Cell Modeling Workshop 2019

Dates: May 8 - May 10, 2019
Location: Pittsburgh Supercomputing Center

Workshop details:   Home | Apply | Agenda | Instructors

This workshop covered 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 learned 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 focused 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 lasted three full days, and attendees were 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.

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) 

 

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