Visual Evaluation of Computational Models of the Biological Mesoscale

Guillermo Garcia-Escribano
Visual Evaluation of Computational Models of the Biological Mesoscale

Information

Abstract

Currently available techniques for capturing macromolecules on atomic level are not appropriate for large structures on the biological mesoscale. Therefore, those structures, such as viruses or cell organelles, have to be assembled from molecular building blocks using software tools. The goal of recent projects like cellPACK is to create models with these tools, allowing the scientific community to iteratively give feedback and edit the models, in order to eventually generate the most suitable illustration consistent with the current state of knowledge. For that purpose, we need to discern the values for properties like distribution, density or opacity that make a model preferable to others. This thesis aims to create a software program for visual evaluation of the quality of the assembled structures. The program will extract the information about the quality of spatial distribution of molecules in the scenes produced by packing tools and plot it into a set of 2D representations. These will convey the statistical information about the distribution and enable the visual comparison of generated models, which vary not only due to the stochastic nature of the packing algorithms but also because of the use of different parameter settings.

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BibTeX

@bachelorsthesis{Escribano_2017,
  title =      "Visual Evaluation of Computational Models of the Biological
               Mesoscale",
  author =     "Guillermo Garcia-Escribano",
  year =       "2017",
  abstract =   "Currently available techniques for capturing macromolecules
               on atomic level are not appropriate for large structures on
               the biological mesoscale. Therefore, those structures, such
               as viruses or cell organelles, have to be assembled from
               molecular building blocks using software tools. The goal of
               recent projects like cellPACK is to create models with these
               tools, allowing the scientific community to iteratively give
               feedback and edit the models, in order to eventually
               generate the most suitable illustration consistent with the
               current state of knowledge. For that purpose, we need to
               discern the values for properties like distribution, density
               or opacity that make a model preferable to others.  This
               thesis aims to create a software program for visual
               evaluation of the quality of the assembled structures. The
               program will extract the information about the quality of
               spatial distribution of molecules in the scenes produced by
               packing tools and plot it into a set of 2D representations.
               These will convey the statistical information about the
               distribution and enable the visual comparison of generated
               models, which vary not only due to the stochastic nature of
               the packing algorithms but also because of the use of
               different parameter settings.",
  month =      jun,
  address =    "Favoritenstrasse 9-11/186, A-1040 Vienna, Austria",
  school =     "Institute of Computer Graphics and Algorithms, Vienna
               University of Technology",
  URL =        "https://www.cg.tuwien.ac.at/research/publications/2017/Escribano_2017/",
}