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Protocol
Multi-Objective Optimization Tuning Framework for Kinetic Parameter Selection and Estimation
Semi-mechanistic kinetic (i.e., dynamic) models based on first principles are particularly relevant in biology, as they can explain and predict functional behavior that arises from varying concentrations of th...
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Protocol
Stochastic Differential Equations for Practical Simulation of Gene Circuits
The Chemical Langevin Equation approach allows simple stochastic simulation of gene circuits under many practical situations where the number of molecules of the species involved is not extremely low. Here, we...
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Article
Open AccessFlux-dependent graphs for metabolic networks
Cells adapt their metabolic fluxes in response to changes in the environment. We present a framework for the systematic construction of flux-based graphs derived from organism-wide metabolic networks. Our grap...
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Article
Open AccessPFA toolbox: a MATLAB tool for Metabolic Flux Analysis
Metabolic Flux Analysis (MFA) is a methodology that has been successfully applied to estimate metabolic fluxes in living cells. However, traditional frameworks based on this approach have some limitations, par...
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Article
Open AccessMulti-objective optimization framework to obtain model-based guidelines for tuning biological synthetic devices: an adaptive network case
Model based design plays a fundamental role in synthetic biology. Exploiting modularity, i.e. using biological parts and interconnecting them to build new and more complex biological circuits is one of the key...
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Article
Open AccessValidation of an FBA model for Pichia pastoris in chemostat cultures
Constraint-based metabolic models and flux balance analysis (FBA) have been extensively used in the last years to investigate the behavior of cells and also as basis for different industrial applications. In this...
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Article
Open AccessTopology analysis and visualization of Potyvirus protein-protein interaction network
One of the central interests of Virology is the identification of host factors that contribute to virus infection. Despite tremendous efforts, the list of factors identified remains limited. With omics techniq...
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Article
Reaction rate reconstruction from biomass concentration measurement in bioreactors using modified second-order sliding mode algorithms
This paper deals with the estimation of unknown signals in bioreactors using sliding observers. Particular attention is drawn to estimate the specific growth rate of microorganisms from measurement of biomass ...
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Article
Open AccessValidation of a constraint-based model of Pichia pastoris metabolism under data scarcity
Constraint-based models enable structured cellular representations in which intracellular kinetics are circumvented. These models, combined with experimental data, are useful analytical tools to estimate the s...
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Article
Open AccessA possibilistic framework for constraint-based metabolic flux analysis
Constraint-based models allow the calculation of the metabolic flux states that can be exhibited by cells, standing out as a powerful analytical tool, but they do not determine which of these are likely to be ...
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Article
Open AccessA procedure for the estimation over time of metabolic fluxes in scenarios where measurements are uncertain and/or insufficient
An indirect approach is usually used to estimate the metabolic fluxes of an organism: couple the available measurements with known biological constraints (e.g. stoichiometry). Typically this estimation is done...
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Article
Application of Functional Intervals to the Response Evaluation of Linear Time-Invariant Systems with Fuzzy Input
Functional input uncertainty is investigated for linear time-invariant (LTI) systems. This kind of uncertainty arises, for instance, when actuator's reliability is taken into account. In this case, the system ...
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Chapter
System Identification. Performance and Closed-loop Issues
Many of the most fruitful control design methods lie in the availability of a process model. Obtaining this model becomes, in many practical, cases a non-trivial task. Physical insight into the process may pro...
