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High performance computational tools for Motif discovery

High performance computational tools for Motif discovery

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International symposium on Parallel and Distributed Processing (IPDPS)

作者： N.E. Baldwin R.L. Collins M.A. Langston C.T. Symons M.R. Leuze B.H. Voy Department of Computer Science University of Tennessee Knoxville USA Oak Ridge National Laboratory USA

Summary form only given. We highlight a fruitful interplay between biology and computation. The sequencing of complete genomes from multiple organisms has revealed that most differences in organism complexity are due to elements of gene regulation that reside in the non protein coding portions of genes. Both within and between species, transcription factor binding sites and the proteins that recognize them govern the activity of cellular pathways that mediate adaptive responses and survival. Experimental identification of these regulatory elements is by nature a slow process. The availability of complete genomic sequences, however, opens the door for computational methods to predict binding sites and expedite our understanding of gene regulation at a genomic level. Just as with traditional experimental approaches, the computational identification of the molecular factors that control a gene's expression level has been problematic. As a case in point, the identification of putative motifs is a challenging combinatorial task. For it, powerful new motif finding algorithms and high performance implementations are described. Heavy use is made of graph algorithms, some of which are exceedingly computationally intensive and involve the use of emergent mathematical methods. An approach to fully dynamic load balancing is developed in order to make effective use of highly parallel platforms.

关键词： High performance computing Sequences DNA Genomics bioinformatics Gene expression Proteins computational intelligence Society Mice Humans

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Approximating edit distance efficiently

Approximating edit distance efficiently

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Annual ieee symposium on Foundations of Computer Science

作者： Z. Bar-Yossef T.S. Jayram R. Krauthgamer R. Kumar Department of Electrical Engineering Technion-Israel Institute of Technology Haifa Israel IBM Almaden Research Center San Jose CA USA

Edit distance has been extensively studied for the past several years. Nevertheless, no linear-time algorithm is known to compute the edit distance between two strings, or even to approximate it to within a modest factor. Furthermore, for various natural algorithmic problems such as low-distortion embeddings into normed spaces, approximate nearest-neighbor schemes, and sketching algorithms, known results for the edit distance are rather weak. We develop algorithms that solve gap versions of the edit distance problem: given two strings of length n with the promise that their edit distance is either at most k or greater than /spl lscr/, decide which of the two holds. We present two sketching algorithms for gap versions of edit distance. Our first algorithm solves the k vs. (kn)/sup 2/3/ gap problem, using a constant size sketch. A more involved algorithm solves the stronger k vs. /spl lscr/ gap problem, where /spl lscr/ can be as small as O(k/sup 2/) - still with a constant sketch - but works only for strings that are mildly "nonrepetitive". Finally, we develop an n/sup 3/7/-approximation quasilinear time algorithm for edit distance, improving the previous best factor of n/sup 3/4/ (Cole and Hariharan, 2002); if the input strings are assumed to be nonrepetitive, then the approximation factor can be strengthened to n/sup 1/3/.

关键词： Approximation algorithms computational biology Text processing Algorithm design and analysis Genomics bioinformatics Web search Books Dynamic programming Heuristic algorithms

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New for 2004

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ieee Transactions on Pattern Analysis and Machine intelligence 2004年第2期26卷 288-288页

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Measurements and computational intelligence in biomedical engineering

Measurements and computational intelligence in biomedical en...

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ieee International symposium on computational intelligence for Measurement Systems and Applications

作者： Micheli-Tzanakou, E Rutgers State Univ Dept Biomed Engn Piscataway NJ 08854 USA

ISBN: (纸本)0780377834

We have used advanced signal processing and innovative image processing methods that are used outside the operating room. The software is written in C++ in a windows environment and can be used on any PC. Applications will be discussed along with computational intelligence as used for diagnostic purposes and as visualization aids inside and outside the operating room. Subjects to be discussed, include blood cell classification, mammography, evoked potentials, ophthalmology, EEG and field potentials in Parkinson's disease. The latter methods along with 3D reconstruction of MRI images of Parkinson's patients, are currently used in the operating room for target assessment and electrode placement.

关键词： Application software Biomedical engineering Biomedical measurements Biomedical signal processing Blood Cells (biology) computational intelligence Image processing Mammography Visualization

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Using easel for modeling and simulating the interactions of cells in order to better understand the basics of biological processes and to predict their likely behaviors 2

Using easel for modeling and simulating the interactions of ...

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2nd International computational Systems bioinformatics Conference

作者： Stojkovic, V Steele, G Lupton, W MSU Baltimore MD USA

ISBN: (纸本)0769520006

Modeling, simulation, visualization, and animation play a significant role in the study of bioinformatics. Research in this area is generally multidisciplinary in nature and collaboratively conducted by researchers with expertise in biology, bioinformatics, computer science, artificial intelligence, mathematics, and statistics. Easel programming language is used for modeling, simulation, visualization, and animation of interactions of cells in order to better understand the basics of biological processes and to predict their likely behaviors. This paper presents a computer science - modeling, simulation, visualization, and animation approach to such research. The paper provides a brief overview of the basic ideas in the "Message Passing" Easel program to demonstrate the transmission of signals between cells based on their physical proximity.

关键词： bioinformatics

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Marked regulatory graphs: A formal framework to simulate biological regulatory networks with simple automata 14

Marked regulatory graphs: A formal framework to simulate bio...

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14th ieee International Workshop on Rapid Systems Prototyping

作者： Bassano, V Bernot, G Univ Evry LaMI Evry France

ISBN: (纸本)0769519431

In the field of biological regulation, models obtained from experimental biology are usually complex networks of induction and repression between genes. Due to the development of high throughput genomic, it is now necessary to treat large scale networks. The challenge is to automatically analyze their behaviour. Here, we propose a formal framework to define this Biological Regulatory Networks. Our model is derived from R. Thomas representation, where a biological regulatory network can be seen as a discrete model. We propose a formal definition of such representation. We separate the static part (description of the systems)from the dynamic one (we develop two semantics, synchronous or asynchronous, to illustrate our method). A software environment to support this framework is also described. This software, developed to be used by biologists, can be used to rapidly obtain a prototype describing the behaviour of the system, to product simulations and to automatize proofs of properties.

关键词： Automata bioinformatics Biological system modeling Complex networks computational biology Genomics Large-scale systems Software prototyping Throughput Virtual prototyping

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Development and assessment of bioinformatics tools for species conservation and habitat management

Development and assessment of bioinformatics tools for speci...

引用

ieee Conference on bioinformatics

作者： M.A. Sutton L. Deneke J. Eme W. Bennett F. Wray Departments of Biology and Computer Science University of West Florida USA Departments of Biology University of West Florida USA

This project represents an interdisciplinary approach to integrating computational methods into the knowledge-discovery process associated with understanding biological systems impacted by the loss or destruction of sensitive habitats. We specifically developed bioinformatics tools for the study of (1) beach mouse communities and (2) marginal fish habitats. Data mining was used in these projects to intelligently query databases and to elucidate broad patterns that facilitate overall data interpretation. Visualization techniques that were developed present mined data in ways where context, perceptual cues, and spatial reasoning skills can be applied to uncover significant trends in behavioral patterns, habitat use, species diversity, and community composition.

关键词： bioinformatics biology computing Biological systems Mice Marine animals Data mining computational intelligence Deductive databases Spatial databases Visual databases

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HMM based handwritten text recognition using biometrical data acquisition pen

HMM based handwritten text recognition using biometrical dat...

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ieee International symposium on computational intelligence in Robotics and Automation (CIRA)

作者： O. Rohlik P. Mautner V. Matousek J. Kempf Department of Computer Science and Engineering University of West Bohemia Pilsen Czech Republic Department of Microelectronic Systems University of Applied Sciences Regensburg Germany

Development of new text and graphical input devices is considered to be important part of human-computer interaction by many researchers worldwide. The paper presents our experience with the text recognition methods that we have developed for a new designed electronic pen that produces signals corresponding to the movement of the pen on paper. Signals are described by a set of primitives and hidden Markov models are used for word recognition. Results of tests are discussed as well as other possible application areas of our electronic pen.

关键词： Hidden Markov models Text recognition bioinformatics Character recognition Writing Handwriting recognition Data acquisition Computer science Data engineering Signal design

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Using Easel for modeling and simulating the interactions of cells in order to better understand the basics of biological processes and to predict their likely behaviors

Using Easel for modeling and simulating the interactions of ...

引用

ieee Conference on bioinformatics

作者： V. Stojkovic G. Steele W. Lupton M. S. U. Baltimore MD USA

Modeling, simulation, visualization, and animation play a significant role in the study of bioinformatics. Research in this area is generally multidisciplinary in nature and collaboratively conducted by researchers with expertise in biology, bioinformatics, computer science, artificial intelligence, mathematics, and statistics. Easel programming language is used for modeling, simulation, visualization, and animation of interactions of cells in order to better understand the basics of biological processes and to predict their likely behaviors. This paper presents a computer science modeling, simulation, visualization, and animation approach to such research. The paper provides a brief overview of the basic ideas in the "Message Passing" Easel program to demonstrate the transmission of signals between cells based on their physical proximity.

关键词： Biological system modeling Predictive models Cells (biology) Biological processes computational modeling Visualization Animation bioinformatics Computer science Collaboration

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Rubdes: A rule based distributed event system

引用

18th International symposium on Computer and Information Sciences, ISCIS 2003

作者： Sahingoz, Ozgur Koray Erdogan, Nadia Air Force Academy Computer Engineering Department Yesilyurt Istanbul Turkey Istanbul Technical University Computer Engineering Department Ayazaga Istanbul80626 Turkey

ISBN: (纸本)3540204091

In the last years, event-based communication paradigm has been largely studied and considered as a promising approach to develop the communication infrastructure of distributed systems. RUBDES (Rule Based Distributed Event System) is a distributed event system that allows the use of composite events in publish/subscribe computational model. In this system, an event is represented as an object and a rule is represented as an expression or a function that is evaluated or executed depending on the occurrence of events. This paper presents the design details of RUBDES and usage of Rule Definition Language (RDL) to describe composite events and event filters. © Springer-Verlag Berlin Heidelberg 2003.

关键词： Artificial intelligence

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