Cell Modeling Workshop 2018

Dates: March 7 - March 9, 2018
Location: Allen Institute, Seattle WA 

Workshop details:   Home   Apply  Agenda  Instructors

Application deadline: January 21 2018


Jointly sponsored by MMBioS and the Allen Institute for Cell Science

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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.

A laptop with the ability to install cell modeling software is required for the tutorial sessions. Please see the software installation instructions.

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)

The application deadline has passed.

Successful participants will receive a Certificate of Completion.

Applicants offered workshop positions will be notified by email no later than February 1, 2018.

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


Housing information will be available soon. For planning purposes, the following hotels are near the Allen Institute for Cell Science:

  • Marriot Courtyard Hotel, 925 Westlake Avenue North, Seattle WA 98109
    Distance from Workshop location: 0.2 miles, ~5 minute walk
  • Marriot Residence Inn, 800 Fairview Avenue North Seattle WA 98109
    Distance from Workshop location: 0.3 miles, ~6 minute walk
  • Four points by Sheraton Downtown, 601 Roy St., Seattle, WA, 98109
    Distance from Workshop location: 0.5 miles, ~12minute walk
  • The Maxwell Hotel - A Staypineapple Hotel, 300 Roy St, Seattle, WA 98109
    Distance from Workshop location: 0.7 miles, ~15 minute walk
  • Inn at Queen Anne, 505 1st Avenue North, Seattle, WA 98109
    Distance from Workshop location: 0.9 miles, ~22 minute walk


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

A flier (PDF) for the 2018 Cell Modeling workshop is available for printing.