Lily Chylek 

Cornell University & Los Alamos National Laboratory

Title: Modeling, visualizing, and annotating immunoreceptor signaling
systems

Abstract: Immunoreceptor signaling is complex, and new computational
modeling approaches, such as rule-based modeling, are needed to advance
our understanding of these systems. However, for computational models of
biochemical systems to be more widely understood and (re)used,
conventions for visualization and annotation are needed. To this end, we
have developed the concepts of an extended contact map and a model
guide. An extended contact map represents the scope of a model by
providing an illustration of each molecule, molecular component, direct
physical interaction, post-translational modification, and
enzyme-substrate relationship considered in a model. Elements of a map
can be associated with elements of an underlying rule-based model
through a model guide, which also serves to document biological
knowledge and model assumptions. We are using these methods in
development of rule-based models for immunoreceptor signaling, with the
goal of analyzing receptor aggregation and downstream phosphorylation
events that can be monitored experimentally.