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检索条件"任意字段=IEEE Computational Systems Bioinformatics Conference"

共 881 条记录，以下是641-650 订阅

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Algorithms for estimating information distance with application to bioinformatics and linguistics

Algorithms for estimating information distance with applicat...

引用

Canadian conference on Electrical and Computer Engineering;Technology Driving Innovation, 2004

作者： Kaltchenko, Alexei Department of Physics Wilfrid Laurier University Waterloo Ont. N2L3C5 Canada

ISBN: (纸本)0780382536

We review unnormalized and normalized information distances based on incomputable notions of Kolmogorov complexity and discuss how Kolmogorov complexity can be approximated by data compression algorithms. We argue that optimal algorithms for data compression with side information can be successfully used to approximate the normalized distance. Next, we discuss an alternative information distance, which is based on relative entropy rate (also known as Kullback-Leibler divergence), and compression-based algorithms for its estimation. We conjecture that in bioinformatics and computational Linguistics this alternative distance is more relevant and important than the ones based on Kolmogorov complexity.

关键词： computational complexity

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bioinformatics and computational systems biology: At the cross roads of biology, engineering and computation

Bioinformatics and computational systems biology: At the cro...

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26th Annual International conference of the ieee-Engineering-in-Medicine-and-Biology-Society

作者： Subramaniam, S Univ Calif San Diego La Jolla CA 92093 USA

ISBN: (纸本)0780384393

Summary form only given. We are witnessing the emergence of the "data rich" era in biology. The myriad data in biology ranging from sequence strings to complex phenotypic and disease-relevant data pose a huge challenge to modern biology. The standard paradigm in biology that deals with hypothesis to experimentation (low throughput data) to models is being gradually replaced by data to hypothesis to models and experimentation to more data and models. And unlike data in physical sciences, that in biological sciences is almost guaranteed to be highly heterogeneous and incomplete. In order to make significant advances in this data rich era, it is essential that there be robust data repositories that allow interoperable navigation, query and analysis across diverse data, and a plug-and-play tools environment that will facilitate seamless interplay of tools and data. Further, the integrated data will enable the reconstruction and modeling of biological systems. This talk with address several of the challenges posed by enormous need for scientific data integration and modeling in biology with specific exemplars and possible strategies. The issues addressed will include: architecture of data and knowledge repositories; flat, relational and object-oriented databases ; ontologies in biology; reduction and analysis of data; legacy knowledge integration with data and systems level modeling in biology.

关键词： computational systems biology bioinformatics Roads Biology computing Biological system modeling Object oriented modeling computational biology Data analysis systems biology Sequences

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The application of grid technology in systems biology: Parameter estimation

The application of grid technology in systems biology: Param...

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Proceedings - Seventh International conference on High Performance Computing and Grid in Asia Pacific Region, HPCAsia 2004

作者： Dhar, Pawan K. Bioinformatics Institute Singapore Singapore Dept. of Biochemistry National University of Singapore Singapore

ISBN: (纸本)076952138X

The systems biology is a recent scientific discipline that arose from the need to combine biology with mathematics, physics, chemistry and computer science. Partly driven by the availability of a morass of data and partly driven by the availability of computational resources, the field of systems biology was reborn few years ago. Recently, a number of computational methods have been developed to model cellular pathways and networks. One of the major issues in building mathematical models of cellular processes is the difficulty of estimating parameters. Due to a wide numerical range within which parameters operate, it takes a large number of iterations to find the biologically relevant values. In this paper I will describe how grid technology can be used to salvage this situation and help in building robust in-silico models.

关键词： Parameter estimation

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Proceedings of the Third ieee International conference on Cognitive Informatics = ICCI 2004

Proceedings of the Third IEEE International Conference on Co...

引用

Proceedings of the Third ieee International conference on Cognitive Informatics, ICCI 2004

ISBN: (纸本)0769521908

The proceedings contain 31 papers from the Proceedings of the Third ieee International conference on Cognitive Informatics ICCI 2004. The topics discussed include: language, logic, and the brain;on autonomous computing and cognitive processes;is entropy suitable to characterize data and signals for cognitive informatics?;on the cognitive informatics foundations of software engineering;a parallel language for cognitive informatics;concept formation and learning: a cognitive informatics perspective;specification of the RTPA grammar and its recognition;formal description of the cognitive process of problem solving;and cognitive bioinformatics: computational cognitive model for dynamic problem solving.

关键词： Cognitive systems

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SUPERCONTIGS: a contig scaffolding tool

SUPERCONTIGS: a contig scaffolding tool

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Proceedings of the ieee computational systems bioinformatics conference, CSB

作者： D. Puiu CSBC Virginia Commonwealth University USA

SUPERCONTIGS is a genome-finishing tool that orders, orients and groups contigs based on clone pair information and an alignment with a related genome. The program can be used in the genome finishing and gap closing process. SUPERCONTIGS is a Perl script that runs on Unix-like systems. It is available at http://***/csbc/bccl/*** as a copy-left public domain program.

