Outreach


2014 Events


Computational Methods for Spatially Realistic Microphysiological Simulations

Workshop Dates: April 28 - 30, 2014
Location: Pittsburgh Supercomputing Center, 300 South Craig Street, Pittsburgh, PA 15213

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:

  1. 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.
  2. 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).
  3. 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.
  4. The newest version of CellBlender, our MCell model creation and visualization framework (Czech et al., Methods in Molecular Biology 500: 237-287, 2009).

Additional information can be found on the MMBioS page.




2013 Events


Computational Methods for Spatially Realistic Microphysiological Simulations

Workshop Dates: May 20 - May 22, 2013
Location: Pittsburgh Supercomputing Center, 300 South Craig Street, Pittsburgh, PA 15213

This workshop is organized by the Center for Multiscale Modeling of Biological Systems 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. The lastest version of the MCell simulation environment will be introduced, including new Monte Carlo methods for 3-D simulation of reactions in solution and on arbitrarily shaped biological surfaces.

Additional information can be found on the MMBioS page.




Spatial Rule-based Modeling of Cellular Biochemistry with MCell/ BioNetGen/ CellBlender

Event: GLBIO 2013
Date: May 14, 2013

In this tutorial we will introduce several simulation tools for the modeling of complex and spatially realistic biochemical and cellular systems: BioNetGen, MCell and CellBlender.

BioNetGen is a software for the specification and simulation of rule-based models of biochemical systems, including signal transduction, metabolic, and genetic regulatory networks; MCell (Monte Carlo cell) is a simulation package that uses spatially realistic 3D cellular models and specialized Monte Carlo algorithms to simulate the movements and reactions of molecules within and between cells — cellular microphysiology. Its companion program CellBlender is an integrated MCell model development, simulation and analysis package.

Additional information can be found on the MMBioS page.

 
 
  • News and Events

    October 24, 2014: Postdoctoral Research Position Available

    Postdoctoral Research Fellow position available in the Biomedical Applications Group at the Pittsburgh Supercomputing Center (PSC).

    April 27, 2014: CellBlender 1.0 Release Candidate 3

    CellBlender 1.0 RC3 is available from our Downloads page.

    February 19, 2014: New MCell Workshop

    Registration open for the new MCell workshop on April 28-30, 2014.

    February 11, 2014: MCell 3.2.1 Now Available

    New MCell versions for OS X, Windows, and Linux (including 64-bit) are available from our Downloads page.

    November 18, 2013: Forums

    The MCell and CellBlender forums are now live.

    October 11, 2013: Downloads now available through MMBioS

    MCell and Cellblender are now available on mmbios.org. See the Downloads page.

    September 30, 2013: MCell 3.2 Now Available

    New MCell versions for OS X, Windows, and Linux (including 64-bit) are available from our Downloads page.

    September 30, 2013: MCell Source Code Available on Github

    The source code for MCell is available from our github repository.

    September 9, 2013: Added Outreach page and New Documentation

    Documentation from the 2013 MCell workshop was added. A new outreach tab has been added, highlighting recent workshops and presentations.