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  • Articles  (131)
  • Oxford University Press  (131)
  • American Chemical Society
  • Blackwell Publishing Ltd
  • Computer Science  (131)
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  • Articles  (131)
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  • 1
    Publication Date: 2012-09-08
    Description: : The application of docking to large-scale experiments or the explicit treatment of protein flexibility are part of the new challenges in structural bioinformatics that will require large computer resources and more efficient algorithms. Highly optimized fast Fourier transform (FFT) approaches are broadly used in docking programs but their optimal code implementation leaves hardware acceleration as the only option to significantly reduce the computational cost of these tools. In this work we present Cell-Dock, an FFT-based docking algorithm adapted to the Cell BE processor. We show that Cell-Dock runs faster than FTDock with maximum speedups of above 200 x , while achieving results of similar quality. Availability and implementation: The source code is released under GNU General Public License version 2 and can be downloaded from http://mmb.pcb.ub.es/~cpons/Cell-Dock . Contact: djimenez@ac.upc.edu or juanf@bsc.es Supplementary Information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 2
    Publication Date: 2012-07-19
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 3
    Publication Date: 2016-03-26
    Description: : Supervised classification based on support vector machines (SVMs) has successfully been used for the prediction of cis -regulatory modules (CRMs). However, no integrated tool using such heterogeneous data as position-specific scoring matrices, ChIP-seq data or conservation scores is currently available. Here, we present LedPred, a flexible SVM workflow that predicts new regulatory sequences based on the annotation of known CRMs, which are associated to a large variety of feature types. LedPred is provided as an R/Bioconductor package connected to an online server to avoid installation of non-R software. Due to the heterogeneous CRM feature integration, LedPred excels at the prediction of regulatory sequences in Drosophila and mouse datasets compared with similar SVM-based software. Availability and implementation: LedPred is available on GitHub: https://github.com/aitgon/LedPred and Bioconductor: http://bioconductor.org/packages/release/bioc/html/LedPred.html under the MIT license. Contact: aitor.gonzalez@univ-amu.fr Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 4
    Publication Date: 2015-08-28
    Description: The gap between processor and memory speeds is one of the greatest challenges that current designers face in order to develop more powerful computer systems. In addition, the scalability of the Dynamic Random Access Memory (DRAM) technology is very limited nowadays, leading one to consider new memory technologies as candidates for the replacement of conventional DRAM. Phase-Change Memory (PCM) is currently postulated as the prime contender due to its higher scalability and lower leakage. However, compared with DRAM, PCM also exhibits some drawbacks, like lower endurance or higher dynamic energy consumption and write latency, that need to be mitigated before it can be used as the main memory technology for the next generation of computers. This work addresses the PCM endurance constraint. For this purpose, we present an analysis of conventional cache replacement policies in terms of the amount of writebacks to main memory that they imply and we also propose some new replacement algorithms for the last-level cache (LLC) with the goal of cutting down the write traffic to memory and consequently, to increase PCM lifetime without degrading system performance. In this paper, we target general purpose processors provided with this kind of non-volatile main memory and we exhaustively evaluate our proposed policies in both single- and multi-core environments. Experimental results show that, on average, compared with a conventional Least Recently Used (LRU) algorithm, some of our proposals manage to reduce the amount of writes to main memory up to 20–30% depending on the scenario evaluated, which leads to memory endurance extensions of up to 20–45%, also reducing the energy consumption in the memory hierarchy by up to 9% and hardly degrading performance.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
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  • 5
    Publication Date: 2015-06-14
    Description: : Diseases caused by zoonotic viruses (viruses transmittable between humans and animals) are a major threat to public health throughout the world. By studying virus migration and mutation patterns, the field of phylogeography provides a valuable tool for improving their surveillance. A key component in phylogeographic analysis of zoonotic viruses involves identifying the specific locations of relevant viral sequences. This is usually accomplished by querying public databases such as GenBank and examining the geospatial metadata in the record. When sufficient detail is not available, a logical next step is for the researcher to conduct a manual survey of the corresponding published articles. Motivation: In this article, we present a system for detection and disambiguation of locations (toponym resolution) in full-text articles to automate the retrieval of sufficient metadata. Our system has been tested on a manually annotated corpus of journal articles related to phylogeography using integrated heuristics for location disambiguation including a distance heuristic, a population heuristic and a novel heuristic utilizing knowledge obtained from GenBank metadata (i.e. a ‘metadata heuristic’). Results: For detecting and disambiguating locations, our system performed best using the metadata heuristic (0.54 Precision, 0.89 Recall and 0.68 F-score). Precision reaches 0.88 when examining only the disambiguation of location names. Our error analysis showed that a noticeable increase in the accuracy of toponym resolution is possible by improving the geospatial location detection. By improving these fundamental automated tasks, our system can be a useful resource to phylogeographers that rely on geospatial metadata of GenBank sequences. Contact: davy.weissenbacher@asu.edu
