Speaker: Dr. Björn Sommer (Universität Konstanz)
Multiscale modeling and visualization of cellular environments is an important topic from a scientific as well as educational perspective. It plays an important role in analyzing and understanding metabolic processes, structural molecular complexes or the targeting of drugs.
The CELLmicrocosmos project combines different information layers for multiple purposes:
At the molecular level, the MembraneEditor is used by many projects to model heterogeneous membranes as a base for molecular simulations and analyses [SDGS11]. Showing small parallels to cellVIEW [LAPV15], the CellExplorer is a software tool which can be used to visualize and explore cell environments at the mesoscopic level. Combined with the PathwayIntegration, cytological networks can be localized and integrated into these cell environments [KoGS16, SKSH10]. In the recent years we developed a number of new cytological visualization approaches which can be explored on multiple scales: from the local computer, to web browsers, to mobile phones and Head-‐mounted displays, and to large-‐scale virtual environments like the CAVE2 [FNTT13, KoGS16, SBHG14, SHKC16, SWXC15]. In this context we are currently working with the CeBiTec Bielefeld on the visualization of a Chlamydomas rheinhardtii cell.
[FNTT13] FEBRETTI, Alessandro; NISHIMOTO, Arthur; THIGPEN, Terrance; TALANDIS, Jonas; LONG, Lance; PIRTLE, J. D.; PETERKA, Tom; VERLO, Alan; et al.:
CAVE2: a hybrid reality environment for immersive simulation and information analysis. In: IS&T/SPIE lectronic Imaging : International Society for Optics and Photonics, 2013, pp. 864903-‐864903–12
[KoGS16] KOVANCI, Gökhan; GHAFFAR, Mehmood; SOMMER, Björn: Web-‐based hybrid-‐ dimensional Visualization and Exploration of Cytological Localization Scenarios. In: Journal of Integrative Bioinformatics 13 (2016), no. 4, p. 298
[LAPV15] LE MUZIC, Mathieu; AUTIN, Ludovic; PARULEK, Julius; VIOLA, Ivan: cellVIEW: a tool for illustrative and multi-‐scale rendering of large biomolecular datasets. In: Proceedings of the Eurographics Workshop on Visual Computing for Biology and Medicine : Eurographics Association, 2015, pp. 61–70
[SBHG14] SOMMER, Björn; BENDER, Christian; HOPPE, Tobias; GAMROTH, Christian; JELONEK, Lukas: Stereoscopic cell visualization: from mesoscopic to molecular scale. In: Electronic Imaging, Proceedings of Stereoscopic Displays and Applications XXVIII 23 (2014), no. 1, pp. 011007-‐1-‐011007-‐10
[SDGS11] SOMMER, B.; DINGERSEN, T.; GAMROTH, C.;SCHNEIDER, S. E.; RUBERT, S.; KRÜGER, J.; DIETZ, K. J.: CELLmicrocosmos 2.2 MembraneEditor: a modular interactive
shape-‐based software approach to solve heterogeneous Membrane Packing Problems. In: Journal of Chemical Information and Modeling 5 (2011), no. 51, pp. 1165–1182
[SHKC16] SOMMER, Björn; HAMACHER, Andreas; KALUZA, Owen; CZAUDERNA, Tobias;
KLAPPERSTÜCK, Matthias; BIERE, Niklas; CIVICO, Marco; THOMAS, Bruce; et al.: Stereoscopic Space Map – Semi-‐immersive Configuration of 3D-‐stereoscopic Tours
in Multi-‐display Environments. In: Electronic Imaging, Proceedings of Stereoscopic Displays and Applications XXVII 2016 (2016), no. 5, pp. 1–9
[SKSH10] SOMMER, Björn; KÜNSEMÖLLER, Jörn; SAND, Norbert; HUSEMANN, Arne; RUMMING, Madis; KORMEIER, Benjamin: CELLmicrocosmos 4.1: an interactive approach to integrating spatially localized metabolic networks into a virtual 3D cell environment. In: FRED, Ana; FILIPE, Joaquim; GAMBOA, Hugo (eds.): BIOSTEC 2010, 2010,pp. 90–95
[SWXC15] SOMMER, Björn; WANG, Stephen Jia; XU, Lifeng; CHEN, Ming; SCHREIBER, Falk: Hybrid-‐Dimensional Visualization and Interaction -‐ Integrating 2D and 3D Visualization with Semi-‐Immersive Navigation Techniques. In: Big Data Visual Analytics (BDVA), 2015 : IEEE, 2015, pp. 1–8