Global network identification from reconstructed dynamical structure subnetworks: Applications to biochemical reaction networks

In this paper we consider the problem of network reconstruction, with applications to biochemical reaction networks. We consider the problem of global network reconstruction when there are a limited number of sensors that can be used to simultaneously measure state information. We introduce dynamical structure functions as a way to formulate the network reconstruction problem and motivate their usage with an example physical system from synthetic biology. In particular, we argue that in synthetic biology research, network verification is paramount to robust circuit operation and thus, network reconstruction is an invaluable tool. Nonetheless, we argue that existing approaches for reconstruction are hampered by limited numbers of biological sensors with high temporal resolution. In this way, we motivate the global network reconstruction problem using partial network information and prove that by performing a series of reconstruction experiments, where each experiment reconstructs a subnetwork dynamical structure function, the global dynamical structure function can be recovered under certain conditions. We illustrate these reconstruction techniques on a recently developed four gene biocircuit, an event detector, used for implementing temporal logic.