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 6
    Publication Date: 2015-06-14
    Description: : The design of genetic markers is of particular relevance in crop breeding programs. Despite many economically important crops being polyploid organisms, the current primer design tools are tailored for diploid species. Bread wheat, for instance, is a hexaploid comprising of three related genomes and the performance of genetic markers is diminished if the primers are not genome specific. PolyMarker is a pipeline that generates SNP markers by selecting candidate primers for a specified genome using local alignments and standard primer design tools to test the viability of the primers. A command line tool and a web interface are available to the community. Availability and implementation: PolyMarker is available as a ruby BioGem: bio-polyploid-tools . Web interface: http://polymarker.tgac.ac.uk . Contact: Ricardo.Ramirez-Gonzalez@tgac.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 7
    Publication Date: 2013-02-13
    Description: Motivation: Data collection in spreadsheets is ubiquitous, but current solutions lack support for collaborative semantic annotation that would promote shared and interdisciplinary annotation practices, supporting geographically distributed players. Results: OntoMaton is an open source solution that brings ontology lookup and tagging capabilities into a cloud-based collaborative editing environment, harnessing Google Spreadsheets and the NCBO Web services. It is a general purpose, format-agnostic tool that may serve as a component of the ISA software suite. OntoMaton can also be used to assist the ontology development process. Availability: OntoMaton is freely available from Google widgets under the CPAL open source license; documentation and examples at: https://github.com/ISA-tools/OntoMaton . Contact: isatools@googlegroups.com
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 8
    Publication Date: 2013-02-02
    Description: Counter-based power models have attracted the interest of researchers because they became a quick approach to know the insights of power consumption. Moreover, they allow one to overpass the limitations of measurement devices. In this paper, we compare different Top-down and Bottom-up Counter-based modeling methods. We present a qualitative and quantitative evaluation of their properties. In addition, we study how to extend them to support the currently ubiquitous dynamic voltage and frequency scaling (DVFS) mechanism. We propose a simple method to generate DVFS agnostic power models from the DVFS-specific models. The proposed method is applicable to models generated using any methodology and allows the reduction of the modeling time without affecting the fundamental properties of the models. The study is performed on an 18 DVFS states Intel ® Core™ 2 platform using the SPECcpu2006, NAS and LMBENCH benchmark suites. In our testbed, a 6 x reduction on the modeling time only increments 1% point on average the error in the predictions.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
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  • 9
    Publication Date: 2016-03-03
    Description: The motif discovery problem (MDP) is an important biological optimization problem that has been addressed in numerous ways. However, it is important to note that when we address real complex optimization problems, we should adequately formulate them in order to provide real applicability to the developed techniques. In the particular case of MDP, as we do not know the size of the motifs and the number of repetitions that can be found in the sequences, we must not make any length or pattern-repetition assumptions. In addition, if we consider that it is practically impossible to adequately formulate an optimization problem with a single-objective function formulation, multiobjective optimization can be a good methodology to be considered. In this paper, we propose a novel hybrid multiobjective algorithm for tackling the MDP. Our main objective is to study the results achieved by our algorithm, analysing its performance when different motif occurrence models are considered. As we will see, experimental results on different sets of real instances will point out the advantages and disadvantages of each model, also checking how a more realistic definition of the optimized problem provides better quality biological results.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
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  • 10
    Publication Date: 2016-01-21
    Description: Precision medicine will revolutionize the way we treat and prevent disease. A major barrier to the implementation of precision medicine that clinicians and translational scientists face is understanding the underlying mechanisms of disease. We are starting to address this challenge through automatic approaches for information extraction, representation and analysis. Recent advances in text and data mining have been applied to a broad spectrum of key biomedical questions in genomics, pharmacogenomics and other fields. We present an overview of the fundamental methods for text and data mining, as well as recent advances and emerging applications toward precision medicine.
    Print ISSN: 1467-5463
    Electronic ISSN: 1477-4054
    Topics: Biology , Computer Science
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