Based on the SEIR model and the modeling of urban transportation networks, a general-purpose simulator for the spread of epidemics in Chinese cities is built. The Chinese public transportation system between over 340 prefectural-level cities is modeled as a multi-layer bi-partite network, with layers representing different means of transportation (airlines, railways, sail routes and buses), and nodes divided into two categories (central cities, peripheral cities). At each city, an open-system SEIR model tracks the local spread of the disease TRANS
, with population in- and out-flow exchanging with the overlying transportation network. The model accounts for (1) different transmissivities of the epidemic on different transportation media, (2) the transit of inbound flow at cities, (3) cross-infection MESHD
on public transportation vehicles due to path overlap, and the realistic considerations that (4) the infected population are not entering public transportation and (5) the recovered population are not subject to repeated infections. The model could be used to simulate the city-level spread in China (and potentially other countries) of an arbitrary epidemic, characterized by its basic reproduction number TRANS
, incubation period TRANS
, infection MESHD
period and zoonotic force, originated from any Chinese prefectural-level city(s), during the period before effective government interventions are implemented. Flowmaps are input into the system to trigger inter-city dynamics, assuming different flow strength, determined from empirical observation, within/between the bi-partite divisions of nodes. The model is used to simulate the 2019 Coronavirus epidemic in Wuhan; it shows that the framework is robust and reliable, and simulated results match public city-level datasets to an extraordinary extent.