We have recently developed a tool, called as the bifurcation discovery tool (BDT), which can be used to search the parameter space to look for interesting dynamical behavior, such as multistability, and oscillations. The analysis and algorithms are described in the following paper. 

V. Chickarmane, S. Paladugu, F. Bergman and H.M. Sauro, “Bifurcation Discovery Tool,” Bioinformatics, 21(18), 3688-3690, 2005.

Documentation:
BDT Tutorial Document

You can download the BDT from here.

As part of the Biospice project, we built an optimizer, which is based on the systems biology workbench. The optimizer fits time series concentration data, to a model and returns the best fitted parameter values and their standard deviations, using Monte-Carlo techniques. We have implemented several local, global and hybrid search algorithms, such as Levenberg-Marquardt, Simplex, Simulated Annealing, Genetic Algorithms and Simplex-Genetic hybrids.

Preprints:
Chickarmane et al 2004, Technical Paper on Optimization
Documentation