Skip to main content

ManyCell: A Multiscale Simulator for Cellular Systems

  • Conference paper
  • 1315 Accesses

Part of the Lecture Notes in Computer Science book series (LNBI,volume 7605)


The emergent properties of multiscale biological systems are driven by the complex interactions of their internal compositions usually organized in hierarchical scales. A common representation takes cells as the basic units which are organized in larger structures: cultures, tissues and organs. Within cells there is also a great deal of organization, both structural (organelles) and biochemical (pathways). A software environment capable of minimizing the computational cost of simulating large-scale multiscale models is required to help understand the functional behaviours of these systems. Here we present ManyCell, a multiscale simulation software environment for efficient simulation of such cellular systems. ManyCell does not only allow the integration and simulation of models from different biological scales, but also combines innovative multiscale methods with distributed computing approaches to accelerate the process of simulating large-scale multiscale agent-based models. Thereby opening up the possibilities of understanding the functional behaviour of cellular systems in an efficient way.


  • multiscale
  • simulation
  • modelling
  • agent-based
  • ODE
  • software

This is a preview of subscription content, access via your institution.

Buying options

USD   29.95
Price excludes VAT (USA)
  • DOI: 10.1007/978-3-642-33636-2_22
  • Chapter length: 4 pages
  • Instant PDF download
  • Readable on all devices
  • Own it forever
  • Exclusive offer for individuals only
  • Tax calculation will be finalised during checkout
USD   74.99
Price excludes VAT (USA)
  • ISBN: 978-3-642-33636-2
  • Instant PDF download
  • Readable on all devices
  • Own it forever
  • Exclusive offer for individuals only
  • Tax calculation will be finalised during checkout
Softcover Book
USD   95.00
Price excludes VAT (USA)


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. Dada, J.O., Mendes, P.: Multi-scale modelling and simulation in systems biology. Integr. Biol. 3(2), 86–96 (2011)

    CrossRef  Google Scholar 

  2. Pope, S.: Computation efficient implementation of combustion chemistry using in situ adaptive tabulation. Combustion Theory Modelling 1, 41–63 (1997)

    MathSciNet  CrossRef  MATH  Google Scholar 

  3. Hoops, S., et al.: Copasi—a complex pathway simulator. Bioinformatics 22(24), 3067–3074 (2006)

    CrossRef  Google Scholar 

  4. Dada, J.O., Mendes, P.: Design and Architecture of Web Services for Simulation of Biochemical Systems. In: Paton, N.W., Missier, P., Hedeler, C. (eds.) DILS 2009. LNCS, vol. 5647, pp. 182–195. Springer, Heidelberg (2009)

    CrossRef  Google Scholar 

  5. Hucka, M., et al.: The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19(4), 524–531 (2003)

    CrossRef  Google Scholar 

  6. Le Novère, N., et al.: Biomodels database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Res. 34, 689–691 (2006)

    CrossRef  Google Scholar 

  7. Dada, J.O., et al.: SBRML: a markup language for associating systems biology data with models. Bioinformatics 26(7), 932–938 (2010)

    CrossRef  Google Scholar 

  8. van Engelen, R.A., Gallivany, K.A.: The gsoap toolkit for web services and peer-to-peer computing networks. In: 2nd IEEE International Symposium on Cluster Computing and the Grid, pp. 128–135 (2002)

    Google Scholar 

  9. Da-Jun, T., Tang, F., Lee, T., Sarda, D., Krishnan, A., Goryachev, A.: Parallel Computing Platform for the Agent-Based Modeling of Multicellular Biological Systems. In: Liew, K.-M., Shen, H., See, S., Cai, W. (eds.) PDCAT 2004. LNCS, vol. 3320, pp. 5–8. Springer, Heidelberg (2004)

    CrossRef  Google Scholar 

  10. Chen, K.C., et al.: Integrative analysis of cell cycle control in budding yeast. Mol. Biol. Cell. 15(8), 3841–3862 (2004)

    CrossRef  Google Scholar 

Download references

Author information

Authors and Affiliations


Editor information

Editors and Affiliations

Rights and permissions

Reprints and Permissions

Copyright information

© 2012 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Dada, J.O., Mendes, P. (2012). ManyCell: A Multiscale Simulator for Cellular Systems. In: Gilbert, D., Heiner, M. (eds) Computational Methods in Systems Biology. CMSB 2012. Lecture Notes in Computer Science(), vol 7605. Springer, Berlin, Heidelberg.

Download citation

  • DOI:

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-33635-5

  • Online ISBN: 978-3-642-33636-2

  • eBook Packages: Computer ScienceComputer Science (R0)