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Evolutionary computation for predicting optimal reaction knockouts and enzyme m...

One of the main purposes of Metabolic Engineering is the quantitative prediction of cell behaviour under selected genetic modifications. These methods can then be used to support adequate strain optimization algorithms in a outer layer. The purpose of the present study is to explore methods in which dynamical models provide for phenotype simulation methods, that will be used as a basis for strain optimization a...

A software platform for evolutionary computation with pluggable parallelism and...

This paper proposes the Java Evolutionary Computation Library (JECoLi), an adaptable, flexible, extensible and reliable software framework implementing metaheuristic optimization algorithms, using the Java programming language. JECoLi aims to offer a solution suited for the integration of Evolutionary Computation (EC)-based approaches in larger applications, and for the rapid and efficient benchmarking of EC al...

OptFlux : an open-source software platform for in silico metabolic engineering

Background: Over the last few years a number of methods have been proposed for the phenotype simulation of microorganisms under different environmental and genetic conditions. These have been used as the basis to support the discovery of successful genetic modifications of the microbial metabolism to address industrial goals. However, the use of these methods has been restricted to bioinformaticians or other ex...

Evolutionary approaches for strain optimization using dynamic models under a me...

One of the purposes of Systems Biology is the quantitative modeling of biochemical networks. In this effort, the use of dynamical mathematical models provides for powerful tools in the prediction of the phenotypical behavior of microorganisms under distinct environmental conditions or subject to genetic modifications. The purpose of the present study is to explore a computational environment where dynamical mod...

OptFlux : a software for metabolic engineering

Implementing metaheuristic optimization algorithms with JECoLi

This work proposes JECoLi - a novel Java-based library for the implementation of metaheuristic optimization algorithms with a focus on Genetic and Evolutionary Computation based methods. The library was developed based on the principles of flexibility, usability, adaptability, modularity, extensibility, transparency, scalability, robustness and computational efficiency. The project is opensource, so JECoLi is m...

A study on the effects of using gene-reaction rules on in silico strain optimiz...

To identify a set of genetic manipulations that will result in a microbial strain with improved production capabilities of a metabolite / product of industrial interest, is one of the greatest challenges in Metabolic Engineering. This problem represents a complex combination between the development of accurate metabolic and regulatory models / networks, plus the need for appropriate simulation and optimization ...

A software tool for the simulation and optimization of dynamic metabolic models

In Systems Biology, there is a growing need for simulation and optimization tools for the prediction of the phenotypical behavior of microorganisms. In this paper, an open-source software platform is proposed to provide support for research in Metabolic Engineering, by implementing tools that enable the simulation and optimization of dynamic metabolic models using ordinary differential equations. Its main funct...

Nonsense mutation in TITF1 in a Portuguese family with benign hereditary chorea

Benign hereditary chorea (BHC) is an autosomaldominant disorder of early onset characterized by a slowly progressing or nonprogressing chorea, without cognitive decline or other progressive neurologic dysfunction, but also by the existence of heterogeneity of the clinical presentation within and among families. The genetic cause of BHC is the presence of either point mutations or deletions in the thyroid transc...

Angio-CT in atheromatous carotid disease.

CT angiography is a diagnostic tool, which is rapidly becoming an important modality for non-invasive evaluation of the neurovasculature. The aim of this article is to review this method, including acquisition and image processing protocols and its application for the evaluation of atherosclerotic stenosis of the carotid artery. Illustrative cases are shown and a revision of the literature is also made. ; CT a...