Illustrative Visualization of Biochemical Processes Featuring Multiple Temporal Scales

Mathieu Le Muzic, Julius Parulek, Manuela Waldner, Ivan Viola
Illustrative Visualization of Biochemical Processes Featuring Multiple Temporal Scales
Poster shown at Eurographics Workshop on Visual Computing for Biology (2014-09-04-2014-09-05) In . 2014.

Information

Abstract

Scientific illustrators are commonly using structural description of molecular compounds when depicting complex biochemical processes. However, computational biology also provides procedural models describing the function of biological processes which are not currently used in the production pipeline. Instead, animators utilize scientific knowledge to manually animate and reproduce the functioning of cellular biology. We would like to explore the use of such models in order to generate explanatory illustrations that would show how molecular machinery works. Particle-based simulations provide the means for spatially representing the dynamics of biochemical processes. They compute the positions of each single particle and are supposed to mimic a realistic behaviour of the metabolites. Current mesoscale visualization also allows to directly show the results of such simulations by mapping the positions of particles in a virtual 3D environment. Nevertheless, some biochemical processes, like the DNA repair for instance, exhibit temporal multiscale aspects because they comprise diffusion rates which are much greater in comparison with reaction rates. As a result, it is challenging to produce a clear and coherent visualization out of this type of simulation. Indeed, when viewing the process at the pace which would let us see the reactions, it becomes impossible for the human eye to keep track of individual elements because of the very large diffusion displacements. On the other hand, if one would playback the simulation slow enough to be see a steady motion of individual elements, then only a very few number of reactions would occur in a reasonable amount of time. In this work we propose to solve the problem associated with multiple temporal scales by providing means for spatial. With this approach we aim at showing the two different temporal scale at the same time by using advanced trajectory smoothing mechanism. This would allow us to see individual elements while showing a world full of reactions, hence enabling us to communicate complex biological processes and molecular machineries in a comprehensive way.

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BibTeX

@misc{lemuzic_2014_ipv,
  title =      "Illustrative Visualization of Biochemical Processes
               Featuring Multiple Temporal Scales",
  author =     "Mathieu Le Muzic and Julius Parulek and Manuela Waldner and
               Ivan Viola",
  year =       "2014",
  abstract =   "Scientific illustrators are commonly using structural
               description of molecular compounds when depicting complex
               biochemical processes. However, computational biology also
               provides procedural models describing the function of
               biological processes which are not currently used in the
               production pipeline. Instead, animators utilize scientific
               knowledge to manually animate and reproduce the functioning
               of cellular biology. We would like to explore the use of
               such models in order to generate explanatory illustrations
               that would show how molecular machinery works.
               Particle-based simulations provide the means for spatially
               representing the dynamics of biochemical processes. They
               compute the positions of each single particle and are
               supposed to  mimic a realistic behaviour of the metabolites.
               Current mesoscale visualization also allows to directly show
               the results of such simulations by mapping the positions of
               particles in a virtual 3D environment. Nevertheless, some
               biochemical processes, like the DNA repair for instance,
               exhibit temporal multiscale aspects because they comprise
               diffusion rates which are much greater in comparison with
               reaction rates. As a result, it is challenging to produce a
               clear and coherent visualization out of this type of
               simulation. Indeed, when viewing the process at the pace
               which would let us see the reactions, it becomes impossible
               for the human eye to keep track of individual elements
               because of the very large diffusion displacements. On the
               other hand, if one would playback the simulation slow enough
               to be see a steady motion of individual elements, then only
               a very few number of reactions would occur in a reasonable
               amount of time. In this work we propose to solve the problem
               associated with multiple temporal scales by providing means
               for spatial. With this approach we aim at showing the two
               different temporal scale at the same time by using advanced
               trajectory smoothing mechanism. This would allow us to see
               individual elements while showing a world full of reactions,
               hence enabling us to communicate complex biological
               processes and molecular machineries in a comprehensive way. ",
  event =      "Eurographics Workshop on Visual Computing for Biology",
  note =       "Poster presented at Eurographics Workshop on Visual
               Computing for Biology (2014-09-04--2014-09-05)",
  URL =        "https://www.cg.tuwien.ac.at/research/publications/2014/lemuzic_2014_ipv/",
}