Similar to most scientific studies, biological analyses demand a great deal of computations and simulations involving sophisticated tools that are often found geographically distributed over the Internet. A worldwide ...
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Similar to most scientific studies, biological analyses demand a great deal of computations and simulations involving sophisticated tools that are often found geographically distributed over the Internet. A worldwide effort in genomics research has resulted in a powerful collection of publicly available sequence analysis tools. These tools often require specialized local services and domain knowledge to function correctly, rendering them unlikely candidates for integration into remote database applications. Thus, integration of heterogeneous "functions" still remains an open problem. Providing a reasonable framework for seamless integration of these tools with database query engines will enable application developers to exploit and harness the power of these effective analysis tools. In this paper, we present an integration framework for such tools by enabling access to them in a user transparent way as part of database queries. In our system, such online tools are abstracted as remote user defined functions (RUDF). An extended SQL DDL language, called the Internet Function Definition Language (IFDL), is presented for the specification and definition of RUDFs. The interface between database system and the Internet is implemented using a layer based on a language called the Hypertext Query Language (HTQL). The separation of IFDL, DDL, HTQL and SQL DML offers several optimization opportunities and makes it possible to develop an architecture for interoperability of heterogeneous databases with RUDFs in more simple and efficient ways.
In this paper Mle develop data mining techniques to predict 3D contact potentials among protein residues (or amino acids) based oil the hierarchical nucleation propagation model of protein folding. We apply! a hybrid ...
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ISBN:
(纸本)0769508626
In this paper Mle develop data mining techniques to predict 3D contact potentials among protein residues (or amino acids) based oil the hierarchical nucleation propagation model of protein folding. We apply! a hybrid approach, using a Hidden Markov Model to extract folding initiation sites, and then apply association mining to discover contact potentials. The new hybrid approach achieves accuracy results better than those reported previously.
Trends in parallel computing indicate that heterogeneous parallel computing will be one of the most widespread platforms for computation-intensive applications. A heterogeneous computing environment offers considerabl...
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Blocked multiple sequence alignment refers to the construction of multiple alignment by first aligning conserved regions into what we call "blocks" and then aligning the regions between successive blocks to ...
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ISBN:
(纸本)0769508626
Blocked multiple sequence alignment refers to the construction of multiple alignment by first aligning conserved regions into what we call "blocks" and then aligning the regions between successive blocks to form a final alignment. instead of starting from low order pairwise alignments tr-e propose a nat way to form blocks by searching for closely related regions in all input sequences, allowing internal spaces in blocks as well as some degree of mismatch. We address the problem of semi-conserved patterns (patterns that do riot appear in all input sequences) by introducing into the process two similarity thresholds that ar-e adjusted dynamically according to the input. A method to central the number of blocks is also presented to deal with the situation when input sequences hate so many similar regions that it becomes impractical to form blocks by frying every combination. BMA is an implementation of this approach, and (our. experimental results indicate that this approach is efficient, particularly on large numbers of long sequences with well-conserved regions.
The proceedings contain 40 papers. The special focus in this conference is on Algorithms. The topics include: Web information retrieval - an algorithmic perspective;computationalbiology - algorithms and more;polygon ...
ISBN:
(纸本)354041004X
The proceedings contain 40 papers. The special focus in this conference is on Algorithms. The topics include: Web information retrieval - an algorithmic perspective;computationalbiology - algorithms and more;polygon decomposition for efficient construction of minkowski sums;an approximation algorithm for hypergraph max k-cut with given sizes of parts;offline list update is NP-hard;computing largest common point sets under approximate congruence;online algorithms for caching multimedia streams;on recognizing cayley graphs;fast algorithms for even/odd minimum cuts and generalizations;efficient algorithms for centers and medians in interval and circular-arc graphs;exact point pattern matching and the number of congruent triangles in a three-dimensional pointset;range searching over tree cross products;the minimum range assignment problem on linear radio networks;property testing in computational geometry;on r-trees with low stabbing number;K-D trees are better when cut on the longest side;on multicriteria online problems;online scheduling revisited;constant ratio approximation algorithms for the rectangle stabbing problem and the rectilinear partitioning problem;I/O-efficient well-separated pair decomposition and its applications;higher order delaunay triangulations;on representations of algebraic-geometric codes for list decoding;minimizing a convex cost closure set;preemptive scheduling with rejection;simpler and faster vertex-connectivity augmentation algorithms;scheduling broadcasts in wireless networks;jitter regulation in an internet router with delay consideration;approximation of curvature-constrained shortest paths through a sequence of points;resource constrained shortest paths;on the competitiveness of linear search;maintaining a minimum spanning tree under transient node failures;minimum depth graph embedding.
The proceedings contain 179 papers. The special focus in this conference is on Personal Computer Based Networks of Workstations, Advances in Parallel, Distributed computational Models and Video Processing. The topics ...
ISBN:
(纸本)354067442X
The proceedings contain 179 papers. The special focus in this conference is on Personal Computer Based Networks of Workstations, Advances in Parallel, Distributed computational Models and Video Processing. The topics include: MPI collective operations over IP multicast;an open market-based architecture for distributed computing;the multicluster model to the integrated use of multiple workstation clusters;parallel information retrieval on an SCI-based pc-now;a pc-now based parallel extension for a sequential DBMS;the heterogeneous bulk synchronous parallel model;a new computation of shape moments via quadtree decomposition;a java applet to visualize algorithms on reconfigurable mesh;a hardware implementation of pram and its performance evaluation;a non-binary parallel arithmetic architecture;multithreaded parallel computer model with performance evaluation;a high performance microprocessor for multimedia computing;a novel superscalar architecture for fast DCT implementation;computing distance maps efficiently using an optical bus;advanced data layout optimization for multimedia applications;parallel parsing of mpeg video in a multi-threaded multiprocessor environment;parallelization techniques for spatial-temporal occupancy maps from multiple video streams;heuristic solutions for a mapping problem in a TV-anytime server network;a programming environment for real-time parallel vision;parallel low-level image processing on a distributed memory system;congestion-free routing of streaming multimedia content in BMIN-based parallel systems;performance of on-chip multiprocessors for vision tasks;specification techniques for automatic performance analysis tools and controlling distributed shared memory consistency from high level programming languages.
Initially, different areas of research in computer science based on models inspired by nature are approached. The area entitled "evolutionary computation" is discussed in a general view. After this, emphasis...
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Initially, different areas of research in computer science based on models inspired by nature are approached. The area entitled "evolutionary computation" is discussed in a general view. After this, emphasis is placed on the human tendency to copy and to find answers to new problems by adopting similar solutions from other equivalent issues that have already been resolved by nature. Finally, we demonstrate that, in the case of evolutionary computation, even if success is achieved in many cases, most of what nature has attained was either severely simplified or truncated in the simulation process. Also, in several cases, a more detailed and more faithful copy could have yielded better results for already-existing systems or for new ones.
In this paper, we develop data mining techniques to predict 3D contact potentials among protein residues (or amino acids) based on the hierarchical nucleation-propagation model of protein folding. We apply a hybrid ap...
详细信息
In this paper, we develop data mining techniques to predict 3D contact potentials among protein residues (or amino acids) based on the hierarchical nucleation-propagation model of protein folding. We apply a hybrid approach, using a hidden Markov model (HMM) to extract folding initiation sites, and then apply association mining to discover contact potentials. The new hybrid approach achieves accuracy results better than those reported previously.
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