Computational Methods for Spatially Realistic Microphysiological Simulations
June 15-19, 2009
Registration deadline: May 17, 2009
This workshop will cover theory and practice for the design and simulation of models focused on diffusion-reaction systems such as neurotransmission, signaling cascades, and other forms of biochemical networks (e.g., Coggan et al., 2005, Science 309:446-451; He et al., 2006, Nature 444:102-105). Current versions of the MCell/DReAMM simulation environment (www.mcell.psc.edu and www.mcell.cnl.salk.edu) will be introduced, including new Monte Carlo methods for 3-D simulation of reactions in solution and on arbitrarily shaped biological surfaces. We will also introduce participants to a recently developed model creation pipeline (Czech et al., Methods in Molecular Biology, Systems Biology, In Press) which leverages in silico model creation via blender (www.blender.org) and allows the creation and simulation of complex MCell models in just a few hours (see sidebar for an example of a dendrite created and simulated in silico).
This workshop has been extended to five full days, and attendees are strongly encouraged to bring ideas/data for their own simulation projects. The daily schedule will include theoretical and practical lectures, instructor-guided hands-on tutorials, and opportunities for one-on-one interaction with the instructors on individual project development. The primary instructors will be Joel Stiles (National Resource for Biomedical Supercomputing) and Thomas Bartol (Computational Neurobiology Laboratory, The Salk Institute), the original developers of MCell and DReAMM.
Workshop content will be targeted to graduate student, postdoctoral, and faculty-level attendees. Space is limited.
