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Weicai Ye, Ying Chen, Yongdong Zhang, Yuesheng Xu
MOTIVATION: The sequence alignment is a fundamental problem in bioinformatics. BLAST is a routinely used tool for this purpose with over 118 000 citations in the past two decades. As the size of bio-sequence databases grows exponentially, the computational speed of alignment softwares must be improved. RESULTS: We develop the heterogeneous BLAST (H-BLAST), a fast parallel search tool for a heterogeneous computer that couples CPUs and GPUs, to accelerate BLASTX and BLASTP-basic tools of NCBI-BLAST...
January 13, 2017: Bioinformatics
Robin Kobus, Christian Hundt, André Müller, Bertil Schmidt
BACKGROUND: Metagenomic sequencing studies are becoming increasingly popular with prominent examples including the sequencing of human microbiomes and diverse environments. A fundamental computational problem in this context is read classification; i.e. the assignment of each read to a taxonomic label. Due to the large number of reads produced by modern high-throughput sequencing technologies and the rapidly increasing number of available reference genomes software tools for fast and accurate metagenomic read classification are urgently needed...
January 3, 2017: BMC Bioinformatics
D Matenine, G Cote, J Mascolo-Fortin, Y Goussard, P Despres
PURPOSE: Iterative reconstruction algorithms in computed tomography (CT) require a fast method for computing the intersections between the photons' trajectories and the object, also called ray-tracing or system matrix computation. This work evaluates different ways to store the system matrix, aiming to reconstruct dense image grids in reasonable time. METHODS: We propose an optimized implementation of the Siddon's algorithm using graphics processing units (GPUs) with a novel data storage scheme...
June 2016: Medical Physics
A Hagan, A Modiri, M Svatos, A Sawant
PURPOSE: True 4D IMRT planning, based on simultaneous spatiotemporal optimization has been shown to significantly improve plan quality in lung radiotherapy. However, the high computational complexity associated with such planning represents a significant barrier to widespread clinical deployment. We introduce an early prototype GPU-enabled Eclipse workstation for inverse planning. To our knowledge, this is the first GPUintegrated Eclipse system demonstrating the potential for clinical translation of GPU computing on a major commercially-available TPS...
June 2016: Medical Physics
T Liu, H Lin, L Su, C Shi, X Tang, B Bednarz, X Xu
PURPOSE: (1) To perform phase space (PS) based source modeling for Tomotherapy and Varian TrueBeam 6 MV Linacs, (2) to examine the accuracy and performance of the ARCHER Monte Carlo code on a heterogeneous computing platform with Many Integrated Core coprocessors (MIC, aka Xeon Phi) and GPUs, and (3) to explore the software micro-optimization methods. METHODS: The patient-specific source of Tomotherapy and Varian TrueBeam Linacs was modeled using the PS approach...
June 2016: Medical Physics
B Li, Z Tian, L Zhou, S Jiang, X Jia
PURPOSE: While compressed sensing-based cone-beam CT (CBCT) iterative reconstruction techniques have demonstrated tremendous capability of reconstructing high-quality images from undersampled noisy data, its long computation time still hinders wide application in routine clinic. The purpose of this study is to develop a reconstruction framework that employs modern consensus optimization techniques to achieve CBCT reconstruction on a multi-GPU platform for improved computational efficiency...
June 2016: Medical Physics
R Yang, B Fallone, J St Aubin
PURPOSE: To develop a Graphic Processor Unit (GPU) accelerated deterministic solution to the Linear Boltzmann Transport Equation (LBTE) for accurate dose calculations in radiotherapy (RT). A deterministic solution yields the potential for major speed improvements due to the sparse matrix-vector and vector-vector multiplications and would thus be of benefit to RT. METHODS: In order to leverage the massively parallel architecture of GPUs, the first order LBTE was reformulated as a second order self-adjoint equation using the Least Squares Finite Element Method (LSFEM)...
June 2016: Medical Physics
Willem Jan Palenstijn, Jeroen Bédorf, Jan Sijbers, K Joost Batenburg
While iterative reconstruction algorithms for tomography have several advantages compared to standard backprojection methods, the adoption of such algorithms in large-scale imaging facilities is still limited, one of the key obstacles being their high computational load. Although GPU-enabled computing clusters are, in principle, powerful enough to carry out iterative reconstructions on large datasets in reasonable time, creating efficient distributed algorithms has so far remained a complex task, requiring low-level programming to deal with memory management and network communication...
