Cell Modeling Workshop 2017

Dates: June 26 - June 28, 2017
Location: Pittsburgh Supercomputing Center, 300 S Craig St, Pittsburgh PA 

Workshop details:   Home   Apply  Agenda  Instructors    Google Maps 

Application deadline: June 2

Deadline to apply and request travel support: April 18


This workshop will cover theory and practice for the design and simulation of cell 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 latest 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 construct and simulate rule-based models using 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 intracellular organization that can be used to compare cell populations and as the basis for cell simulations.
  4. The newest version of CellBlender, our MCell model creation and visualization framework (Czech et al., Methods in Molecular Biology 500: 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.

Please see the preprint of Spatial Stochastic Modeling with MCell and CellBlender for a concise explanation of the theory and motivations for using spatial stochastic modeling as well as detailed steps for creating basic and intermediate CellBlender models.

Workshop instructors:

  • James Faeder (University of Pittsburgh)
  • Thomas Bartol (Salk Institute for Biological Studies)
  • Robert F. Murphy (Carnegie Mellon University)
  • Jacob Czech (Pittsburgh Supercomputing Center)
  • Bob Kuczewski (Salk Institute for Biological Studies)
  • Ivan Cao-Berg (Carnegie Mellon University0

The application deadline is June 2, 2017.  Registration and housing will be free of charge for attendees from non-profit academic institutions. Participants are expected to cover their own travel  and meals. 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.


Housing in three person apartments at the University of Pittsburgh Bouquet Gardens (check-in June 25; check-out June 28) will be provided for participants only. Those preferring a single room or any other arrangements (e.g., early arrival or late departure) need to arrange and pay for their own housing. Participants are responsible for any incidental charges related to their stay in the residence hall.

If you have any questions, please contact This email address is being protected from spambots. You need JavaScript enabled to view it..


CellBlender 1.2 bundle

Data sets