Alejandro F. Villaverde

TL;DR: This contribution aims to compare and highlight the different perspectives and contributions from these fields, with emphasis on two key questions: why are reverse engineering problems so hard to solve, and what methods are available for the particular problems arising from systems biology.

TL;DR: This paper shows how to analyse the structural identifiability of a very general class of nonlinear models by extending methods originally developed for studying observability by implementing STRIKE-GOLDD, a method implemented in a MATLAB toolbox.

TL;DR: Meigo as discussed by the authors is an R and Matlab optimization toolbox that implements metaheuristics capable of solving diverse problems arising in systems biology and bioinformatics, such as continuous nonlinear programming (cNLP) and mixed-integer programming (MINLP) problems, and variable neighborhood search (VNS) for Integer Programming (IP) problems.

TL;DR: MIDER is a method for inferring network structures with information theoretic concepts that may be applied to any type of network, cellular or otherwise and provides a representation of the network in which the distance among nodes indicates their statistical closeness.

TL;DR: MEIGO is presented, an R and Matlab optimization toolbox that implements metaheuristics capable of solving diverse problems arising in systems biology and bioinformatics and its open and modular structure allows the addition of further methods.