adaptive dynamics agent-based modelling artificial life automated analysis Bayesian inference bioinformatics branching processes Classification classification coalescent combinatorial search comparative genomics computational biology database analysis tools databases differential equations diffusion diffusion controlled reactions dynamic systems extended Kalman filter FEM fermentation processes fluid dynamics Food Web Models Fortran game theory genome analysis genome scale metabolic models geometry-reaction interplay (GRIP) graph theory high performance computing identifiability Image analysis Kalman filter kinetics linear programing linear systems machine learning markov models Mathematica Matrix modelling maximum likelihood Maxsim2 metabolic flux analysis methods model checking model discrimination model reduction models moment closure methods net Networks networks NLME non-linear effects of electro-mechanical coupling non-linear filtering observability ode ODE modelling of individuals and/or ecosystems optimization Parameter Estimation parameter estimation particle filter particle simulations PathwayLab pde Population dynamics population dynamics probability theory qualitative networks Quantification reaction models regression SBGN SBML SDE sde sequential Monte Carlo methods Spatial marked point processes Spatio-temporal modelling spin systems Statistical analysis statistical inference statistical physics Statistics structural bioinformatics system identification Time series uncertainty unscented Kalman filter wavelets