Speaker: Prof. Art Olson (The Scripps Research Institute, CA USA)
The ability to create structural models of cells and cellular components at the molecular level is being driven by advances ranging from proteomics and expression profiling to ever more powerful imaging approaches. It is being enabled by technology leaps in computation, informatics, and visualization.
Our CellPACK program is a tool for generating structural models of cellular environments at molecular and atomic level. Recently we have implemented a GPU-based implementation of CellPACK that speeds up the process by orders of magnitude, in what we have termed “instant packing.” This enables interactive exploration and manipulation of components of the packings. Visualization of these models is also enabled by GPU-based efficient representations, renderings and levels of detail. The ability to model complex cellular components such as a bacterial nucleoid and distinct phases is a significant challenge that we continue to work on. Our Lab’s recent lattice-based method for rapidly producing bacterial nucleoids is a prototype for other rule-based generative structure builders. Use of GPU-based physics engines enables real time interaction with dynamic models. Flexx is a real-time constraint solver from NVidia. It is capable of interactive constraint minimization of up to 1 million particles in real time. Such systems can quickly resolve clashes and identify interactions in the crowded cellular environment.
In a parallel effort to CellPACK, we have developed CellPAINT, which has its origins in David Goodsell’s watercolor paintings of cellular environments and processes. Cellpaint uses a painting metaphore to enable creation of Goodsell-like images interactively within a Unity game-engine. These images can be animated using a simple Brownian motion-based diffusion model. Recently we have expanded this interactive interface into 3D, and have also implemented it in a Virtual Reality environment.
The talk will include live interactive demonstrations of the current state of our software.