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检索条件"任意字段=16th International Conference on DNA Computing and Molecular Programming, DNA 16"

共 108 条记录，以下是71-80 订阅

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2014 IEEE international conference on Cluster computing, CLUSTER 2014

2014 IEEE International Conference on Cluster Computing, CLU...

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16th IEEE international conference on Cluster computing, CLUSTER 2014

ISBN: (纸本)9781479955480

the proceedings contain 60 papers. the topics discussed include: scalable replay with partial-order dependencies for message-logging fault tolerance;applying frequency analysis techniques to DAG-based workflows to benchmark and predict resource behavior on non-dedicated clusters;memory management for billions of small objects in a distributed in-memory storage;software technologies coping with memory hierarchy of GPGPU clusters for stencil computations;disk cache-aware task scheduling for data-intensive and many-task workflow;scalable graph500 design with MPI-3 RMA;SWAPHI-LS: Smith-Waterman algorithm on xeon phi coprocessors for long dna sequences;boosting the performance of remote GPU virtualization using InfiniBand connect-IB and PCIe 3.0;leveraging deep memory hierarchies for data staging in coupled data-intensive simulation workflows;and load analysis and cost estimation of parallel constrained producer-consumer algorithms.

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ProSOM:: core promoter prediction based on unsupervised clustering of dna physical profiles

ProSOM:: core promoter prediction based on unsupervised clus...

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16th ISMB conference on Intelligent Systems for molecular Biology

作者： Abeel, thomas Saeys, Yvan Rouze, Pierre Van de Peer, Yves Univ Ghent VIB Dept Plant Syst Biol B-9052 Ghent Belgium Univ Ghent Dept Mol Genet B-9052 Ghent Belgium Univ Ghent Lab Associe INRA B-9052 Ghent Belgium

Motivation: More and more genomes are being sequenced, and to keep up with the pace of sequencing projects, automated annotation techniques are required. One of the most challenging problems in genome annotation is the identification of the core promoter. Because the identification of the transcription initiation region is such a challenging problem, it is not yet a common practice to integrate transcription start site prediction in genome annotation projects. Nevertheless, better core promoter prediction can improve genome annotation and can be used to guide experimental work. Results: Comparing the average structural profile based on base stacking energy of transcribed, promoter and intergenic sequences demonstrates that the core promoter has unique features that cannot be found in other sequences. We show that unsupervised clustering by using self-organizing maps can clearly distinguish between the structural profiles of promoter sequences and other genomic sequences. An implementation of this promoter prediction program, called ProSOM, is available and has been compared with the state-of-the-art. We propose an objective, accurate and biologically sound validation scheme for core promoter predictors. ProSOM performs at least as well as the software currently available, but our technique is more balanced in terms of the number of predicted sites and the number of false predictions, resulting in a better all-round performance. Additional tests on the ENCODE regions of the human genome show that 98 of all predictions made by ProSOM can be associated with transcriptionally active regions, which demonstrates the high precision.

关键词： Forecasting

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16th international Colloquium on Automata, Languages and programming, 1989

16th International Colloquium on Automata, Languages and Pro...

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16th international Colloquium on Automata, Languages and programming, 1989

ISBN: (纸本)9783540513711

the proceedings contain 51 papers. the special focus in this conference is on Automata, Languages and programming. the topics include: Completion of finite codes with finite deciphering delay;relational semantics for recursive types and bounded quantification;a singly-exponential stratification scheme for real semi-algebraic varieties and its applications;about primitive recursive algorithms;the definability of equational graphs in monadic second-order logic;Dominoes and the regularity of dna splicing languages;causal trees;infinite normal forms: Preliminary version;on recent trends in algebraic specification;limitations of the upward separation technique (preliminary version);automata with storage on infinite words;parallel algorithmic techniques for combinatorial computation;on dice and coins: models of computation for random generation;an optimal probabilistic algorithm for synchronous Byzantine agreement;finding triconnected components by local replacements: Extended abstract;an improved algorithm for approximate string matching;a pointer-free data structure for merging heaps and min-max heaps;structured operational semantics and bisimulation as a congruence: Extended abstract;parallel retrieval of scattered information;Tensor rank is NP-complete;lower bounds for the low hierarchy: Extended abstract;the complexity of nonlinear separable optimization;general methods for the analysis of the maximum size of dynamic data structures: Extended abstract;how to share concurrent asynchronous wait-free variables: Preliminary version;a new approach to formal language theory by kolmogorov complexity: Preliminary version;dynamic algorithms in D.E. Knuth's model: A probabilistic analysis;completing the temporal picture;lower bounds for computations with the floor operation;programming, transforming, and proving with function abstractions and memories;automata theory meets circuit complexity;partial communations.

