Tutorial Presentations

Tutorial presentations given by MMBioS investigators are listed on this page.

Many software packages developed by MMBioS partners include online tutorials; see the listing for each package on the Software page

Tutorial on CellOrganizer

Greg Johnson (MMBioS)

Cellular Dynamics and Modeling Meeting, Cold Spring Harbor Laboratory
March 5, 2015


Microphysiological Simulation Using MCell

Jacob Czech and Markus Dittrich (MMBios)

Cellular Dynamics and Modeling Meeting, Cold Spring Harbor Laboratory
March 5, 2015


Rule-Based Modeling with BioNetGen and RuleBender

James Faeder, Jose Juan Tapia, John Sekar and Leonard Harris (MMBioS)

Cellular Dynamics and Modeling Meeting, Cold Spring Harbor Laboratory
March 2, 2015


Modeling Complex Biochemical Systems in Time and Space

James Faeder, Jose Juan Tapia and Robert Sheehan (MMBioS)

8th International q-bio Conference on Cellular Information Processing
August 13, 2014

The consequences of protein-protein interactions are difficult to specify and track with conventional modeling approaches based on reaction rate equations – simulated using either ODE’s or stochastic chemical kinetics – because of the combinatorially large number of protein phosphoforms and protein complexes that these interactions potentially generate. Rule-based modeling languages such as BioNetGen and Kappa have been developed to address this problem and to allow development of cell regulatory networks based on concise descriptions of biochemical interactions that take the form of rules.


Cell Organizer: Building Models of Cell Structure from Microscope Images and Using them for High-Content Screening and Cell Simulations


Gregory Johnson and Devin Sullivan (Carnegie Mellon University, Pittsburgh, PA, USA)

CYTO 2013
May 18, 2013


CellOrganizer is an open source software system that can learn models of the size, shape and spatial distribution of cellular components directly from images.  These models are generative, which means that they can be used to synthesize new images of cells that are statistically similar to the ones they were trained on.  Such images are useful for testing image analysis algorithms, and can be used as the basis for spatially-realistic cell simulations using systems such as Virtual Cell and MCell.  Perhaps most importantly, CellOrganizer models represent a transportable means of representing the results of High Content Screening (HCS) assays that is not dependent on a specific instrument, assay or cell type.  This tutorial will focus on how to use CellOrganizer and how to interface it with other software. 

See the tutorial


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

glbio mcell tutorial 2013

James Faeder and Markus Dittrich (MMBioS) 

Great Lakes Bioinformatics Conference 2013
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.

See the tutorial: