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Parallel Computing Platform for the Agent-Based Modeling of Multicellular Biological Systems

  • Conference paper
Parallel and Distributed Computing: Applications and Technologies (PDCAT 2004)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 3320))

Abstract

Agent-based simulation of large multicellular biological systems has become a viable option owing to affordable parallel computers, such as Beowulf-style clusters. We describe a scalable modular software platform that (i) provides for an easy integration of different solvers computing internal dynamics of the cells, and (ii) dynamically adapts to the changing loads on the cluster nodes using a load balancing algorithm. Simulations of systems of about 100,000 bacterial cells have been shown to be feasible using the platform.

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Author information

Authors and Affiliations

  1. Bioinformatics Institute, Matrix L7, 30 Biopolis St, Singapore

    Toh Da-Jun, Francis Tang, Travis Lee, Deepak Sarda, Arun Krishnan & Andrew Goryachev

Authors
  1. Toh Da-Jun
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  2. Francis Tang
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  3. Travis Lee
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  4. Deepak Sarda
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  5. Arun Krishnan
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  6. Andrew Goryachev
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Editor information

Editors and Affiliations

  1. Nanyang Centre for Supercomputing and Visualisation School of Mechanical and Production Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639 798, Singapore

    Kim-Meow Liew

  2. School of Computer Science, The University of Adelaide,  

    Hong Shen

  3. Asia Pacific Science and Technology Center, Sun Microsystems Inc., 50 Nanyang Avenue, N3-1c-10, 639798, Singapore

    Simon See

  4. School of Computer Engineering, Nanyang Technological University, 639798, Singapore

    Wentong Cai

  5. Southwest Jiaotong University,  

    Pingzhi Fan

  6. Tohoku University ,  

    Susumu Horiguchi

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© 2004 Springer-Verlag Berlin Heidelberg

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Cite this paper

Da-Jun, T., Tang, F., Lee, T., Sarda, D., Krishnan, A., Goryachev, A. (2004). Parallel Computing Platform for the Agent-Based Modeling of Multicellular Biological Systems. In: Liew, KM., Shen, H., See, S., Cai, W., Fan, P., Horiguchi, S. (eds) Parallel and Distributed Computing: Applications and Technologies. PDCAT 2004. Lecture Notes in Computer Science, vol 3320. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-30501-9_2

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  • DOI: https://doi.org/10.1007/978-3-540-30501-9_2

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-24013-6

  • Online ISBN: 978-3-540-30501-9

  • eBook Packages: Computer ScienceComputer Science (R0)

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