tested experimentally and suggest specific experiments.
Journal ArticleDOI
VirtualLeaf: An Open-Source Framework for Cell-Based Modeling of Plant Tissue Growth and Development
TL;DR: This work presents a step-by-step introduction to building models with VirtualLeaf, providing basic example models of leaf venation and meristem development and a set of biologically intuitive C++ objects that provide useful abstractions for building biological simulations of developmental processes.
Journal ArticleDOI
Study of blood flow impact on growth of thrombi using a multiscale model
Zhiliang Xu,Nan Chen,Shawn C. Shadden,Jerrold E. Marsden,Malgorzata M. Kamocka,Elliot D. Rosen,Mark Alber +6 more
TL;DR: An extended multiscale model is introduced for studying the formation of platelet thrombi in blood vessels and simulations indicate that increase in flow rates leads to greater structural heterogeneity of the clot.
References
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Book
Design Patterns: Elements of Reusable Object-Oriented Software
TL;DR: The book is an introduction to the idea of design patterns in software engineering, and a catalog of twenty-three common patterns, which most experienced OOP designers will find out they've known about patterns all along.
Journal ArticleDOI
Simulation of biological cell sorting using a two-dimensional extended Potts model.
François Graner,James A. Glazier +1 more
TL;DR: This work simulates the sorting of a mixture of two types of biological cells using a modified version of the large-Q Potts model with differential adhesivity and finds long-distance cell movement leading to sorting with a logarithmic increase in the length scale of homogeneous clusters.
Journal ArticleDOI
Simulation of the differential adhesion driven rearrangement of biological cells
James A. Glazier,François Graner +1 more
TL;DR: Simulation of the differential adhesion driven rearrangement of biological cells shows that self-organization due to few basic cell properties alone are enough to explain a number of biological phenomena.
Journal ArticleDOI
Percolation, Morphogenesis, and Burgers Dynamics in Blood Vessels Formation
Andrea Antonio Gamba,Davide Carlo Ambrosi,Antonio Coniglio,A. de Candia,S. Di Talia,Enrico Giraudo,Guido Serini,Luigi Preziosi,Federico Bussolino +8 more
TL;DR: A simple model is proposed which reproduces many features of the biological system and shows that both the model and the real system exhibit a fractal behavior at small scales, followed at large scale by a random percolation behavior due to the coalescence of aggregates.
Journal ArticleDOI
A cell-centered approach to developmental biology
TL;DR: A cell-centered approach to developmental biology Why can / should we use the potts model as discussed by the authors, and how to use the Potts model in the context of developmental biology.
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