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Johannes Koster, Sven Rahmann
We present the q-group index, a novel data structure for read mapping tailored towards graphics processing units (GPUs) with a small memory footprint and efficient parallel algorithms for querying and building. On top of the q-group index we introduce PEANUT, a highly parallel GPU-based read mapper. PEANUT provides the possibility to output both the best […]
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Mahsa Bayati, Jaydeep P. Bardhan, David M. King, Miriam Leeser
For modeling proteins in conformational states, two methods of representation are used: internal coordinates and Cartesian coordinates. Each of these representations contain a large amount of structural and simulation information. Different processing steps require one or the other representation. Our goal is to rapidly translate between these coordinate spaces so that a scientist can choose […]
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Dinghua Li, Chi-Man Liu, Ruibang Luo, Kunihiko Sadakane, Tak-Wah Lam
MEGAHIT is a NGS de novo assembler for assembling large and complex metagenomics data in a time- and cost-efficient manner. It finished assembling a soil metagenomics dataset with 252Gbps in 44.1 hours and 99.6 hours on a single computing node with and without a GPU, respectively. MEGAHIT assembles the data as a whole, i.e., it […]
Mikhail A. Farkov
The vast majority of problems faced by bioinformatics are very complex and time consuming. They require the use of modern high-performance computational systems and the development of algorithms for such system. Heterogeneous computing systems which include graphics processing unit (GPU) occupy a separate niche. Such systems allow to accelerate solving of some task significantly. The […]
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Abdul Hafeez
Detection and identification of important biological targets, such as DNA, proteins, and diseased human cells are crucial for early diagnosis and prognosis. The key to discriminate healthy cells from the diseased cells is the biophysical properties that differ radically. Micro and nanosystems, such as solid-state micropores and nanopores can measure and translate these properties of […]
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Tomas Ekeberg, Stefan Engblom, Jing Liu
The classical method of determining the atomic structure of complex molecules by analyzing diffraction patterns is currently undergoing drastic developments. Modern techniques for producing extremely bright and coherent X-ray lasers allow a beam of streaming particles to be intercepted and hit by an ultrashort high energy X-ray beam. Through machine learning methods the data thus […]
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Jianbin Fang, Ana Lucia Varbanescu, Baldomero Imbernon, Jose M. Cecilia, Horacio Perez-Sanchez
Currently, medical research for the discovery of new drugs is increasingly using Virtual Screening (VS) methods. In these methods, the calculation of the non-bonded interactions, such as electrostatic or van der Waals, plays an important role, representing up to 80% of the total execution time. These are computationally intensive operations, and massively parallel in nature, […]
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Quan Zhou, Wenlin Chen, Shiji Song, Jacob R. Gardner, Kilian Q. Weinberger, Yixin Chen
The past years have witnessed many dedicated open-source projects that built and maintain implementations of Support Vector Machines (SVM), parallelized for GPU, multi-core CPUs and distributed systems. Up to this point, no comparable effort has been made to parallelize the Elastic Net, despite its popularity in many high impact applications, including genetics, neuroscience and systems […]
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Gary K. Chen, Eric Chi, John Ranola, Kenneth Lange
The primary goal in cluster analysis is to discover natural groupings of objects. The field of cluster analysis is crowded with diverse methods that make special assumptions about data and address different scientific aims. Despite its shortcomings in accuracy, hierarchical clustering is the dominant clustering method in bioinformatics. Biologists find the trees constructed by hierarchical […]
Richard Wilton, Tamas Budavari, Ben Langmead, Sarah Wheelan, Steven L. Salzberg, Alex Szalay
MOTIVATION: In computing pairwise alignments of biological sequences, software implementations employ a variety of heuristics that decrease the computational effort involved in computing potential alignments. A key element in achieving high processing throughput is to identify and prioritize potential alignments where high-scoring mappings can be expected. These tasks involve list-processing operations that can be efficiently […]
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Esin Yavuz, James Turner, Thomas Nowotny
A major challenge in computational neuroscience is to achieve high performance for real-time simulations of full size brain networks. Recent advances in GPU technology provide massively parallel, low-cost and efficient hardware that is widely available on the computer market. However, the comparatively low-level programming that is necessary to create an efficient GPU-compatible implementation of neuronal […]
Rahul Shirude, Valmik B. Nikam, B.B. Meshram
Bioinformatics is the field of science which applies computer science and information technology to the problems of biological science. One of the most useful applications of bioinformatics is sequence analysis. Sequence analysis, which is the process of subjecting a DNA, RNA to any wide range of analytical approaches, involves methodologies like sequence alignment and searches […]
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