CellOrganizer

This workshop covers 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. The workshop focuses on the following tools:

• The MCell simulation environment, including new Monte Carlo methods for 3-D simulation of reactions in solution and on arbitrarily shaped biological surfaces. The newest version of CellBlender our MCell model creation and visualization framework.
• The BioNetGen software for specifying, simulating, and analyzing biochemical networks using a modular, rule-based approach.
• The CellOrganizer system for creating image-derived models of cell shape and intracellular organization that can be used to compare cell populations and to create cell simulations for diverse cell geometries to explore the effect of variation in cell organization on microphysiology.

This workshop will span four full days, and attendees are 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 for individual project development.