Computational Methods for Spatially Realistic Microphysiological Simulations

Workshop Dates: Mon, May 20 - Wed, May 22, 2013
Location: Pittsburgh Supercomputing Center, 300 South Craig Street, Pittsburgh, PA 15213
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Application Deadline: April 7th, 2013

Application is now closed (please contact for any potential late applications)

This workshop is organized by the Center for Multiscale Modeling of Biological Systems and 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 lastest 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. Our new MCell model creation and visualization framework called CellBlender 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. Due to space constraints, the number of participants will be limited.

If you have any questions, please contact Pat Sudac