Multi-scale modelling in computational biomedicine

The inherent complexity of biomedical systems is well recognized; they are multi-scale, multi-science systems, bridging a wide range of temporal and spatial scales. This article reviews the currently emerging field of multi-scale modelling in computational biomedicine. Many exciting multi-scale models exist or are under development. However, an underpinning multi-scale modelling methodology seems to be missing. We propose a direction that complements the classic dynamical systems approach and introduce two distinct case studies, transmission of resistance in human immunodeficiency virus spreading and in-stent restenosis in coronary artery disease.

[1]  Gordon Clapworthy,et al.  The virtual physiological human: building a framework for computational biomedicine I. Editorial. , 2008, Philosophical transactions. Series A, Mathematical, physical, and engineering sciences.

[2]  T. Silander,et al.  Bayesian network analysis of resistance pathways against HIV-1 protease inhibitors. , 2007, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

[3]  P. Maini,et al.  Multiscale modeling in biology , 2007 .

[4]  Alfons G. Hoekstra,et al.  Scale-Splitting Error in Complex Automata Models for Reaction-Diffusion Systems , 2008, ICCS.

[5]  Werner Dubitzky,et al.  Distributed, High-Performance and Grid Computing in Computational Biology : International Workshop, GCCB 2006, Eilat, Israel, January 21, 2007 : proceedings , 2007 .

[6]  Paul A. Fishwick,et al.  Handbook of Dynamic System Modeling , 2007 .

[7]  Peter M. A. Sloot,et al.  A complex automata model of HIV-1 co-receptor tropism: Understanding mutation rate pressure , 2007 .

[8]  Roland Eils,et al.  Computational Systems Biology , 2006 .

[9]  Akhil Bidani,et al.  Multiscale model for pulmonary oxygen uptake and its application to quantify hypoxemia in hepatopulmonary syndrome. , 2007, Journal of theoretical biology.

[10]  Zhiliang Xu,et al.  A multiscale model of thrombus development , 2008, Journal of The Royal Society Interface.

[11]  D R Hose,et al.  Modelling the interaction of haemodynamics and the artery wall: current status and future prospects. , 2008, Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie.

[12]  Robert Jacob,et al.  A Multilingual Programming Model for Coupled Systems , 2008 .

[13]  E Weinan,et al.  Heterogeneous multiscale methods: A review , 2007 .

[14]  David Gavaghan,et al.  Multi-scale computational modelling in biology and physiology , 2007, Progress in Biophysics and Molecular Biology.

[15]  Martin Hofmann-Apitius,et al.  Knowledge environments representing molecular entities for the virtual physiological human , 2008, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences.

[16]  Alfons G. Hoekstra,et al.  Towards a Complex Automata Framework for Multi-scale Modeling: Formalism and the Scale Separation Map , 2007, International Conference on Computational Science.

[17]  Peter M. A. Sloot,et al.  Modeling Dynamic Systems with Cellular Automata , 2007, Handbook of Dynamic System Modeling.

[18]  P. Hunter,et al.  Bioinformatics, multiscale modeling and the IUPS Physiome Project , 2008, Briefings Bioinform..

[19]  A. Barabasi,et al.  Taming complexity , 2005 .

[20]  Tianhai Tian,et al.  A multi-scaled approach for simulating chemical reaction systems. , 2004, Progress in biophysics and molecular biology.

[21]  Mauricio Barahona,et al.  Chemistry across scales: from molecules to cells , 2007, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences.

[22]  Dawn Walker,et al.  Towards a Complex Automata Multiscale Model of In-Stent Restenosis , 2009, ICCS.

[23]  Mitchell H. Gail,et al.  A Method for Obtaining Short-Term Projections and Lower Bounds on the Size of the AIDS Epidemic , 1988 .

[24]  Bernard P. Zeigler,et al.  Theory of Modeling and Simulation: Integrating Discrete Event and Continuous Complex Dynamic Systems , 2000 .

[25]  Peter V Coveney,et al.  Rapid and accurate prediction of binding free energies for saquinavir-bound HIV-1 proteases. , 2008, Journal of the American Chemical Society.

[26]  Peter M. A. Sloot,et al.  Cellular Automata Model of Drug Therapy for HIV Infection , 2002, ACRI.

