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Protocol
Automated Biocircuit Design with SYNBADm
SYNBADm is a Matlab toolbox for the automated design of biocircuits using a model-based optimization approach. It enables the design of biocircuits with pre-defined functions starting from libraries of biologi...
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Protocol
Synthetic Gene Circuit Analysis and Optimization
Synthetic biology aims at engineering synthetic circuits with pre-defined target functions. From a systems (model-based) perspective, the following problems are of central importance: (1) given the model of a ...
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Article
Open AccessUsing optimal control to understand complex metabolic pathways
Optimality principles have been used to explain the structure and behavior of living matter at different levels of organization, from basic phenomena at the molecular level, up to complex dynamics in whole pop...
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Article
A dual-parameter identification approach for data-based predictive modeling of hybrid gene regulatory network-growth kinetics in Pseudomonas putida mt-2
Data integration to model-based description of biological systems incorporating gene dynamics improves the performance of microbial systems. Bioprocess performance, typically predicted using empirical Monod-ty...
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Article
Hybrid parallel multimethod hyperheuristic for mixed-integer dynamic optimization problems in computational systems biology
This paper describes and assesses a parallel multimethod hyperheuristic for the solution of complex global optimization problems. In a multimethod hyperheuristic, different metaheuristics cooperate to outperfo...
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Article
Open AccessParameter estimation in models of biological oscillators: an automated regularised estimation approach
Dynamic modelling is a core element in the systems biology approach to understanding complex biosystems. Here, we consider the problem of parameter estimation in models of biological oscillators described by d...
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Article
A cloud-based enhanced differential evolution algorithm for parameter estimation problems in computational systems biology
Metaheuristics are gaining increasing recognition in many research areas, computational systems biology among them. Recent advances in metaheuristics can be helpful in locating the vicinity of the global solut...
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Article
Open AccessParameter identifiability analysis and visualization in large-scale kinetic models of biosystems
Kinetic models of biochemical systems usually consist of ordinary differential equations that have many unknown parameters. Some of these parameters are often practically unidentifiable, that is, their values ...
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Article
Open AccessParameter estimation in large-scale systems biology models: a parallel and self-adaptive cooperative strategy
The development of large-scale kinetic models is one of the current key issues in computational systems biology and bioinformatics. Here we consider the problem of parameter estimation in nonlinear dynamic mod...
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Chapter and Conference Paper
A Heuristic Method to Optimize High-Dimensional Expensive Problems: Application to the Dynamic Optimization of a Waste Water Treatment Plant
The mathematical description of industrial processes usually requires the use of models consisting of large systems of differential and algebraic equations. The numerical simulations of such models may lead to...
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Chapter and Conference Paper
Evaluation of Parallel Differential Evolution Implementations on MapReduce and Spark
Global optimization problems arise in many areas of science and engineering, computational and systems biology and bioinformatics among them. Many research efforts have focused on develo** parallel metaheuri...
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Chapter and Conference Paper
PREMER: Parallel Reverse Engineering of Biological Networks with Information Theory
A common approach for reverse engineering biological networks from data is to deduce the existence of interactions among nodes from information theoretic measures. Estimating these quantities in a multidimensi...
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Chapter and Conference Paper
Implementing Parallel Differential Evolution on Spark
Metaheuristics are gaining increased attention as an efficient way of solving hard global optimization problems. Differential Evolution (DE) is one of the most popular algorithms in that class. However, its ap...
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Article
Open AccessRobust and efficient parameter estimation in dynamic models of biological systems
Dynamic modelling provides a systematic framework to understand function in biological systems. Parameter estimation in nonlinear dynamic models remains a very challenging inverse problem due to its nonconvexi...
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Article
Open AccessEnabling network inference methods to handle missing data and outliers
The inference of complex networks from data is a challenging problem in biological sciences, as well as in a wide range of disciplines such as chemistry, technology, economics, or sociology. The quantity and q...
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Article
Reaction network realizations of rational biochemical systems and their structural properties
In this paper, a frequently used representation of mass-action type reaction networks is extended to a more general system class where the reaction rates are in rational function form. An algorithm is given to...
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Article
Open AccessOptimal programs of pathway control: dissecting the influence of pathway topology and feedback inhibition on pathway regulation
Adjusting the capacity of metabolic pathways in response to rapidly changing environmental conditions is an important component of microbial adaptation strategies to stochastic environments. In this work, we u...
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Article
Open AccessBioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology
Dynamic modelling is one of the cornerstones of systems biology. Many research efforts are currently being invested in the development and exploitation of large-scale kinetic models. The associated problems of...
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Article
Open AccessMulticriteria global optimization for biocircuit design
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...
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Article
Open AccessMEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics
Optimization is the key to solving many problems in computational biology. Global optimization methods, which provide a robust methodology, and metaheuristics in particular have proven to be the most efficient...
