Features
Summary of the current features
Network visualization linking to Cytoscape
Maximum flexibility for the definition of models and observation functions.
Multi-experiment tasks with local (experiment dependent) and global information.
Multiple types of experimental noise conditions and, accordingly, different types of cost functions for parameter estimation and experimental design.
Maximum flexibility for the definition of unknowns: parameters and initial conditions that may be local (experiment dependent) or global for all tasks.
Several approaches to performing identifiability analysis: i) local and global sensitivity analysis, ii) ranking of parameters, iii) sensitivity clustering, iv) the Fisher Information Matrix (FIM) to asymptotic analyses; v) the plot of two-dimensional projections of the parameter estimation cost function and vi) the robust analysis by means of a Monte-Carlo based approach.
Regularization techniques for parameter estimation.
Parameter estimation post-analysis: goodness of fit analysis, autocorrelation of the residuals.
Sequential-parallel optimal experimental designs: to compute what, how and when to measure.
Parameter estimation and optimal experimental design with general non-linear constraints.
A suite of state of the art numerical methods for simulation to cover a broad range of problems: integration of stiff, non-stiff and/or sparse dynamic systems.
A collection of methods to compute parametric sensitivities: direct methods, finite differences schemes of several orders.
A suite of state of the art numerical methods for optimization to cover a broad range of problems: constrained convex and multimodal, multi-objective nonlinear optimization problems.
The possibility of adding your optimizers to AMIGO2.
Exact jacobian information to accelerate the convergence of local methods.
Enables an enhanced operating mode by automatically interfacing to C.
Full C mode for parameter estimation.
Constrained multi-objective dynamic optimization with the control vector parameterization approach.
Maximum flexibility in the definition of objective functions, linear and non-linear constraints.
Generates reports and plots according to user requirements.