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

共 878 条记录，以下是71-80 订阅

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Intelligent Mobile Web Service for bioinformatics systems

Intelligent Mobile Web Service for Bioinformatics Systems

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International conference on Informative and Cybernetics for computational Social systems (ICCSS)

作者： Chuang, Chen-Chia Jeng, Jin-Tsong Hsiao, Chih-Ching Ho, Yu-Yang Liu, Yue-Shiang Natl Ilan Univ Dept Elect Engn Yilan 260 Taiwan Kao Yuan Univ Dept Informat Technol Kaohsiung Taiwan Natl Formosa Univ Dept Comp Sci & Informat Engn Huwei Township Yunlin Taiwan

ISBN: (纸本)9781467372459

In this paper, to integrate android systems, intelligent computing and web service on an intelligent mobile web service computing systems for bioinformatics is proposed. That is, users can send parameters to control the intelligent computing system under Matlab/C#/Java and query from client-side to server-side in the proposed bioinformatics systems with their android phone. Besides, the proposed system can also deal with disease genes search under web service with bioinformatics web. At the same time, web service is important communication protocol in the proposed systems. Consequently, the proposed systems can provide that user can modify parameters for controlling the proposed intelligent computing, deal with disease genes search under web service with bioinformatics web and obtain results from the proposed systems by android phone arbitrarily.

关键词： Android systems Web Service bioinformatics mobile computing

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Predicting Time Sequences in Gene Expression Using Dynamic Neuro-Fuzzy Networks

Predicting Time Sequences in Gene Expression Using Dynamic N...

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ieee conference on computational Intelligence in bioinformatics and computational Biology CIBCB

作者： Ahmadi, Ali Tari, Sadaf Iranpour KN Toosi Univ Technol Fac Comp Engn Tehran Iran

ISBN: (纸本)9781479969265

Gene regulation at the cellular level is a dynamic process;and neural networks with the capability of being trained and regulated based on training data, and fuzzy systems with their interpretability, are suitable algorithms for this type of computations. In this research, methods based on neuro-fuzzy networks were employed for predicting the complicated relationships that exist among genes. In the proposed method, genes that have the greatest effect on each other are found and considered as regulatory genes. Then the types of their relationships including those with inhibitory, activating, and neutralizing effects are determined, and the gene regulatory network is mapped. The standard microarray dataset related to 12 typical genes that influence the germination cycle of the yeast species Saccharomyces cerevisiae was used for training. Obtained results were validated using previous biological laboratory results. It was found that the proposed method reduced the number of extracted rules for input-output space fragmentation by 15%, which substantially reduced the required computations, while the sum square error of the algorithm declined by -0.3 compared to the method that resembled the proposed algorithm the most.

关键词： bioinformatics gene expression gene regulatory network neuro-fuzzy networks

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Evaluating Workflow Management systems: A bioinformatics Use Case

Evaluating Workflow Management Systems: A Bioinformatics Use...

引用

2018 ieee International conference on bioinformatics and Biomedicine, BIBM 2018

作者： Larsonneur, Elise Mercier, Jonathan Wiart, Nicolas Floch, Edith Le Delhomme, Olivier Meyer, Vincent Institut de Biologie Francois Jacob CEA Université Paris-Saclay EvryF-91057 France

ISBN: (纸本)9781538654880

Biological knowledge discovery is a tedious task which relies on computationally intensive analyses to process huge volumes of data and metadata. This task can be facilitated by a well-designed workflow management system, capable of deploying and efficiently orchestrating the scientific analysis. However choosing the right workflow management system remains a critical challenge. In this study, we propose ten metrics for evaluating the efficiency of workflow management systems, and show how the Pegasus-mpi-cluster and Snakemake workflow management systems gave the best overall performance, closely followed by Nextflow. © 2018 ieee.

关键词： bioinformatics

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A Scalable Architecture for Intrusion-Detection systems Based on a Broadband Network of Embedded Set-Top Boxes

A Scalable Architecture for Intrusion-Detection Systems Base...