关键词： bioinformatics Genomics Cloning Assembly Sequences Visualization Libraries Filters Biological cells Cryptography

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computational methods for predicting intramolecular G-quadruplexes in nucleotide sequences

Computational methods for predicting intramolecular G-quadru...

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Proceedings of the ieee computational systems bioinformatics conference, CSB

作者： L. D'Antonio P. Bagga Computer Science Department Ramapo College of New Jersey Bioinformatics Department Ramapo College of New Jersey

Guanine-rich sequences, including those that form G-quadruplexes, are abundant in regions of biological significance. In order to map putative G-quadruplex elements within mammalian genes we have created a suite of computational tools. This suite contains algorithms to search genes for occurrences of the G-quadruplex motif and determine their distribution near RNA processing sites.

关键词： RNA Biology computing Educational institutions bioinformatics Computer science Stability Proteins Chemical elements Chemistry

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Using blocks+ database in Needleman-Wunsch algorithm

Using blocks+ database in Needleman-Wunsch algorithm

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NAFIPS 2004 - Annual Meeting of the North American Fuzzy Information Processing Society: Fuzzy Sets in the Heart of the Canadian Rockies

作者： Zhihua, Du Feng, Lin Bioinformatics Research Center Nanyang Technological University Nanyang Avenue Singapore Singapore

This paper describes a novel approach of computing pairwise sequence alignment for guarantee that the generated alignment satisfies some particular blocks should be aligned together. This approach can increase the accuracy of the resulting alignment by incorporating prior knowledge about the sequences. It brings into the alignment the method used by biologists which consists in forcing the alignment of occurrences certain biological structures or the function. In the first part, the problem of this algorithm is outlined. Later, a general introduction of related work is described. Finally, a modified Needleman-Wunsch algorithm and experimental results are presented. The importance of this process lies on its effect of keeping common blocks in sequences to be aligned accurately.

关键词： computational methods

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computational dissection of regulatory networks using diverse high-throughput data

Computational dissection of regulatory networks using divers...

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Proceedings of the ieee computational systems bioinformatics conference, CSB

作者： R. Shamir School of Computer Science Sackler Faculty of Exact Sciences Tel-Aviv University Tel-Aviv Israel

Summary form only given. The maturation of high-throughput technologies and the availability of whole genome sequences make it possible to apply holistic computational approaches to the study of biological systems. The use of high-throughput technologies requires the development of advanced computational methods and tools that would enable the elicitation of significant biological knowledge from the vast amounts of data generated by these methods. Our group has been developing a battery of such methodologies and incorporated some of them in several tools such as CLICK, PRIMA, SAMBA, EXPANDER, SHARP, Binding Site Evolution and MetaReg.

关键词： Computer networks bioinformatics Genomics Algorithm design and analysis Fungi Proteins Biological system modeling Gene expression Sequences Biology computing

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A markov model based gene discrimination approach in trypanosomes

A markov model based gene discrimination approach in trypano...

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Proceedings of the ieee computational systems bioinformatics conference, CSB

作者： A. Griggs S. Gopal Department of Biological Sciences Rochester Institute of Technology Rochester NY USA

The trypanosomes are a class of eukaryotic parasites that diverged from Saccharomyces cerevisiae about 800 million years ago. Many possible gene structures are present within these genomes but most appear to be non-functional and do not code for proteins. Initial analyses of these genomes suggest that over 70% of the putative genes have no biological function.

关键词： bioinformatics Organisms Biological information theory Genomics Biological system modeling Biology Proteins Signal analysis Sequences Linear discriminant analysis

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A knowledge base for computational pathway reconstruction

A knowledge base for computational pathway reconstruction

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Proceedings of the ieee computational systems bioinformatics conference, CSB

作者： Peng Wang Zhengchang Su Phuongan Dam Ying Xu Computational Systems Biology Laboratory Department of Biochemistry and Molecular Biology University of Georgia USA

ISBN: (纸本)0769521940

The Synechococcus WH8102 knowledge base (http://***/WH8J02) is a Web based relational database developed to facilitate computational effort to reconstruct regulatory pathways and serve as a gateway for biologist to access the data. It is the repertoire that integrates a variety of knowledge derived both from literature and computational prediction. Those data are organized in hierarchical fashion. The basic building blocks are functional annotation and structure prediction of individual molecule. Those data are then organized into clusters based on computationally predicted operon, regulon and molecular complexes. Finally all data are complied into pathways derived from combined efforts of literature mining and computational prediction. A number of tools have been developed to facilitate the data retrieval including a SQL query engineer and several viewers to browse genome, molecular complexes and pathways.

关键词： bioinformatics Genomics Biology computing Relational databases Proteins Visual databases computational systems biology Information retrieval Displays Laboratories

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