We present explicit and online Model Predictive Controllers (MPCs) for an excitable cell simulator based on the nonlinear FitzHugh-Nagumo model. Despite the plant’s nonlinearity, we are able to formulate the model predictive control problem as an instance of quadratic programming, using a PieceWise Affine (PWA) abstraction of the plant. The speed-versus-accuracy tradeoff for the explicit and on...

1Laboratory of Computational Biology and Bioinformatics, Institute of Public Health and Environment, School of Public Health, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 151-742, Korea 2Molecular Recognition Research Center, Korea Institute of Science and Technology, Hwarangno 14-gil, Seongbuk-gu, Seoul 136-791, Korea 3High-performance Biocomputing Team, Supercomputing RandD Center...

Bologna Biocomputing Group, University of Bologna, via S. Giacomo 9/2, I-40126, Bologna, Italy, Department of Biological, Geological and Environmental Sciences (BIGEA), University of Bologna, via Selmi 3, I-40126, Bologna, Italy, Department of Computer Science and Engineering, University of Bologna, Mura A. Zamboni 7, I-40126, Bologna, Italy, Health Science and Technologies-ICIR, University of ...

Precision medicine research efforts both in basic science discovery and clinical implementation are well underway and promise to provide individualized preventions and treatments, improving overall health care delivery. To achieve these goals, advances in data capture and analysis are needed spanning different types of 'omic and clinical data. The efforts to enhance precise treatments for all m...

We were pleased to see PLoS Conference Postcards return to the Pacific Symposium on Biocomputing (PSB), held January 4–11, 2011. This year we received a Postcard from A. Murat Eren, a PhD student at the University of New Orleans, in which he discusses a software package designed for use in microbial ecology research. We hope to see Conference Postcards at ISMB 2011, and if you would like to con...

We consider a realization of the XOR logic gate in a process biocatalyzed by an enzyme which can be inhibited by a substrate when the latter is inputted at large enough concentrations. A model is developed for describing such systems in an approach suitable for evaluation of the analog noise amplification properties of the gate. The obtained data are fitted for gate quality evaluation within th...

The study of genetic regulatory networks has become an important field of research in biomathematics and biocomputing. With the early progresses made in biotechnology, there will be more and more data available concerning the expression of genes ; the understanding of such complex systems will then become crucial. However, even though several serious models have been proposed ([3], [1]), these ...

Synthesis of chiral amines by amine dehydrogenase has the advantages environmental friendliness, high stereoselectivity, and mild reaction conditions. However, low catalytic activity, which greatly limits its application in large-scale synthesis amines. In this study, a novel was obtained modifying substrate specificity leucine via computer-aided protein engineering strategy. Furthermore, conse...

Multiple sequence alignment (MSA), used in biocomputing to study similarities between different genomic sequences, is known to require important memory and computation resources. Nowadays, researchers are aligning thousands of these sequences, creating new challenges in order to solve the problem using the available resources efficiently. Determining the efficient amount of resources to allocat...

MOTIVATION Predicting the ground state of biopolymers is a notoriously hard problem in biocomputing. Model systems, such as lattice proteins, are simple tools and valuable to test and improve new methods. Best known are models with sequences composed from a binary (hydrophobic and polar) alphabet. The major drawback is the degeneracy, i.e. the number of different ground state conformations. R...