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Designing the Cloud-Based DOE Systems biology Knowledgebase

Designing the Cloud-Based DOE Systems Biology Knowledgebase

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ieee International symposium on Parallel and Distributed Processing Workshops and Phd Forum (IPDPSW)

作者： Carina Lansing Yan Liu Jian Yin Abigail Corrigan Zoe Guillen Kerstin Kleese van Dam Ian Gorton Fundamental and Computational Science Division Pacific Northwest National Laboratory Richland WA USA

Systems biology research, even more than many other scientific domains, is becoming increasingly data-intensive. Not only have advances in experimental and computational technologies lead to an exponential increase in scientific data volumes and their complexity, but increasingly such databases are providing the basis for new scientific discoveries. To engage effectively with these community resources, integrated analyses, synthesis and simulation software is needed, supported by scientific workflows. In order to provide a more collaborative, community driven research environment for this heterogeneous setting, the Department of Energy (DOE) has decided to develop a federated, cloud based cyber infrastructure the Systems biology Knowledgebase (Kbase). In this context the Pacific Northwest National Laboratory (PNNL) has been defining and testing the basic federated cloud-based system architecture and developed a prototype implementation. Community wide accessibility of biological data and the capability to integrate and analyze this data within its changing research context were seen as key technical functionalities the Kbase needs to enable. In this paper we describe the results of our investigations into the design of this cloud based federated infrastructure for: 1) Semantics driven data discovery, access and integration 2) Data annotation, publication and sharing 3) Workflow enabled data analysis 4) Project based collaborative working We describe our approach, exemplary use cases and our prototype implementation that demonstrates the feasibility of this approach.

关键词： Communities Collaboration Computer architecture Semantics bioinformatics Genomics

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GenAMap: Visualization strategies for structured association mapping

GenAMap: Visualization strategies for structured association...

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ieee symposium on Biological Data Visualization (BioVis)

作者： Ross E. Curtis Peter Kinnaird Eric P. Xing Computational Biology Joint Carnegie Mellon-University of Pittsburgh USA Human Computer Interaction Institute Carnegie Mellon University Qatar Machine Learning Department Carnegie Mellon University Qatar

Association mapping studies promise to link DNA mutations to gene expression data, possibly leading to innovative treatments for diseases. One challenge in large-scale association mapping studies is exploring the results of the computational analysis to find relevant and interesting associations. Although many association mapping studies find associations from a genome-wide collection of genomic data to hundreds or thousands of traits, current visualization software only allow these associations to be explored one trait at a time. The inability to explore the association of a genomic location to multiple traits hides the inherent interaction between traits in the analysis. Additionally, researchers must rely on collections of in-house scripts and multiple tools to perform an analysis, adding time and effort to find interesting associations. In this paper, we present a novel visual analytics system called GenAMap. GenAMap replaces the time-consuming analysis of large-scale association mapping studies with exploratory visualization tools that give geneticists an overview of the data and lead them to relevant information. We present the results of a preliminary evaluation that validated our basic approach.

关键词： Genomics bioinformatics Data visualization Algorithm design and analysis Heating Gene expression

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An Efficient and Scalable Implementation of SNP-Pair Interaction Testing for Genetic Association Studies

An Efficient and Scalable Implementation of SNP-Pair Interac...

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ieee International symposium on Parallel and Distributed Processing Workshops and Phd Forum (IPDPSW)

作者： Lars Koesterke Dan Stanzione Matt Vaughn Stephen M. Welch Waclaw Kusnierczyk Jinliang Yang Cheng-Ting Yeh Dan Nettleton Patrick S. Schnable Texas Advanced Computing Center University of Technology Austin TX USA Department of Agronomy Kansas State University Manhattan KS USA Iowa State University Ames IA USA

This paper describes a scalable approach to one of the most computationally intensive problems in molecular plant breeding, that of associating quantitative traits with genetic markers. The fundamental problem is to build statistical correlations between particular loci in the genome of an individual plant and the expressed characteristics of that individual. While applied to plants in this paper, the problem generalizes to mapping genotypes to phenotypes across all biology. In this work, a formulation of a statistical approach for identifying pair wise interactions is presented. The implementation, optimization and parallelization of this approach are then presented, with scalability results.

关键词： bioinformatics computational modeling Indexes Genomics DNA Electronic mail

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Tight Certification Techniques for Digit-by-Rounding Algorithms with Application to a New 1/sqrt(x) Design

Tight Certification Techniques for Digit-by-Rounding Algorit...