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High Performance Genomic Sequencing: A Filtered Approach 8

High Performance Genomic Sequencing: A Filtered Approach

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8th international conference on Practical Applications of Computational Biology & Bioinformatics (PACBB)

作者： Retamosa, German de Pedro, Luis Gonzalez, Ivan Tamames, Javier Univ Autonoma Madrid High Performance & Comp Networking Dept E-28049 Madrid Spain CSIC Natl Biotechnol Res Ctr Madrid Spain

ISBN: (纸本)9783319075815;9783319075808

Protein and dna homology detection systems are an essential part in computational biology applications. these algorithms have changed over the time from dynamic programming approaches by finding the optimal local alignment between two sequences to statistical approaches with different kinds of heuristics that minimize former executions times. However, the continuously increasing size of input datasets is being projected into the use of High Performance computing (HPC) hardware and software in order to address this problem. the aim of the research presented in this paper is to propose a new filtering methodology, based on general-purpose graphical processor units (GP-GPUs) and multi-core processors, for removing those sequences considered irrelevant in terms of homology and similarity. the proposed methodology is completely independent from the homology detection algorithm. this approach is very useful for researchers and practitioners because they do not need to understand a new algorithm. this design has been approved by the National Biotechnology Research Center of Spain (CNB).

关键词： Comparison and alignment methods BLAST High Performance computing GP-GPU

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K-group A* for multiple sequence alignment with quasi-natural gap costs

K-group A* for multiple sequence alignment with quasi-natura...

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Proceedings - 16th IEEE international conference on Tools with Artificial Intelligence, ICTAI 2004

作者： Zhou, Rong Hansen, Eric A. Dept. of Comp. Sci. and Engineering Mississippi State University Mississippi State MS 39762 United States

ISBN: (纸本)076952236X

Alignment of multiple protein or dna sequences is an important problem in Bioinformatics. Previous work has shown that the A* search algorithm can find optimal alignments for up to several sequences, and that a K-group generalization of A* can find approximate alignments for much larger numbers of sequences. In this paper, we describe the first implementation of K-group A* that uses quasinatural gap costs, the cost model used in practice by biologists. We also introduce a new method for computing gap-opening costs in profile alignment. Our results show that K-group A* can efficiently find optimal or close-to-optimal alignments for small groups of sequences, and, for large numbers of sequences, it can find higher-quality alignments than the widely-used CLUSTAL family of approximate alignment tools. this demonstrates the benefits of A* in aligning large numbers of sequences, as typically compared by biologists, and suggests that K-group A* could become a practical tool for multiple sequence alignment. © 2004 IEEE.

关键词： dna sequences

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A Novel Autonomous molecular Mechanism Based on Spatially Localized dna Computation 15th

A Novel Autonomous Molecular Mechanism Based on Spatially Lo...

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15th international conference on Bio-Inspired computing: theories and Applications, BIC-TA 2020

作者： Wang, Yue Qian, Mengyao Hu, Wenxiao Wang, Luhui Dong, Yafei School of Computer Science Shaanxi Normal University Xi’an Shaanxi710119 China College of Life Science Shaanxi Normal University Xi’an Shaanxi710119 China

ISBN: (纸本)9789811613531

Contemporary dna synthesis technology matures, and the development provides intriguing possibilities for dynamic manipulation of dna self-assembly, which plays a pivotal role in the behavior of designing versatile nanodevices and generating controllable networks. Similarly, in synthetic molecular circuits, the spatially localized architecture furnishes a different strategy, allowing for immobilized dna molecules in close vicinity to each other. Herein, the formal modeling language was utilized to mark the address with a specific sequence of location tags, thus a set of routes were precisely arranged at the nanoscale. Beyond building a collection of separate modules, computer simulations were used to explore further complex assemblies of the building blocks. By orchestrating a series of dna strand displacement operations locally, autonomous movement and addressing operations were realized, completing the group transport and partition storage of dissimilar molecules. the nanodevice gives the dna molecule its mechanical properties and follows an embedded "molecular program". the simulation results of the Visual DSD tool provided qualitative and quantitative proof for the operation of the system. © 2021, Springer Nature Singapore Pte Ltd.

关键词： dna

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A Review of dna Cryptography: From a Data Protection Perspective

A Review of DNA Cryptography: From a Data Protection Perspec...

