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Issue No.05 - Sept.-Oct. (2012 vol.32)
pp: 50-61
L. Autin , Scripps Res. Inst., La Jolla, CA, USA
G. Johnson , Scripps Res. Inst., La Jolla, CA, USA
J. Hake , Univ. of California, San Diego, La Jolla, CA, USA
A. Olson , Scripps Res. Inst., La Jolla, CA, USA
M. Sanner , Scripps Res. Inst., La Jolla, CA, USA
ABSTRACT
The uPy Python extension module provides a uniform abstraction of the APIs of several 3D computer graphics programs (called hosts), including Blender, Maya, Cinema 4D, and DejaVu. A plug-in written with uPy can run in all uPy-supported hosts. Using uPy, researchers have created complex plug-ins for molecular and cellular modeling and visualization. uPy can simplify programming for many types of projects (not solely science applications) intended for multihost distribution. It's available at http://upy.scripps.edu. The first featured Web extra is a video that shows interactive analysis of a calcium dynamics simulation. YouTube URL: http://youtu.be/wvs-nWE6ypo. The second featured Web extra is a video that shows rotation of the HIV virus. YouTube URL: http://youtu.be/vEOybMaRoKc.
INDEX TERMS
Biomedical image processing, Three dimensional displays, Adaptation models, Computational modeling, Data visualization, Graphical user interfaces, Molecular biophysics,Cinema 4D, Biomedical image processing, Three dimensional displays, Adaptation models, Computational modeling, Data visualization, Graphical user interfaces, Molecular biophysics, computer graphics, uPy, Python, software plug-ins, scientific data visualization, 3D molecular visualization, Blender, Maya
CITATION
L. Autin, G. Johnson, J. Hake, A. Olson, M. Sanner, "uPy: A Ubiquitous CG Python API with Biological-Modeling Applications", IEEE Computer Graphics and Applications, vol.32, no. 5, pp. 50-61, Sept.-Oct. 2012, doi:10.1109/MCG.2012.93
REFERENCES
1. G. McGill,“Molecular Movies ... Coming to a Lecture Near You,” Cell, vol. 133, no. 7, 2008, pp. 1127–1132.
2. M.F. Sanner, “Python: A Programming Language for Software Integration and Development,” J. Molecular Graphics and Modeling, vol. 17, no. 1, 1999, pp. 57–61.
3. G.T. Johnson et al., “ePMV Embeds Molecular Modeling into Professional Animation Software Environments,” Structure, vol. 19, no. 3, 2011, pp. 293–303.
4. A. Gillet et al., “Tangible Interfaces for Structural Molecular Biology,” Structure, vol. 13, no. 3, 2005, pp. 483–491.
5. Z. Yu et al., “Feature-Preserving Adaptive Mesh Generation for Molecular Shape Modeling and Simulation,” J. Molecular Graphics and Modeling, vol. 26, no. 8, 2008, pp. 1370–1380.
6. T. Hayashi et al., “Three-Dimensional Electron Microscopy Reveals New Details of Membrane Systems for Ca2+ Signaling in the Heart,” J. Cell Science, vol. 122, no. 7, 2009, pp. 1005–1013.
7. Y.H. Cheng et al., “Finite Element Analysis of the Time-Dependent Smoluchowski Equation for Acetylcholinesterase Reaction Rate Calculations,” Biophysical J., vol. 92, no. 10, 2007, pp. 3397–3406.
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