E-CELL: software environment for whole-cell simulation. - Masaru Tomita; Kenta Hashimoto; Koichi Takahashi; Thomas Simon Shimizu; Yuri Matsuzaki; Fumihiko Miyoshi; Kanako Saito; Sakura Tanida; Katsuyuki Yugi; J. Craig Venter; Clyde A. Hutchison III (Bioinform., 1999)

STOCHSIM: modelling of stochastic biomolecular processes. - Nicolas Le Novère; Thomas Simon Shimizu (Bioinform., 2001)

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. - Michael Hucka; Andrew Finney; Herbert M. Sauro; H. Bolouri; John C. Doyle 001; Hiroaki Kitano; Adam P. Arkin; Benjamin J. Bornstein; Dennis Bray; Athel Cornish-Bowden; Autumn A. Cuellar; Serge Dronov; et al. (Bioinform., 2003)