In 2000, development began on a prototype platform for supporting multilevel modeling, under the leadership of Professor Taishin Nomura at the BioDynamics Laboratory of Osaka University. The platform was named insilicoIDE (ISIDE) in 2006, and at the same time, insilicoML (ISML) was developed as the model description language. In 2007, development began on the insilicoSim simulator and insilicoDB database with the aid of the MEXT Global Center of Excellence program for “an In Silico Medicine-Oriented Worldwide Open Platform” at Osaka University (Leader: Prof. Taishin Nomura, Osaka University, 2007–2011).
In 2010, the PhysioDesigner project was started by Dr. Hiroaki Kitano in collaboration with Prof. Taishin Nomura, SBI and all developers of ISIDE. PhysioDesigner officially took over the development stream from ISIDE in 2011. All functions implemented on ISIDE were reimplemented on PhysioDesigner and new features were added. PHML was also developed concurrently with PhysioDesigner, inheriting ISML specifications.
Since 2010, support has been provided by the MEXT Grant-in-Aid for Scientific Research on Innovative Areas, “HD Physiology” project (Manager: Prof. Yoshihisa Kurachi, Osaka University, 2010–1014), which has accelerated the development of PhysioDesigner.