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Computer Arithmetic (ARITH)

作者： Ping Tak Peter Tang J. Adam Butts Ron O. Dror David E. Shaw D. E. Shaw Research New York NY USA Center for Computational Biology and Bioinformatics Columbia University New York NY USA

Digit-by-rounding algorithms enable efficient hardware implementations of algebraic functions such as the reciprocal, square root, or reciprocal square root, but certifying the correctness of such algorithms is a nontrivial endeavor. Traditionally, sufficient conditions for correctness are derived as closed-form formulae relating key design parameters. These sufficient conditions, however, often prove stricter than necessary, excluding correct and efficient designs. In this paper, we present a rigorous, computer-aided method for correctness certification that better approximates the necessary conditions, lowering the risk of rejecting correct designs. We also present two specific applications of this method. First, when applied to a conventional digit-by-rounding reciprocal square root design, our method enabled a fourfold reduction in lookup table size relative to the minimum dictated by a standard sufficient condition. Second, our method certified the correctness of a novel reciprocal square root design that we developed to parallelize two computational steps whose sequential execution lies on the critical path of conventional designs. The difficulty in deriving closed-form sufficient conditions to ascertain this design's correctness provided the original motivation for development of the new certification method.

关键词： Algorithm design and analysis Tiles Trajectory Convergence Testing computational efficiency Approximation algorithms

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2005 ieee symposium on computational intelligence in bioinformatics and computational biology (ieee CIBCB 2005)

2005 IEEE symposium on Computational Intelligence in Bioinfo...

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作者： Fogel, Gary B. Natural Selection Inc. United States

The issues taken into count in ieee CIBCB 2005 symposium, held in La Jolla, Calif., at the Embassy Suites Hotel La Jolla San Diego on November 14-15, 2005, are discussed. The CIBCB symposium series aims to bring together researchers from around the world to discuss applications of computational intelligence in bioinformatics. The event was officially opened with a keynote lecture related to regulating the regulators: variations and silencing in transcription factor genes given by Dr. Terry Gaasterland, professor of computational biology of the University of California and the directors of the Scripps Genome Center The event also highlighted how alternative splicing and microRNA expression modify transcription factor protein production and binding.

关键词： Artificial intelligence

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Finding multiple global optima exploiting differential evolution's niching capability

Finding multiple global optima exploiting differential evolu...

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ieee symposium on Differential Evolution (SDE)

作者： Michael G. Epitropakis Vassilis P. Plagianakos Michael N. Vrahatis Computational Intelligence Laboratory Department of Mathematics University of Patras Greece Department of Computer Science and Biomedical Informatics University of Central Greece Greece

Handling multimodal functions is a very important and challenging task in evolutionary computation community, since most of the real-world applications exhibit highly multi-modal landscapes. Motivated by the dynamics and the proximity characteristics of Differential Evolution's mutation strategies tending to distribute the individuals of the population to the vicinity of the problem's minima, we introduce two new Differential Evolution mutation strategies. The new mutation strategies incorporate spatial information about the neighborhood of each potential solution and exhibit a niching formation, without incorporating any additional parameter. Experimental results on eight well known multimodal functions and comparisons with some state-of-the-art algorithms indicate that the proposed mutation strategies are competitive and very promising, since they are able to reliably locate and maintain many global optima throughout the evolution process.

关键词： Strontium Accuracy Evolution (biology) Space exploration Benchmark testing Optimization Evolutionary computation

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Proceedings of the 2006 ieee symposium on computational intelligence in bioinformatics and computational biology, CIBCB'06

Proceedings of the 2006 IEEE Symposium on Computational Inte...

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3rd computational intelligence in bioinformatics and computational biology symposium, CIBCB

ISBN: (纸本)1424406234

The proceedings contain 66 papers. The topics discussed include: predicting protein-protein interface using desolvation energy similarity matching;a hidden Markov model approach to identifying HTH motifs using protein sequence and predicted solvent accessibility;a method to integrate, assess and characterize the protein-protein interactions;fuzzy C-means for inferring functional coupling of proteins from their phylogenetic profiles;protein-protein interface residue prediction with SVM using evolutionary profiles and accessible surface areas;a swarm intelligence based algorithm for proteomic pattern detection of ovarian cancer;feature selection approach for quantitative prediction of transcriptional activities;integrating affymetrix microarray data sets using probe-level test statistic for predicting prostate cancer;and a differential evolution approach for protein folding.

关键词： Evolutionary algorithms

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Performance of different approaches for predicting the subcellular locations of proteins: A review

Performance of different approaches for predicting the subce...

