Research Highlights

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  • Top: Scripted in uPy, ePMV can interoperate any Python wrapped algorithms on the same model through a single interface.
  • Bottom: The highly developed uPy plugin, ePMV, allows a user to visualize an idea (the proverbial napkin sketch) as a press-ready image. Data from a variety of sources can combine with user-sculpted models (cubes, spheres, lathed shapes, etc. that represent unknown structures) in an interface that allows for easy assembly, lighting, animation, and high-quality rendering.

Bringing modeling and animation into one interface and improving interdisciplinary collaborations: Increasingly complex research has made it more difficult to prepare data for analysis, publication, education, and outreach. Many scientists must also wade through what seems like black-boxes with mysterious code that works “magic” to generate results with computational algorithms from diverse sources in order to supplement their laboratory (bench) work. This creates barriers between researchers and what they want to accomplish with their data: integration and visualization. To ease this problem, NBCR researchers have developed the embedded Python Molecular Viewer (ePMV)– an open-source plugin scripted in their newly released Python adaptor module the ubiquitous Python API (uPy). ePMV runs molecular modeling software directly inside of professional 3-D animation applications. Running inside of the animation program allows ePMV to provide access to the capabilities of both molecular modeling and 3-D animation simultaneously (Johnson 2011). Uniting host animation software and scientific algorithms in this way makes it possible for users from varied backgrounds to assemble professional quality visuals and to perform computational experiments in a single interface with relative ease. By enabling this easy exchange of algorithms, ePMV facilitates interdisciplinary research, smooths communication between broadly diverse specialties, and provides a common platform to frame and visualize the increasingly detailed intersection(s) of cellular and molecular biology.

Currently, ePMV can be used in the Blender, Cinema 4D, and Maya software animation packages, others to follow. In addition, being scripted in uPy enables ePMV to integrate the FETK (finite element toolkit) package component GAMer (geometric preserving adaptive meshing tool) into Blender for mesh visualization and refinement. uPy also facilitates the integration of Mcell (by the Bartol group, http://www.mcell.cnl.salk.edu/)—a modeling tool for realistic simulation of cellular signaling in the complex 3-D subcellular microenvironment in and around living cells—into Blender, with the ability to utilize ePMV inside the Blender/Mcell environment. ePMV is included in the PMV MGLToolsPckgs (1.5.6) and thus does not require an additional download. More information on ePMV can be found on its website.

References: Johnson, G.T. and Autin, L., et al., ePMV embeds molecular modeling into professional animation software environments. Structure, 2011. 19(3): p. 293-303.

NBCR Researchers: Michel Sanner (Core Lead - Visualization and Visual Workflow Environment to Enhance Multiscale Modeling and Simulation), Graham Johnson, David Goodsell, Ludovic Autin, Art Olson, Tom Bartol (Service Project Lead)

Figure:

  • Top: Scripted in uPy, ePMV can interoperate any Python wrapped algorithms on the same model through a single interface.
  • Bottom: The highly developed uPy plugin, ePMV, allows a user to visualize an idea (the proverbial napkin sketch) as a press-ready image. Data from a variety of sources can combine with user-sculpted models (cubes, spheres, lathed shapes, etc. that represent unknown structures) in an interface that allows for easy assembly, lighting, animation, and high-quality rendering.