A first version of sysBio, an open source package for modeling and simulation of biological systems. It provides ability to convert reactions into ordinary differential equations (ODEs) and ability to
Molecular dynamics (MD) and related techniques have been used for computer simulations of biomolecular systems for over 40 years, but only recently due to advances in computer hardware, simulation sof
Protein synthesis involves translation initiation, elongation, termination, and ribosome recycling, and each step is controlled intricately by many signaling proteins. Translation initiation can be co
The epithelial-mesenchymal transition (EMT) is a cellular process critical for wound healing, cancer metastasis and embryonic development. Recent efforts have identified the role of hybrid epithelial/
ODE simulations of chemical systems perform poorly when some of the species have extremely low concentrations. Stochastic simulation methods, which can handle this case, have been impractical for larg