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Security of Information and Networks (SIN), international conference on

作者： Parth Parmar Jekil Gadhiya Satvik Vats Deepak Kumar Verma Krunal Vaghela Computer Engineering Marwadi University Rajkot India Computer Science and Engineering Graphic Era Hill University Dehradun India

the rate of development in today's IT industry is unprecedented. Information is being stored and transformed at a faster and faster rate. therefore, the importance of protecting sensitive data is growing. Everyone is concerned about preventing hackers from gaining access to their personal data. Several algorithms from the fields of classical cryptography and steganography can be used to conceal data. dna cryptography is an emerging field that aims to protect information kept in dna. dna cryptography takes use of dna's innate computing power at the molecular level. In this paper, we are exploring diverse cryptographic algorithms and methods that are used to secure the stored data in dna. the paper represents the critical review that includes merits and demerits of the diverse cryptographic algorithms for securing the data in dna.

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16th international conference on Bio-Inspired computing: theories and Applications, BIC-TA 2021

16th International Conference on Bio-Inspired Computing: The...

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16th international conference on Bio-Inspired computing: theories and Applications, BIC-TA 2021

ISBN: (纸本)9789811912528

the proceedings contain 67 papers. the special focus in this conference is on Bio-Inspired computing: theories and Applications. the topics include: Firefly Algorithm with Opposition-Based Learning;a Multi-direction Prediction Multi-objective Hybrid Chemical Reaction Optimization Algorithm for Dynamic Multi-objective Optimization;optimal Overbooking Appointment Scheduling in Hospitals Using Evolutionary Markov Decision Process;an Improved Bare-Bones Multi-objective Artificial Bee Colony Algorithm;surrogate-Assisted Artificial Bee Colony Algorithm;a Hybrid Multi-objective Coevolutionary Approach for the Multi-user Agile Earth Observation Satellite Scheduling Problem;a Node Influence Based Memetic Algorithm for Community Detection in Complex Networks;water Wave Optimization with Distributed-Learning Refraction;a Differential Evolution Algorithm for Multi-objective Mixed-Variable Optimization Problems;Implementation and Application of NSGA-III Improved Algorithm in Multi-objective Environment;solving Satellite Range Scheduling Problem with Learning-Based Artificial Bee Colony Algorithm;Synchronization of Chaos with a Single Driving Variable Feedback Control Based on dna Strand Displacement;an Optimization Method of Course Scheduling Problem Based on Improved Genetic Algorithm;A Multi-UUV Formation Control and Reorganization Method Based on Path Tracking Controller and Improved Ant Colony Algorithm;an Effective Data Balancing Strategy Based on Swarm Intelligence Algorithm for Malicious Code Detection and Classification;an Optimization Task Scheduling Model for Multi-robot Systems in Intelligent Warehouses;feature Selection Method Based on Ant Colony Optimization Algorithm and Improved Neighborhood Discernibility Matrix;a Cuckoo Quantum Evolutionary Algorithm for the Graph Coloring Problem;attribute Selection Method Based on Artificial Bee Colony Algorithm and Neighborhood Discrimination Matrix Optimization;black Widow Spider Algorithm Based on Differential Evolution and

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16th international conference on Bio-Inspired computing: theories and Applications, BIC-TA 2021

16th International Conference on Bio-Inspired Computing: The...

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16th international conference on Bio-Inspired computing: theories and Applications, BIC-TA 2021

ISBN: (纸本)9789811912559

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Construction of Four-Variable Chaotic System Based on dna Strand Displacement 16th

Construction of Four-Variable Chaotic System Based on DNA ...

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16th international conference on Bio-Inspired computing: theories and Applications, BIC-TA 2021

作者： Ji, Haoping Wang, Yanfeng Sun, Junwei Henan Key Lab of Information-Based Electrical Appliances Zhengzhou University of Light Industry Zhenzhou450002 China School of Electrical and Information Engineering Zhengzhou University of Light Industry Zhenzhou450002 China

ISBN: (纸本)9789811912559

As a typical dna nanotechnology, dna strand displacement reaction has attracted many scholars to investigate. In this paper, a four-variable chaotic system is proposed by multiplication, degradation, and adjustment dna strand displacement modules, and the dynamic behaviors of designed chaotic system are analysed by the software of Matlab and Visual DSD. the simulation results show that our strand displacement chaotic system can realize the production of chaotic signals. Our work uses biological reactions to achieve the construction of chaotic systems, which can provide a reference for the future researches of chaotic system. © 2022, Springer Nature Singapore Pte Ltd.

关键词： Chaotic systems

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