Multistate Model Builder (MSMB): a flexible editor for compact biochemical models. - Alida Palmisano; Stefan Hoops; Layne T. Watson; Thomas C. Jones Jr; John J. Tyson; Clifford A. Shaffer (BMC Syst. Biol., 2014)

JigCell Run Manager (JC-RM): a tool for managing large sets of biochemical model parametrizations. - Alida Palmisano; Stefan Hoops; Layne T. Watson; Thomas C. Jones Jr; John J. Tyson; Clifford A. Shaffer (BMC Syst. Biol., 2015)

JigCell Model Connector: building large molecular network models from components. - Thomas C. Jones Jr; Stefan Hoops; Layne T. Watson; Alida Palmisano; John J. Tyson; Clifford A. Shaffer (Simul., 2018)