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Literature DB >> 24806987

uPy: a ubiquitous CG Python API with biological-modeling applications.

Ludovic Autin, Graham Johnson, Johan Hake, Arthur Olson, Michel Sanner.

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.

Entities: Chemical Disease Gene Species

Mesh：

Year: 2012 PMID： 24806987 PMCID： PMC4590990 DOI： 10.1109/MCG.2012.93

Source DB: PubMed Journal: IEEE Comput Graph Appl ISSN： 0272-1716 Impact factor: 2.088

6 in total

1. Python: a programming language for software integration and development.

Authors: M F Sanner
Journal: J Mol Graph Model Date: 1999-02 Impact factor: 2.518

2. Tangible interfaces for structural molecular biology.

Authors: Alexandre Gillet; Michel Sanner; Daniel Stoffler; Arthur Olson
Journal: Structure Date: 2005-03 Impact factor: 5.006

3. Feature-preserving adaptive mesh generation for molecular shape modeling and simulation.

Authors: Zeyun Yu; Michael J Holst; Yuhui Cheng; J Andrew McCammon
Journal: J Mol Graph Model Date: 2008-02-07 Impact factor: 2.518

4. Molecular movies... coming to a lecture near you.

Authors: Gaël McGill
Journal: Cell Date: 2008-06-27 Impact factor: 41.582

5. ePMV embeds molecular modeling into professional animation software environments.

Authors: Graham T Johnson; Ludovic Autin; David S Goodsell; Michel F Sanner; Arthur J Olson
Journal: Structure Date: 2011-03-09 Impact factor: 5.006

6. Three-dimensional electron microscopy reveals new details of membrane systems for Ca2+ signaling in the heart.

Authors: Takeharu Hayashi; Maryann E Martone; Zeyun Yu; Andrea Thor; Masahiro Doi; Michael J Holst; Mark H Ellisman; Masahiko Hoshijima
Journal: J Cell Sci Date: 2009-04-01 Impact factor: 5.285

6 in total

4 in total

uPy: a ubiquitous CG Python API with biological-modeling applications.

1. Python: a programming language for software integration and development.

2. Tangible interfaces for structural molecular biology.

3. Feature-preserving adaptive mesh generation for molecular shape modeling and simulation.

4. Molecular movies... coming to a lecture near you.

5. ePMV embeds molecular modeling into professional animation software environments.

6. Three-dimensional electron microscopy reveals new details of membrane systems for Ca2+ signaling in the heart.

Review 1. A guide to the visual analysis and communication of biomolecular structural data.

2. 3D molecular models of whole HIV-1 virions generated with cellPACK.

3. cellPACK: a virtual mesoscope to model and visualize structural systems biology.

4. LipidWrapper: an algorithm for generating large-scale membrane models of arbitrary geometry.