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作者： Jacq, N. Salzemann, J. Jacq, F. Legré, Y. Medernach, E. Montagnat, J. Maaß, A. Breton, V. Schwichtenberg, H. Sridhar, M. Kasam, V. Zimmermann, M. Hofmann, M. Breton, V. Laboratoire de Physique Corpusculaire Université Blaise Pascal IN2P3-CNRS UMR 6533 24 Avenue des Landais 63177 Aubière France Communication and Systèmes Grenoble France Informatique Signaux et Systèmes Université de Nice Sophia Antipolis CNRS UMR 6070 Sophia Antipolis France Department of Simulation Engineering Fraunhofer Institute for Algorithms and Scientific Computing Sankt Augustin Germany Department of Bioinformatics Fraunhofer Institute for Algorithms and Scientific Computing Sankt Augustin Germany

WISDOM is an international initiative to enable a virtual screening pipeline on a Grid infrastructure. Its first attempt was to deploy large scale in silico docking on a public Grid infrastructure. Protein-ligand docking is about computing the binding energy of a protein target to a library of potential drugs using a scoring algorithm. Previous deployments were either limited to one cluster, to Grids of clusters in the tightly protected environment of a pharmaceutical laboratory or to desktop Grids. The first large scale docking experiment ran on the EGEE Grid production service from 11 July 2005 to 19 August 2005 against targets relevant to research on malaria and saw over 41 million compounds docked for the equivalent of 80 years of CPU time. Up to 1,700 computers were simultaneously used in 15 countries around the world. Issues related to the deployment and the monitoring of the in silico docking experiment as well as experience with Grid operation and services are reported in the paper. The main problem encountered for such a large scale deployment was the Grid infrastructure stability. Although the overall success rate was above 80%, a lot of monitoring and supervision was still required at the application level to resubmit the jobs that failed. But the experiment demonstrated how Grid infrastructures have a tremendous capacity to mobilize very large CPU resources for well targeted goals during a significant period of time. This success leads to a second computing challenge targeting avian flu neuraminidase N1. © Springer Science + Business Media B.V. 2007.

关键词： Grid computing

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Automatic composition of music with methods of computational intelligence

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WSEAS Transactions on Information Science and Applications 2007年第3期4卷 508-515页

作者： Klinger, Roman Rudolph, Günter Fraunhofer Institute for Algorithms and Scientific Computation Department of Bioinformatics Schloss Birlinghoven 53754 Sankt Augustin Germany University of Dortmund Department of Computer Science LS XI - Computational Intelligence 44221 Dortmund Germany

We describe our approach for the automatic composition of monophone melodies on a user given chord sequence. For this purpose we use Markov-chains and other methods to build some initial individuals. These are then optimised with evolutionary algorithms using automatically learned classifiers next to interactive evaluation as fitness functions.

关键词： Computer music

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Reconstruction of chemical molecules from images

Reconstruction of chemical molecules from images

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29th Annual International Conference of IEEE-EMBS, Engineering in Medicine and Biology Society, EMBC'07

作者： Algorri, Maria-Elena Zimmermann, Marc Friedrich, Christoph M. Akle, Santiago Hofmann-Apitius, Martin Department of Digital Systems Instituto Tecnologico Autonomo de Mexico Mexico City Dept. of Bioinformatics Fraunhofer Institute for Algorithms and Scientific Computing Sankt Augustin Germany

ISBN: (纸本)1424407885

We have developed a system for the automatic reconstruction of chemical molecules from images. The system takes as input an electronically produced image of a chemical molecule and produces an SDF file containing the complete chemical description of the molecule. The SDF file can then be read and used by most chemical computer programs. Our system finds extensive application in information extraction problems where the molecule images contained in chemical documents need to be rendered computer readable. We have benchmarked our system against a commercially available product and have also tested it using chemical databases of several thousand images. The system can be parameterized to reconstruct images of different sources and different characteristics. © 2007 IEEE.

关键词： Image reconstruction

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Identifying gene-specific variations in biomedical text

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Journal of bioinformatics and Computational Biology 2007年第6期5卷 1277-1296页

作者： Klinger, Roman Friedrich, Christoph M. Mevissen, Heinz Theodor Fluck, Juliane Hofmann-apitius, Martin Furlong, Laura I. Sanz, Ferran Department of Bioinformatics Fraunhofer Institute for Algorithms and Scientific Computing 53754 Sankt Augustin Schloss Birlinghoven Germany Research Unit on Biomedical Informatics (GRIB) IMIM UPF PRBB E-08003 Barcelona c/ Dr. Aiguader 88 Spain

The influence of genetic variations on diseases or cellular processes is the main focus of many investigations, and results of biomedical studies are often only accessible through scientific publications. Automatic extraction of this information requires recognition of the gene names and the accompanying allelic variant information. In a previous work, the OSIRIS system for the detection of allelic variation in text based on a query expansion approach was communicated. Challenges associated with this system are the relatively low recall for variation mentions and gene name recognition. To tackle this challenge, we integrate the ProMiner system developed for the recognition and normalization of gene and protein names with a conditional random field (CRF)-based recognition of variation terms in biomedical text. Following the newly developed normalization of variation entities, we can link textual entities to Single Nucleotide Polymorphism database (dbSNP) entries. The performance of this novel approach is evaluated, and improved results in comparison to state-of-the-art systems are reported. © 2007 Imperial College Press.

关键词： Conditional random field Named entity recognition Normalization Single nucleotide polymorphism SNP Variants

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Heuristic optimization methods for the tuning of input parameters of simulation models

Heuristic optimization methods for the tuning of input param...

