Institute of Fundamental Technological Research

Rule-based modeling provides a means to represent cell signaling systems in a way that captures site-specific details of molecular interactions. For rule-based models to be more widely understood and (re)used, conventions for model visualization and annotation are needed. We have developed the concepts of an extended contact map and a model guide for illustrating and annotating rule-based models. 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. A map can also illustrate allosteric effects, structural relationships among molecular components, and compartmental locations of molecules. A model guide associates elements of a contact map with annotation and elements of an underlying model, which may be fully or partially specified. A guide can also serve to document the biological knowledge upon which a model is based. We provide examples of a map and guide for a published rule-based model that characterizes early events in IgE receptor (FceRI) signaling. We also provide examples of how to visualize a variety of processes that are common in cell signaling systems but not considered in the example model, such as ubiquitination. An extended contact map and an associated guide can document knowledge of a cell signaling system in a form that is visual as well as executable. As a tool for model annotation, a map and guide can communicate the content of a model clearly and with precision, even for large models.

This paper deals with measurements of convective velocity of large-scale thermal structures, using the thin foil technique and infrared thermography to visualize the thermal pattern on the wall. An image correlation method is proposed to track the displacement of the observed thermal pattern. The idea of the method is similar to that of particle image velocimetry, but the thermal patterns on the heated wall are used, rather than tracing particles. On this basis, the thermal patterns created by the coherent structures of turbulent channel flow are examined. Particular attention is paid to the determination of the optimal parameters of image acquisition, including spatial and temporal separation. An attempt is made to relate momentum and scalar transport analyses by considering the propagation velocity of large-scale temperature structures. The proposed technique appears to be an attractive alternative for non-intrusive analysis of turbulent flow, especially, where opaqueness of channel walls excludes the use of optical methods.