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54th ieee International Midwest Symposium on Circuits and systems (MWSCAS)

作者： Neill, Richard Carloni, Luca P. Columbia Univ Dept Comp Sci New York NY 10027 USA

ISBN: (纸本)9781612848570

As the processing power of set-top box (STB) devices continnes to grow with each new product generation and multiple service operators directly manage millions of these devices through a dedicated broadband network, we propose to harness this massive aggregate computational power to execute large-scale parallel applications. We present a prototype implementation of a heterogeneous distributed embedded system that combines a complete head-end cable system with a DOCSIS broadband network of STBs and an interoperable embedded implementation of Open MPI running on the STB operating system. We demonstrate the operations and performance of this system by reporting the experimental results that we obtained for the execution of various instances of Multiple Sequence Alignment, a parallel bioinformatics application. Based on these results we propose a new distributed embedded system architecture for highly-scalable intrusion-detection systems.

关键词： Broadband communication DOCSIS broadband network Frequency modulation Linux Radio frequency Servers Transform coding bioinformatics bioinformatics application computer networks dedicated broadband network embedded set-top boxes embedded systems head end cable system heterogeneous distributed embedded system intrusion detection systems large scale parallel applications massive aggregate computational power multiple sequence alignment scalable architecture security of data set-top boxes

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A Classification System for Predicting RNA Hairpin Loops

A Classification System for Predicting RNA Hairpin Loops

引用

International Joint conference on bioinformatics, systems Biology and Intelligent Computing

作者： Aldwairi, Monther Duwairi, Rehab Algarqaz, Wafa'a Jordan Univ Sci & Technol Dept Comp Engn Irbid Jordan

ISBN: (纸本)9780769537399

RiboNucleic Acid (RNA) molecules fold back over themselves to form secondary structures which determine the RNA's functionality in living cells. RNA secondary structure can be determined in laboratory by X-ray diffraction and nuclear magnetic resonance (NMR) techniques. However, these techniques are slow and expensive. Therefore, computational approaches are used to predict the secondary structure of RNA molecules. A new approach. RNA-SSP, for predicting RNA secondary structure elements is proposed. It combines computational approaches and machine learning classifiers to predict individual structure elements using a new search heuristic. The approach is implemented and tested for hairpin loops and a methodology for extending the approach to predict the remaining secondary structure elements is proposed. The experiments showed a significant improvement in prediction accuracy to 95% for stem regions and 80% for loops. The overall weighted-average accuracy for predicting hairpin loop sub-structure is 89% with a sensitivity of 85.29%.

关键词： bioinformatics RNA Secondary Structure Prediction computational RNA

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GPU Acceleration of Advanced k-mer Counting for computational Genomics 29

GPU Acceleration of Advanced <i>k</i>-mer Counting for Compu...

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29th Annual ieee International conference on Application-Specific systems, Architectures and Processors (ASAP)

作者： Li, Huiren Ramachandran, Anand Chen, Deming Univ Illinois Dept Elect & Comp Engn 1406 W Green St Urbana IL 61801 USA

ISBN: (纸本)9781538674796

k-mer counting is a popular pre-processing step in many bioinformatic algorithms. KMC2 is one of the most popular tools for k-mer counting. In this work, we leverage the computational power of the GPU to accelerate KMC2. Our goal is to reduce the overall runtime of many genome analysis tasks that use k-mer counting as an essential step. Compared to KMC2 running on a single CPU thread, our implementation using the GPU achieved 4.03x speedup when using one CPU thread, and 5.88x speedup when using four CPU threads. This speedup is significant because accelerating k-mer counting is challenging due to reasons like serialized portions of code and overhead of disk operations.

关键词： Graphics processing units Instruction sets Sequential analysis Kernel bioinformatics Tools Acceleration"

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The Tensor Product model transformation as the link connecting Biological and Cognitive systems with Control Theory 5

The Tensor Product model transformation as the link connecti...

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5th ieee International conference on Cognitive Infocommunications (CogInfoCom)

作者： Szoellosi, Alexandra Baranyi, Peter Hungarian Acad Sci Comp & Automat Res Inst Internet Based Control & Commun Lab 3D H-1051 Budapest Hungary

ISBN: (纸本)9781479972807

The paper investigates and discusses the fact that there exists a significant difference and gap between the conventional mathematical modeling and computational techniques of control theory and the mathematical modeling and computational techniques beneficial of modeling cognitive processes or generally overall biological processes. This difference and gap represents a significant obstacle in designing control systems and theorems for cognitive or overall biological processes and systems. In this context the paper discusses and concludes pointing out the fact that the Tensor Product (TP) model transformation is a possible effective link and connector between the above mentioned two different mathematical modeling concepts.

