Computational Methods for Spatially Realistic Microphysiological Simulations 2014
Dates: Mon, April 28 - Wed, April 30, 2014
Location: Pittsburgh Supercomputing Center, 300 South Craig Street, Pittsburgh, PA
This workshop is organized by the National Center for Multiscale Modeling of Biological Systems (MMBioS) and 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, users 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:
- 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.
- 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).
- 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.
- 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 will last three full days, and attendees are strongly encouraged to bring ideas/data for their own simulation projects. The daily schedule will include theoretical and practical lectures, instructor-guided hands-on tutorials, and opportunities for one-on-one interaction with the instructors on individual project development.
- James Faeder (University of Pittsburgh)
- Thomas Bartol (Salk Institute for Biological Studies)
- Markus Dittrich (Pittsburgh Supercomputing Center)
- Robert F. Murphy (Carnegie Mellon University)
Registration will be free of charge for attendees from non-profit academic institutions. Participants are expected to cover their own travel and housing expenses.
Workshop content will be targeted to graduate student, postdoctoral, and faculty-level attendees. Due to space constraints, the number of participants will be limited.