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4th International Mediterranean Modeling Multiconference, I3M 2007

作者： Affenzeller, Michael Kronberger, Gabriel Winkler, Stephan Ionescu, Mihaela Wagner, Stefan Upper Austrian University of Applied Sciences Campus Hagenberg Heuristic and Evolutionary Algorithms Laboratory Softwarepark 11 A-4232 Hagenberg Austria Johannes Kepler University Linz Institute of Bioinformatics Altenbergerstr. 69 A-4040 Linz Austria

ISBN: (纸本)8890073268

This paper proposes an approach combining Evolutionary Computation and Simulation: An extended problem representation as well as solution manipulation concepts for Evolution Strategies are proposed with the aim to fulfill the needs of input parameter optimization of simulation models;moreover, this approach is not restricted to real-valued parameters. The usage of a parallel infrastructure is also proposed and planned to be realized based on the HeuristicLab framework for heuristic optimization.

关键词： Heuristic methods

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Reconstruction of Chemical Molecules from Images

Reconstruction of Chemical Molecules from Images

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29th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBS 2007), vol.11

作者： Maria-Elena Algorri Marc Zimmermann Christoph M. Friedrich Santiago Akle Martin Hofmann-Apitius Department of Digital Systems Instituto Tecnologico Autonomo de Mexico Mexicali Mexico Department of Bioinformatics Fraunhofer Institute for Algorithms and Scientific Computing Sankt Augustin Germany

关键词： Image reconstruction Optical character recognition software Data mining Chemical products Image recognition Benchmark testing System testing Image databases Image converters Character recognition

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Evolutionary composition of music with learned melody evaluation 5th

Evolutionary composition of music with learned melody evalua...

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Proceedings of the 5th WSEAS International Conference on Computational Intelligence, Man-Machine Systems and Cybernetics, CIMMACS '06

作者： Klinger, Roman Rudolph, Günter Fraunhofer Institute for Algorithms and Scientific Computation Department of Bioinformatics Schloss Birlinghoven Sankt Augustin53754 Germany University of Dortmund Department of Computer Science LS XI - Computational Intelligence Dortmund44221 Germany

We describe our approach for the automatic composition of monophone melodies on a user given chord sequence. For this purpose we use evolutionary algorithms for the music generation with automatically learned classifi... 详细信息

ISBN: (纸本)9608457564

关键词： Data mining

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Microarray layout as quadratic assignment problem

Microarray layout as quadratic assignment problem

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German Conference on bioinformatics, GCB 2006

作者： De Carvalho Jr., Sérgio A. Rahmann, Sven Graduiertenkolleg Bioinformatik Bioinformatics and Genome Research Bielefeld University D-33594 Bielefeld Germany International NRW Graduate School Bioinformatics and Genome Research Bielefeld University D-33594 Bielefeld Germany Algorithms and Statistics for Systems Biology Group Genome Informatics Technische Fakultät Bielefeld University D-33594 Bielefeld Germany

ISBN: (纸本)9783885791775

The production of commercial DNA microarrays is based on a light-directed chemical synthesis driven by a set of masks or micromirror arrays. Because of the natural properties of light and the ever shrinking feature sizes, the arrangement of the probes on the chip and the order in which their nucleotides are synthesized play an important role on the quality of the final product. We propose a new model called conflict index for evaluating microarray layouts, and we show that the probe placement problem is an instance of the quadratic assignment problem (QAP), which opens up the way for using QAP heuristics. We use an existing heuristic called GRASP to design the layout of small artificial chips with promising results. We compare this approach with the best known algorithm and describe how it can be combined with other existing algorithms to design the latest million-probe microarrays.

关键词： Probes

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Improving the layout of oligonucleotide microarrays: Pivot partitioning

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6th International Workshop on algorithms in bioinformatics, WABI 2006

作者： De Carvalho Jr., Sérgio A. Rahmann, Sven International NRW Graduate School in Bioinformatics and Genome Research Germany Graduiertenkolleg Bioinformatik Bielefeld University Germany Technische Fakultät Algorithms and Statistics for Systems Biology Group Bielefeld University D-33594 Bielefeld Germany

ISBN: (纸本)3540395830

The production of commercial DNA microarrays is based on a light-directed chemical synthesis driven by a set of masks or micromirror arrays. Because of the natural properties of light and the ever shrinking feature sizes, the arrangement of the probes on the chip and the order in which their nucleotides are synthesized play an important role on the quality of the final product. We propose a new model called conflict index for evaluating the layout of microarrays. We also present a new algorithm, called Pivot Partitioning, that improves the quality of layouts, according to existing measures, by over 6% when compared to the best known algorithms. © Springer-Verlag Berlin Heidelberg 2006.

关键词： DNA

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Efficient algorithms for range queries in protein sequence analysis 17

Efficient algorithms for range queries in protein sequence a...

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17th Canadian Conference on Computational Geometry, CCCG 2005

作者： Madhusudhanan, N. Gupta, Prosenjit Mitra, Abhijit Algorithms and Computation Theory Laboratory International Institute of Information Technology Gachibowli Hyderabad Andhra Pradesh500 019 India Bioinformatics Research Center International Institute of Information Technology Gachibowli Hyderabad Andhra Pradesh500 019 India

A protein chain consists of a sequence of amino acids. Each amino acid. may occur several times in the chain. Associated with each amino acid. are various categorical attributes like charged, polar, hydrophobic etc. Protein sequences are often subjected to standard sequence analysis. Often statistical criteria are used for evaluation of various protein sequence attributes. Several queries arise during the statistical analysis of such a protein sequence which involves a segment of the protein. We model some of these problems as generalized range searching problems in computational geometry and provide efficient data structures and algorithms for solving them. © 2005 Canadian Conference on Computational Geometry. All rights reserved.

关键词： Amino acids

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