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Morpheus: a user-friendly modeling environment for multiscale and multicellular systems biology

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Bioinformatics

Oxford University Press

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      Abstract

      Summary: Morpheus is a modeling environment for the simulation and integration of cell-based models with ordinary differential equations and reaction-diffusion systems. It allows rapid development of multiscale models in biological terms and mathematical expressions rather than programming code. Its graphical user interface supports the entire workflow from model construction and simulation to visualization, archiving and batch processing.Availability and implementation: Binary packages are available at http://imc.zih.tu-dresden.de/wiki/morpheus for Linux, Mac OSX and MS Windows.Contact: walter.deback@tu-dresden.deSupplementary information: Supplementary data are available at Bioinformatics online.

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      Most cited references 12

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      Simulation of biological cell sorting using a two-dimensional extended Potts model.

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        Chaste: An Open Source C++ Library for Computational Physiology and Biology

        Chaste — Cancer, Heart And Soft Tissue Environment — is an open source C++ library for the computational simulation of mathematical models developed for physiology and biology. Code development has been driven by two initial applications: cardiac electrophysiology and cancer development. A large number of cardiac electrophysiology studies have been enabled and performed, including high-performance computational investigations of defibrillation on realistic human cardiac geometries. New models for the initiation and growth of tumours have been developed. In particular, cell-based simulations have provided novel insight into the role of stem cells in the colorectal crypt. Chaste is constantly evolving and is now being applied to a far wider range of problems. The code provides modules for handling common scientific computing components, such as meshes and solvers for ordinary and partial differential equations (ODEs/PDEs). Re-use of these components avoids the need for researchers to ‘re-invent the wheel’ with each new project, accelerating the rate of progress in new applications. Chaste is developed using industrially-derived techniques, in particular test-driven development, to ensure code quality, re-use and reliability. In this article we provide examples that illustrate the types of problems Chaste can be used to solve, which can be run on a desktop computer. We highlight some scientific studies that have used or are using Chaste, and the insights they have provided. The source code, both for specific releases and the development version, is available to download under an open source Berkeley Software Distribution (BSD) licence at http://www.cs.ox.ac.uk/chaste, together with details of a mailing list and links to documentation and tutorials.
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          Multi-scale modeling of tissues using CompuCell3D.

          The study of how cells interact to produce tissue development, homeostasis, or diseases was, until recently, almost purely experimental. Now, multi-cell computer simulation methods, ranging from relatively simple cellular automata to complex immersed-boundary and finite-element mechanistic models, allow in silico study of multi-cell phenomena at the tissue scale based on biologically observed cell behaviors and interactions such as movement, adhesion, growth, death, mitosis, secretion of chemicals, chemotaxis, etc. 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. We also present a walkthrough of four biological models and their associated simulations that demonstrate the capabilities of the GGH and CompuCell3D. Copyright © 2012 Elsevier Inc. All rights reserved.
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            Author and article information

            Affiliations
            Center for Information Services and High Performance Computing, Technische Universität Dresden, 01062 Dresden, Germany
            Author notes
            *To whom correspondence should be addressed.

            Associate Editor: Martin Bishop

            The authors wish it to be known that, in their opinion, the first two authors should be regarded as Joint First Authors.

            Journal
            Bioinformatics
            Bioinformatics
            bioinformatics
            bioinfo
            Bioinformatics
            Oxford University Press
            1367-4803
            1367-4811
            1 May 2014
            17 January 2014
            17 January 2014
            : 30
            : 9
            : 1331-1332
            24443380
            3998129
            10.1093/bioinformatics/btt772
            btt772
            © The Author 2014. Published by Oxford University Press.

            This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

            Counts
            Pages: 2
            Categories
            Applications Notes
            Systems Biology

            Bioinformatics & Computational biology

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