[27]  D. Noble.  Modeling the Heart--from Genes to Cells to the Whole Organ , 2002, Science.

[28]  Alfons G. Hoekstra,et al.  Toward a Complex Automata Formalism for Multi-Scale Modeling , 2007 .

[29]  Peter Hunter,et al.  A strategy for integrative computational physiology. , 2005, Physiology.

[30]  Dan V. Nicolau,et al.  Modelling and simulation techniques for membrane biology , 2007, Briefings Bioinform..

[31]  Peter M. A. Sloot,et al.  International Journal of Computer Mathematics Stochastic Simulation of Hiv Population Dynamics through Complex Network Modelling Stochastic Simulation of Hiv Population Dynamics through Complex Network Modelling , 2022 .

[32]  Fabio Baruffaldi,et al.  Multiscale investigation of the functional properties of the human femur , 2008, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences.

[33]  Alfons G. Hoekstra,et al.  Multi-scale Modeling with Cellular Automata: The Complex Automata Approach , 2008, ACRI.

[34]  Roeland M. H. Merks,et al.  Models of coral growth: spontaneous branching, compactification and the Laplacian growth assumption. , 2003, Journal of theoretical biology.

[35]  B. Chopard,et al.  A lattice Boltzmann model for particle transport and deposition , 1998 .

[36]  Thomas L. Casavant,et al.  Gene transcript clustering: a comparison of parallel approaches , 2005, Future Gener. Comput. Syst..

[37]  Joc Cing Tay,et al.  A hybrid agent-based approach for modeling microbiological systems. , 2008, Journal of theoretical biology.

[38]  Yves Moreau,et al.  Estimation of an in vivo fitness landscape experienced by HIV-1 under drug selective pressure useful for prediction of drug resistance evolution during treatment , 2008, Bioinform..

[39]  Manfred Krafczyk,et al.  An Agent-Based Coupling Platform for Complex Automata , 2008, ICCS.

[40]  Ian David Lockhart Bogle,et al.  Addressing the challenges of multiscale model management in systems biology , 2007, Comput. Chem. Eng..

[41]  Gernot Plank,et al.  From mitochondrial ion channels to arrhythmias in the heart: computational techniques to bridge the spatio-temporal scales , 2008, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences.

[42]  Peter M. A. Sloot.  ViroLab: From the molecule to the man , 2008 .

[43]  Marian Bubak,et al.  Expanding the Knowledge Economy : Issues , Applications , Case Studies , 2007 .

[44]  K. Burrowes,et al.  Towards a virtual lung: multi-scale, multi-physics modelling of the pulmonary system , 2008, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences.

[45]  Yves Moreau,et al.  Analysis of HIV-1 pol sequences using Bayesian Networks: implications for drug resistance , 2006, Bioinform..

[46]  Marina Vannucci,et al.  Models and computational strategies linking physiological response to molecular networks from large-scale data , 2008, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences.

[47]  Mario-Ubaldo Manto,et al.  Editorial , 2008, The Cerebellum.

[48]  Gregory A Voth,et al.  Multiscale modeling of biomolecular systems: in serial and in parallel. , 2007, Current opinion in structural biology.

[49]  Marian Bubak,et al.  ViroLab: A collaborative decision support system in viral disease treatment , 2008 .

[50]  Ian T. Cameron,et al.  Classification and analysis of integrating frameworks in multiscale modelling , 2004 .

[51]  Gordon Clapworthy,et al.  The virtual physiological human. Editorial. , 2008, Philosophical transactions. Series A, Mathematical, physical, and engineering sciences.

[52]  Katalin M. Hangos,et al.  Multiscale Modeling and Time-Scale Analysis of a Human Limb , 2007, Multiscale Model. Simul..

[53]  S. Deeks,et al.  Treatment of antiretroviral-drug-resistant HIV-1 infection , 2003, The Lancet.

[54]  James Hetherington,et al.  Computational challenges of systems biology , 2004, Computer.

[55]  Marian Bubak,et al.  From molecule to man: Decision support in individualized E-health , 2006, Computer.

[56]  R H Smallwood,et al.  The application of multiscale modelling to the process of development and prevention of stenosis in a stented coronary artery , 2008, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences.