Computational Methods for Spatially Realistic Microphysiological Simulations 2015

Dates: Mon, April 27 - Wed, April 29, 2015
Location: Pittsburgh Supercomputing Center, 300 S Craig St, Pittsburgh PA 

Workshop details:    Home  Agenda  Instructors  Evaluations

Application deadline: April 1, 2015


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.

During the workshop, participants will  learn how to use the tools developed by MMBioS to create, run, and analyze models of cellular microphysiology and apply them to their own research questions. In particular, the workshop will focus on:

  1. The lastest version of the MCell simulation environment, including new Monte Carlo methods for 3-D simulation of reactions in solution and on arbitrarily shaped biological surfaces.
  2. Novel tools to incorporate rule-based modeling techniques into MCell simulations based on the BioNetGen software (Faeder et al., Methods in Molecular Biology, 500:113-167, 2009).
  3. The CellOrganizer system (Murphy, Methods in Cell Biology 110:179-193, 2012) for creating image-derived models of cell shape and organization that can be used in MCell.
  4. The newest version of CellBlender, our MCell model creation and visualization framework (Czech et al., Methods in Molecular Biology 500:
  5. 237-287, 2009).


This workshop lasts three full days, and attendees are strongly encouraged to bring ideas/data for their own simulation projects. The daily schedule includes theoretical and practical lectures, instructor-guided hands-on tutorials, and opportunities for one-on-one interaction with the instructors on individual project development.


Workshop agenda


Workshop instructors:

  • James Faeder (University of Pittsburgh)
  • Thomas Bartol (Salk Institute for Biological Studies)
  • Markus Dittrich (Pittsburgh Supercomputing Center)
  • Robert F. Murphy (Carnegie Mellon University)
  • Jose-Juan Tapia (University of Pittsburgh)
  • Devin Sullivan
  • Jacob Czech (Pittsburgh Supercomputing Center)

The application deadline has passed.  Registration will be free of charge for attendees from non-profit academic institutions. Participants are expected to cover their own travel and housing expenses. Limited travel support is available for participants who may not otherwise be able to attend. To request support, please submit a request explaining the circumstances along with a CV when applying.

Successful participants will receive a Certificate of Completion.

Workshop content is targeted to graduate student, postdoctoral, and faculty-level attendees. Due to space constraints, the number of participants is 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..

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