Prof. Dr. Ina Koch - Goehte-Universität Frankfurt a. M.

The modeling and analysis of often highly intertwined signaling networks deliver valuable insights into the function of the biological system. For the analysis of robustness and vulnerability of the system, the determination of all possible signal flows is obligatory. The detection of signal flows, e.g., from signal initiation to cellular response, can be a demanding task for signaling pathways, which often exhibit cyclic regulations.
In the talk, we introduce the concept of Manatee invariants based on transition invariants in the context of Petri nets to enumerate all signal flows in a network including cyclic structures. To illustrate the conceptual ideas, we consider a small Petri net model of a part of the TNFR1-mediated NF-κB signaling pathway. Furthermore, we emphasize the benefit of Manatee invariants as precursors to further analyses like in silico knockouts.