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ieee International Conference on Multi Topic

作者： Muhammad Taskeen Raza Noor M. Sheikh Muhammad Abuzar Fahiem Ahmed M. Mehdi Department of Electrical Engineering UET Taxila Lahore Pakistan Department of Electrical Engineering University of Engineering & technology Lahore Pakistan Department of Computer Science Lahore College for Women University Lahore Pakistan Institute for Molecular Bioscience University of Queensland Brisbane Australia

Subcellular location of a protein is closely related to its function. Knowing the subcellular localization of proteins is important in molecular cell biology, proteomics, and system biology and drug discovery. Different predictors have been developed that predict presence, location and interaction of molecules using various computational techniques including probabilistic models of Machine Learning and artificial intelligence algorithms. These predictors partially cover the different aspects of exploration of subcellular locations. Some of them are equally well applicable to many types of organisms (human, yeast, mouse, bacteria) while some are specific and focus on better performance in accuracy of the predicted results. Similarly some of the techniques cover “few” number of proteins but more accurately and on the other side some algorithms predict sub cellular locations of “many” proteins at the expense of prediction accuracy. This research is a review of most common and efficient techniques grouped in four in total, which are 1-amino acid composition and order-based predictors 2-sorting signal predictors 3- homology-based predictors and 4-hybrid methods that use several sources of information to predict localization. The work Elucidate the performance and coverage comparisons among the subcellular locations predictors.

关键词： bioinformatics Biological system modeling Analytical models Bayesian methods Genomics Humans

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An identification and prediction methods for feature-subsets of CpG islands methylation based on human peripheral blood leukocytes of chromosome 21q

An identification and prediction methods for feature-subsets...

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Annual International Conference of the ieee Engineering in Medicine and biology Society

作者： Isse Ali Hussein Sheikh ali Mohamoud Bio-Health Informatics Research Group within the Centre for Computational Intelligence De Montfort University South West Thames Regional Genetics Service St Georges Hospital Cranmer Terrace

ISBN: (纸本)9781424441211

The pace of technology has allowed classification of feature-subset of methylated and unmethylated of CpG islands of DNA sequence properties. As methylation of CpG islands is involved in various biological phenomena and function of the DNA methylation is correlated to various human diseases such as cancer, analysis of the CpG islands has become important and useful in characterizing and modelling biological phenomena and understanding mechanism of such diseases. However, analysis of the data associated with the CpG islands is a quite new and challenging subject in bioinformatics, systems biology and epigenetics. In this paper, the problems associated with prediction of methylated and unmethylated CpG islands on human chromosome 21q are addressed. In order to carry out the prediction, a data set of 132 samples of the CpG islands from human peripheral blood leukocytes of chromosomes 21q and 4 different feature sub-sets totalling 44 attributes that characterise the methylated and unmethylated groups is extracted for each sample. Due to the nature of this unbalanced data set, in order to avoid disadvantages of traditional leave-one-out (LOO) and m-fold cross validation methods, the LOO method is modified by incorporating the m-fold cross validation approach. In addition, K-nearest neighbour classifier is then adapted for the prediction. The results gained through 440 different comprehensive analyses shows that the methylated CpG islands can be distinguished from the unmethylated CpG islands by a predictive accuracy of between 75% and 80%. More importantly, the modified LOO identifies more clearly and reliably when the feature sub-sets are combined. Another interesting observation is that the modified-LOO-based analysis reveals that the CpGI-specific feature-set achieve the highest predictive accuracy when combined with the other feature sets, which is not the case in the traditional LOO. This also further supports the robustness of the modified-LOO cross validation appr

关键词： DNA Humans Accuracy bioinformatics Feature extraction Biological cells Genomics

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Radix-8 Digit-by-Rounding: Achieving High-Performance Reciprocals, Square Roots, and Reciprocal Square Roots

Radix-8 Digit-by-Rounding: Achieving High-Performance Recipr...

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Computer Arithmetic (ARITH)

作者： J. Adam Butts Ping Tak Peter Tang Ron O. Dror David E. Shaw D. E. Shaw Research New York NY USA Center for Computational Biology and Bioinformatics Columbia University New York NY USA

We describe a high-performance digit-recurrence algorithm for computing exactly rounded reciprocals, square roots, and reciprocal square roots in hardware at a rate of three result bits - one radix-8 digit - per recurrence iteration. To achieve a single-cycle recurrence at a short cycle time, we adapted the digit-by-rounding algorithm, which is normally applied at much higher radices, for efficient operation at radix 8. Using this approach avoids in the recurrence step the lookup table required by SRT - the usual algorithm used for hardware digit recurrences. The increasing access latency of this table, the size of which grows super linearly in the radix, limits high-frequency SRT implementations to radix 4 or lower. We also developed a series of novel optimizations focused on further reducing the critical path through the recurrence. We propose, for example, decreasing data path widths to a point where erroneous results sometimes occur and then correcting these errors off the critical path. We present a specific implementation that computes any of these functions to 31 bits of precision in 13 cycles. Our implementation achieves a cycle time only 11% longer than the best reported SRT design for the same functions, yet delivers results in five fewer cycles. Finally, we show that even at lower radices, a digit-by-rounding design is likely to have a shorter critical path than one using SRT at the same radix.

关键词： Approximation methods Hardware Optimization Delay Equations Algorithm design and analysis Complexity theory

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