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Visualization of Signal Transduction Processes in the Crowded Environment of the Cell
VISUS - Visualization Research Center, Universität Stuttgart, Germany.ORCID iD: 0000-0003-1511-5006
Institute of Biochemical Engineering and Center Systems Biology, Universität Stuttgart, Germany.
Institute of Biochemical Engineering and Center Systems Biology, Universität Stuttgart, Germany.
VISUS - Visualization Research Center, Universität Stuttgart, Germany.
2009 (English)In: IEEE Pacific Visualization Symposium (PacificVis 2009), 2009, p. 169-176Conference paper, Published paper (Refereed)
Abstract [en]

In this paper, we propose a stochastic simulation to model and analyze cellular signal transduction. The high number of objects in a simulation requires advanced visualization techniques: first to handle the large data sets, second to support the human perception in the crowded environment, and third to provide an interactive exploration tool. To adjust the state of the cell to an external signal, a specific set of signaling molecules transports the information to the nucleus deep inside the cell. There, key molecules regulate gene expression. In contrast to continuous ODE models we model all signaling molecules individually in a more realistic crowded and disordered environment. Beyond spatiotemporal concentration profiles our data describes the process on a mesoscopic, molecular level, allowing a detailed view of intracellular events. In our proposed schematic visualization individual molecules, their tracks, or reactions can be selected and brought into focus to highlight the signal transduction pathway. Segmentation, depth cues and depth of field are applied to reduce the visual complexity. We also provide a virtual microscope to display images for comparison with wet lab experiments. The method is applied to distinguish different transport modes of MAPK (mitogen-activated protein kinase) signaling molecules in a cell. In addition, we simulate the diffusion of drug molecules through the extracellular space of a solid tumor and visualize the challenges in cancer related therapeutic drug delivery.

Place, publisher, year, edition, pages
2009. p. 169-176
Series
IEEE Pacific Visualization Symposium, ISSN 2165-8765, E-ISSN 2165-8773
Keywords [en]
ScientificVis, SignalTransduction
National Category
Media and Communication Technology
Identifiers
URN: urn:nbn:se:liu:diva-143699DOI: 10.1109/PACIFICVIS.2009.4906853ISBN: 978-1-4244-4404-5 (print)OAI: oai:DiVA.org:liu-143699DiVA, id: diva2:1166281
Conference
IEEE Pacific Visualization Symposium (PacificVis 2009), 20-23 April 2009, Beijing, China
Available from: 2017-12-14 Created: 2017-12-14 Last updated: 2018-01-13

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CiteExportLink to record
Permanent link

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Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • oxford
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf