Laboratory of Systems Biology

June 4 – 8, 2012
National Institutes of Health
Bethesda, MD

Part 1 (June 4 – 6)

• Creating quantitative models of cellular signaling using visual tools
• Performing spatially resolved simulations of cellular biochemistry
• Combining biochemical and morphological dynamics

Part 2 (June 6 – 8)

• Using the Simmune software API to develop custom simulations

Part 1 of the course is for experimental biologists who want to learn how to develop and use quantitative computational models of cellular signaling processes. Prior modeling experience is not required due to the unique visual interface of Simmune. Participants should, however, have an active interest in quantitative aspects of cell biological phenomena. The course will provide hands-on guidance using examples such as G-protein coupled receptor signaling, growth factor signaling networks, chemokine sensing, and cellular adhesion.

Part 2 is aimed at computational modelers who want to use the capabilities of the Simmune API in their projects. Programming experience is required. Typically, people participating in the second part may want to join the first part as well.
Participants should ideally bring their own laptops, but computers will also be provided on site.

How To Apply

Please send an email with subject "Course" to simmune@niaid.nih.gov. Include a brief statement of your research interests and specify which part(s) of the course you are interested in.

A limited number of scholarships for travel and lodging are available.

Screenshots of the Simmune Modeling Software

A recent manuscript highlights some of the capabilities of Simmune:
Angermann BR, Klauschen F, Garcia AD, Prustel T, Zhang F, Germain RN, Meier-Schellersheim M. Computational modeling of cellular signaling processes embedded into dynamic spatial contexts. Nat Methods. 2012 Jan 29. Epub ahead of print.

Screenshot of the Simmune modeler visual interface showing the definition of an association reaction between the EGF receptor and Grb2. The conditions under which the association can take place are encoded in the colored tags displayed on the interacting molecules.

Screenshot of the Simmune simulator showing the distribution of adhesion molecules at the interface between two interacting cells. The concentration of the molecules is visualized using a heatmap (blue: low concentration; red: high concentration).

Screenshot of the Simmune simulator showing two interacting cells that have formed a broad contact zone driven by adhesion receptors. The concentration profile of the adhesion receptors along the perimeters of the cells is shown in a cut plane.