Normal mode analysis (NMA) is one of the major simulation techniques used to probe largescale motions in biomolecules. Typical application is for the prediction of functional motions in proteins. Version 2.0 of the Bio3D package now includes extensive NMA facilities (see also the NMA Vignette). ...
Apart from creation, visualization and static properties analysis of Petri nets, MonaLisa allows dynamic simulation of net behavior, rang- ing from simple random transition firing to complex and comprehensive stochastic simulation of biochemical networks. A user-friendly graphi- cal interface, combined ...