Documentation

Startup guide

Find out the requirements to use AMIGO2, how to install the toolbox and how to start running tasks in AMIGO2_startup_guide.pdf.

Theoretical background

Theoretical concepts underlying model parametric identification, optimization based modeling and multi-objective dynamic optimization for biological design as considered in the toolbox can be found in AMIGO2_theory.pdf.

Publications

• Eva Balsa-Canto; David Henriques; Attila Gabor; Julio R. Banga. AMIGO2, a toolbox for dynamic modeling, optimization and control in systems biology Bioinformatics 2016; doi: 10.1093/bioinformatics/btw411 (link)

Theoretical background and examples related to Inverse Optimal Control can be found in:

• Tsiantis, N., E. Balsa-Canto and J. R. Banga. Optimality and identification of dynamic models in systems biology: an inverse optimal control framework. Bioinformatics 2018, doi: 10.1093/bioinformatics/bty139 (link)