Computational Methods for Spatially Realistic Microphysiological Simulations 2013

Dates: Mon, May 20 - Wed, May 22, 2013

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This workshop was organized by the Center for Multiscale Modeling of Biological Systems and covered 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 ( was introduced, including new Monte Carlo methods for 3-D simulation of reactions in solution and on arbitrarily shaped biological surfaces. Also introduced during the workshop were

  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 lasted three full days, and attendees were strongly encouraged to bring ideas/data for their own simulation projects. The daily schedule included 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 were 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).


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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 at This email address is being protected from spambots. You need JavaScript enabled to view it..