Computational Methods for Spatially Realistic Microphysiological Simulations

Workshop Dates: Mon, May 7 - Wed, May 9, 2012
Location: Pittsburgh Supercomputing Center, 300 South Craig Street, Pittsburgh, PA 15213
Registration Deadline: April 9th, 2012
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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. The current version of the MCell simulation environment ( will be introduced, including new Monte Carlo methods for 3-D simulation of reactions in solution and on arbitrarily shaped biological surfaces. During the workshop we will also introduce

  1. Novel tools to incorporate rule-based modeling techniques into MCell simulations based on the BioNetGen Software (Faeder et al., Methods in Molecular Biology, Systems Biology, 2009, ed. Maly, Ivan V. Humana Press, Clifton, NJ, 113-167).
  2. A new MCell model creation and visualization framework based on Blender ( that builds on our previously developed model creation pipeline (Czech et al., Methods in Molecular Biology, Systems Biology, 2009, ed. Maly, Ivan V. Humana Press, Clifton, NJ, 237-287).

This workshop will last three 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 Thomas Bartol (Computational Neurobiology Laboratory, The Salk Institute, original developer of MCell), Jim Faeder (University of Pittsburgh, developer of BioNetGen) and Markus Dittrich (NRBSC, PSC).

Registration will be free of charge for attendees from non-profit academic institutions. Participants are expected to cover their own travel and housing expenses.

Workshop content will be targeted to graduate student, postdoctoral, and faculty-level attendees. Space is limited.

If you have any questions, please contact Pat Sudac

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