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Villaverde A.F.,BioProcess Engineering Group | Barreiro A.,University of Vigo | Raimundez C.,University of Vigo
Automatica | Year: 2010

During the last two decades, important advances have been made in the field of bilateral teleoperation. Different techniques for performing stable teleoperation in non-ideal conditions have been developed, especially in a passivity framework. Until recently, however, no robust solutions for addressing this problem with variable delays and other drawbacks of packet-switched networks have been developed. The requirement of maintaining passivity in these circumstances degrades performance, due to the loss of energy that it involves. In this paper an arrangement is proposed which is capable of eliminating position errors, while maintaining passivity of an Internet-like channel. The behaviour of this new controller is studied by Lyapunov analysis, compared to previous methods, and validated through numerical simulations. © 2010 Elsevier Ltd. All rights reserved. Source

Villaverde A.F.,BioProcess Engineering Group | Ross J.,Stanford University | Moran F.,Complutense University of Madrid | Banga J.R.,BioProcess Engineering Group
PLoS ONE | Year: 2014

The prediction of links among variables from a given dataset is a task referred to as network inference or reverse engineering. It is an open problem in bioinformatics and systems biology, as well as in other areas of science. Information theory, which uses concepts such as mutual information, provides a rigorous framework for addressing it. While a number of information-theoretic methods are already available, most of them focus on a particular type of problem, introducing assumptions that limit their generality. Furthermore, many of these methods lack a publicly available implementation. Here we present MIDER, a method for inferring network structures with information theoretic concepts. It consists of two steps: first, it provides a representation of the network in which the distance among nodes indicates their statistical closeness. Second, it refines the prediction of the existing links to distinguish between direct and indirect interactions and to assign directionality. The method accepts as input time-series data related to some quantitative features of the network nodes (such as e.g. concentrations, if the nodes are chemical species). It takes into account time delays between variables, and allows choosing among several definitions and normalizations of mutual information. It is general purpose: it may be applied to any type of network, cellular or otherwise. A Matlab implementation including source code and data is freely available (http://www.iim.csic.es/∼gingproc/mider.html). The performance of MIDER has been evaluated on seven different benchmark problems that cover the main types of cellular networks, including metabolic, gene regulatory, and signaling. Comparisons with state of the art information-theoretic methods have demonstrated the competitive performance of MIDER, as well as its versatility. Its use does not demand any a priori knowledge from the user; the default settings and the adaptive nature of the method provide good results for a wide range of problems without requiring tuning. © 2014 Villaverde et al. Source

Otero-Muras I.,BioProcess Engineering Group | Banga J.R.,BioProcess Engineering Group
BMC Systems Biology | Year: 2014

Background: One of the challenges in Synthetic Biology is to design circuits with increasing levels of complexity. While circuits in Biology are complex and subject to natural tradeoffs, most synthetic circuits are simple in terms of the number of regulatory regions, and have been designed to meet a single design criterion.Results: In this contribution we introduce a multiobjective formulation for the design of biocircuits. We set up the basis for an advanced optimization tool for the modular and systematic design of biocircuits capable of handling high levels of complexity and multiple design criteria. Our methodology combines the efficiency of global Mixed Integer Nonlinear Programming solvers with multiobjective optimization techniques. Through a number of examples we show the capability of the method to generate non intuitive designs with a desired functionality setting up a priori the desired level of complexity.Conclusions: The methodology presented here can be used for biocircuit design and also to explore and identify different design principles for synthetic gene circuits. The presence of more than one competing objective provides a realistic design setting where every solution represents an optimal trade-off between different criteria. © 2014 Otero Muras and Banga; licensee BioMed Central Ltd. Source

Villaverde A.F.,BioProcess Engineering Group | Egea J.A.,Technical University of Cartagena | Banga J.R.,BioProcess Engineering Group
BMC Systems Biology | Year: 2012

Background: Mathematical models play a key role in systems biology: they summarize the currently available knowledge in a way that allows to make experimentally verifiable predictions. Model calibration consists of finding the parameters that give the best fit to a set of experimental data, which entails minimizing a cost function that measures the goodness of this fit. Most mathematical models in systems biology present three characteristics which make this problem very difficult to solve: they are highly non-linear, they have a large number of parameters to be estimated, and the information content of the available experimental data is frequently scarce. Hence, there is a need for global optimization methods capable of solving this problem efficiently.Results: A new approach for parameter estimation of large scale models, called Cooperative Enhanced Scatter Search (CeSS), is presented. Its key feature is the cooperation between different programs (" threads" ) that run in parallel in different processors. Each thread implements a state of the art metaheuristic, the enhanced Scatter Search algorithm (eSS). Cooperation, meaning information sharing between threads, modifies the systemic properties of the algorithm and allows to speed up performance. Two parameter estimation problems involving models related with the central carbon metabolism of E. coli which include different regulatory levels (metabolic and transcriptional) are used as case studies. The performance and capabilities of the method are also evaluated using benchmark problems of large-scale global optimization, with excellent results.Conclusions: The cooperative CeSS strategy is a general purpose technique that can be applied to any model calibration problem. Its capability has been demonstrated by calibrating two large-scale models of different characteristics, improving the performance of previously existing methods in both cases. The cooperative metaheuristic presented here can be easily extended to incorporate other global and local search solvers and specific structural information for particular classes of problems. © 2012 Villaverde et al.; licensee BioMed Central Ltd. Source

Villaverde A.F.,BioProcess Engineering Group | Banga J.R.,BioProcess Engineering Group
Journal of the Royal Society Interface | Year: 2014

The interplay of mathematical modelling with experiments is one of the central elements in systems biology. The aim of reverse engineering is to infer, analyse and understand, through this interplay, the functional and regulatory mechanisms of biological systems. Reverse engineering is not exclusive of systems biology and has been studied in different areas, such as inverse problem theory, machine learning, nonlinear physics, (bio)chemical kinetics, control theory and optimization, among others. However, it seems that many of these areas have been relatively closed to outsiders. In this contribution, we aim to compare and highlight the different perspectives and contributions from these fields, with emphasis on two key questions: (i) why are reverse engineering problems so hard to solve, and (ii) what methods are available for the particular problems arising from systems biology? © 2013 The Authors. Published by the Royal Society. Source

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