Modelling is at the core of systems biology. Models help to reconcile hypothesis with data gaining new biological knowledge; models can be used to make predictions and reply to what if, when or even where questions and models can also be used to design and control the performance of a particular bioprocess or biosystem.

Many problems of interest in modeling and optimal control of biological systems can be posed as non-linear optimisation problems subject to algebraic and dynamic constraints.  In the context of modelling, this is the case of, e.g. parameter estimation, optimal experimental design, inverse optimal control or dynamic flux balance analysis. In the context of optimal control, model-based metabolic engineering, pattern formation or drug dose optimisation problems can be formulated as (multi-objective) dynamic optimisation problems.

The AMIGO2 toolbox is a multiplatform (MATLAB-based) software tool that automatizes the solution of all those problems, offering a suite of state-of-the-art (multi-objective) global optimisers and advanced simulation approaches.

In this talk, I will introduce what AMIGO2 has to offer to systems biologists and show its features with some illustrative examples.