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Visualisation and analysis of stochastic flow through large network diagrams of biological pathways

CISA Seminar Series
Tom Freeman

Over the last few years we have been developing a graphical language, the modified Edinburgh Pathway Notation scheme (mEPN), with which to logically depict the biological interactions that together make up pathways (1-3). We have used this language to construct a number of large-scale pathways associated with immune signaling and effector systems and have been exploring ways to model the activity of these networks. To this end, we have refactored a highly optimized version of the Signaling Petri Net (SPN) algorithm (4) and implemented it within the program BioLayout Express3D ( We have also built a visualization engine within the tool to permit the analysis of rule-based stochastic flow simulations through large pathway models and network systems. I will discuss this work and how we hope to use this technology for hypothesis generation and testing with respect to signaling pathways and transcription networks underpinning the workings of the immune system.

1. Raza et al., BMC Systems Biology 2008, 2:36
2. Freeman et al., BMC Systems Biology 2010, 4:65
3. Raza et al., BMC Systems Biology 2010, 4:63
4. Ruths et al., PLoS Comput Biol 2008, 4:e1000005

Date and time: 
Monday, 7 June, 2010 - 14:00
60 minutes
Research topics: