Interactively illustrating polymerization using three-level model fusion

Ivan Kolesár, Julius Parulek, Ivan Viola, Stefan Bruckner, Anne-Kristin Stavrum, Helwig Hauser
Interactively illustrating polymerization using three-level model fusion
BMC Bioinformatics 2014, 15(345):1-16, October 2014.

Information

Abstract

Background: Research in cell biology is steadily contributing new knowledge about many aspects of physiological processes, both with respect to the involved molecular structures as well as their related function. llustrations of the spatio-temporal development of such processes are not only used in biomedical education, but also can serve scientists as an additional platform for in-silico experiments.

Results: In this paper, we contribute a new, three-level modeling approach to illustrate physiological processes from the class of polymerization at different time scales. We integrate physical and empirical modeling, according to which approach best suits the different involved levels of detail, and we additionally enable a form of interactive steering, while the process is illustrated. We demonstrate the suitability of our approach in the context of several polymerization processes and report from a first evaluation with domain experts.

Conclusion: We conclude that our approach provides a new, hybrid modeling approach for illustrating the process of emergence in physiology, embedded in a densely filled environment. Our approach of a complementary fusion of three systems combines the strong points from the different modeling approaches and is capable to bridge different spatial and temporal scales.

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BibTeX

@article{Viola_Ivan_IIP,
  title =      "Interactively illustrating polymerization using three-level
               model fusion",
  author =     "Ivan Koles{'a}r and Julius Parulek and Ivan Viola and Stefan
               Bruckner and Anne-Kristin Stavrum and Helwig Hauser",
  year =       "2014",
  abstract =   "Background: Research in cell biology is steadily
               contributing new knowledge about many aspects of
               physiological  processes, both with respect to the involved
               molecular structures as well as their related function.  
               llustrations of the spatio-temporal development of such
               processes are not only used in biomedical education, but
               also can serve scientists as an additional platform for
               in-silico experiments.  Results: In this paper, we
               contribute a new, three-level modeling approach to
               illustrate physiological processes from the class of
               polymerization at different time scales. We integrate
               physical and empirical modeling, according to which approach
               best suits the different involved levels of detail, and we
               additionally enable a form of interactive steering, while
               the process is illustrated. We demonstrate the suitability
               of our approach in the context of several polymerization
               processes and report from a first evaluation with domain
               experts.  Conclusion: We conclude that our approach provides
               a new, hybrid modeling approach for illustrating the process
               of emergence in physiology, embedded in a densely filled
               environment. Our approach of a complementary fusion of three
               systems combines the strong points from the different
               modeling approaches and is capable to bridge different
               spatial and temporal scales.",
  month =      oct,
  issn =       "1471-2105",
  journal =    "BMC Bioinformatics 2014",
  number =     "345",
  volume =     "15",
  pages =      "1--16",
  keywords =   "Multi-agent modeling, L-system modeling, Biochemical
               visualization, Visualization of physiology, Polymerization",
  URL =        "https://www.cg.tuwien.ac.at/research/publications/2014/Viola_Ivan_IIP/",
}