关键词： Tensor Product model transformation Control Theory Biological systems Cognitive systems bioinformatics Intelligent Control Coginformatics

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Oscillatory dynamics in the mitogen-activated protein kinase cascade

Oscillatory dynamics in the mitogen-activated protein kinase...

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2005 ieee computational systems bioinformatics conference, Workshops and Poster Abstracts

作者： Chiam, K.-H. Bhargava, Vipul Rajagopal, Gunaretnam Bioinformatics Institute 30 Biopolis Street #07-01 Singapore 138671 Singapore

ISBN: (纸本)0769524427

We have used quantitative modeling of signaling networks to show that the mitogen-activated protein kinase cascade - a highly-conserved signaling network in eukaryotes - can functions as a low-pass filter by amplifying low-frequency oscillations and attenuating high-frequency oscillations. This filtering function of the kinase cascade is in addition to other known functions such as being an ultrasensitive switch. We show how this low-pass filtering regulates downstream cellular functions and cellular physiology. We also show how the presence of scaffold proteins in the kinase cascade modifies the properties of the low-pass filter. In particular, we find that the presence of scaffold proteins destroys the properties of the low-pass filtering, and instead attenuate all oscillations. In particular, the higher the scaffold concentration, the greater the attenuation. © 2005 ieee.

关键词： Proteins

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Improved pairwise alignment of proteins in the Twilight Zone using local structure predictions

Improved pairwise alignment of proteins in the Twilight Zone...

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2005 ieee computational systems bioinformatics conference, Workshops and Poster Abstracts

作者： Huang, Yao-Ming Bystroff, Christopher Center for Bioinformatics Dept. of Biology Rensselaer Polytechnic Institute Troy NY 12180 United States

ISBN: (纸本)0769524427

Recent advances in the ability to discriminate between homologous and non-homologous proteins in the "Twilight Zone" of sequence similarity, must be accompanied by accurate alignments if they are to be of value to molecular modelers. Pairwise alignments require a measure of evolutionary distance, traditionally modeled using global amino acid substitution matrices. But real differences in the likelihood of substitutions may exist for different structural contexts within proteins, since structure contributes to the selective pressure. HMMSUM (HMMSTR-based Substitution Matrices) is a new model for structure-dependent amino acid substitution probabilities consisting of a set of 281 matrices, one for each of the sequence-structure contexts defined in HMMSTR (a Hidden Markov Model for protein STRucture). HMMSUM does not require the structure of the protein to be known, using HMMSTR predictions instead, Alignments using the HMMSUM compare favorably BLOSUM50 alignments when validated against curated remote homolog alignments from BAUBASE. © 2005 ieee.

关键词： Proteins

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An 8-bit 2 MS/s Successive Approximation Register Analog-To-Digital Converter for bioinformatics and computational Biology Application 12

An 8-bit 2 MS/s Successive Approximation Register Analog-To-...

引用

ieee 12th International conference on Networking, Sensing and Control

作者： Lai, Wen Cheng Huang, Jhin-Fang Hsieh, Cheng Gu Kao, Fan-Tsai Natl Taiwan Univ Sci & Technol Taipei Taiwan

ISBN: (纸本)9781479980697

In this paper, a 1.8-V 8-bit successive approximation register (SAR) analog-to-digital converter (ADC) implemented in TSMC 0.18-um CMOS process is presented. By applying SAR control logic that reduces half comparator and digital circuit power consumption, the proposed SAR ADC achieves low power consumption. Also, bootstrapped switch method is used to solve varying on-resistance of analog sampling switch caused from varying input signal. Measured results show that at the supply voltage of 1.8 V and sampling rate of 2 MS/s, the proposed SAR ADC achieves a signal-to-noise and distortion ratio (SNDR) of 42.7 dB, an effective number of bits (ENOB) of 6.8 bits, a differential nonlinearity (DNL) of 0.98 LSB, an integral nonlinearity (INL) of 2.01 LSB and a power consumption of 128 mu W. The overall chip area is only 0.67 mm(2) with a small ADC core area of 0.226 mm(2) for bioinformatics and computational Application.

关键词： Analog-to-digital converter successive approximation register bio-signals and systems

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