2017: Advanced Structural and Chemical Imaging
Germán Retamosa, Luis de Pedro, Ivan González, Javier Tamames
Homology detection has evolved over the time from heavy algorithms based on dynamic programming approaches to lightweight alternatives based on different heuristic models. However, the main problem with these algorithms is that they use complex statistical models, which makes it difficult to achieve a relevant speedup and find exact matches with the original results. Thus, their acceleration is essential. The aim of this article was to prefilter a sequence database. To make this work, we have implemented a groundbreaking heuristic model based on NVIDIA's graphics processing units (GPUs) and multicore processors...
2016: Evolutionary Bioinformatics Online
Yongbao Li, Zhen Tian, Ting Song, Zhaoxia Wu, Yaqiang Liu, Steve Jiang, Xun Jia
Monte Carlo (MC)-based spot dose calculation is highly desired for inverse treatment planning in proton therapy because of its accuracy. Recent studies on biological optimization have also indicated the use of MC methods to compute relevant quantities of interest, e.g. linear energy transfer. Although GPU-based MC engines have been developed to address inverse optimization problems, their efficiency still needs to be improved. Also, the use of a large number of GPUs in MC calculation is not favorable for clinical applications...
January 7, 2017: Physics in Medicine and Biology
Basile F E Curchod, Aaron Sisto, Todd J Martínez
The ultrafast decay dynamics of 4-(N,N-dimethylamino)benzonitrile (DMABN) following photoexcitation was studied with the ab initio multiple spawning (AIMS) method, combined with GPU-accelerated linear-response time-dependent density functional theory (LR-TDDFT). We validate the LR-TDDFT method for this case and then present a detailed analysis of the first ≈200 fs of DMABN excited-state dynamics. Almost complete nonadiabatic population transfer from S2 (the initially populated bright state) to S1 takes place in less than 50 fs, without significant torsion of the dimethylamino (DMA) group...
January 3, 2017: Journal of Physical Chemistry. A
Robert P Sheridan, Wei Min Wang, Andy Liaw, Junshui Ma, Eric M Gifford
In the pharmaceutical industry it is common to generate many QSAR models from training sets containing a large number of molecules and a large number of descriptors. The best QSAR methods are those that can generate the most accurate predictions but that are not overly expensive computationally. In this paper we compare eXtreme Gradient Boosting (XGBoost) to random forest and single-task deep neural nets on 30 in-house data sets. While XGBoost has many adjustable parameters, we can define a set of standard parameters at which XGBoost makes predictions, on the average, better than those of random forest and almost as good as those of deep neural nets...
December 27, 2016: Journal of Chemical Information and Modeling
Dmytro Bykov, Thomas Kjaergaard
We report porting of the Divide-Expand-Consolidate Resolution of the Identity second-order Møller-Plesset perturbation (DEC-RI-MP2) method to the graphic processing units (GPUs) using OpenACC compiler directives. It is shown that the OpenACC compiler directives implementation efficiently accelerates the rate-determining step of the DEC-RI-MP2 method with minor implementation effort. Moreover, the GPU acceleration results in a better load balance and thus in an overall scaling improvement of the DEC algorithm...
February 5, 2017: Journal of Computational Chemistry
George Kantasis, Christos G Xanthis, Kostas Haris, Einar Heiberg, Anthony H Aletras
Quantitative Magnetic Resonance Imaging (MRI) is a research tool, used more and more in clinical practice, as it provides objective information with respect to the tissues being imaged. Pixel-wise T1 quantification (T1 mapping) of the myocardium is one such application with diagnostic significance. A number of mapping sequences have been developed for myocardial T1 mapping with a wide range in terms of measurement accuracy and precision. Furthermore, measurement results obtained with these pulse sequences are affected by errors introduced by the particular acquisition parameters used...
January 2017: Journal of Magnetic Resonance
Dari Kimanius, Björn O Forsberg, Sjors Hw Scheres, Erik Lindahl
By reaching near-atomic resolution for a wide range of specimens, single-particle cryo-EM structure determination is transforming structural biology. However, the necessary calculations come at increased computational costs, introducing a bottleneck that is currently limiting throughput and the development of new methods. Here, we present an implementation of the RELION image processing software that uses graphics processors (GPUs) to address the most computationally intensive steps of its cryo-EM structure determination workflow...
November 15, 2016: ELife
Jessica A Nash, Albert L Kwansa, James S Peerless, Ho Shin Kim, Yaroslava G Yingling
Nanoparticles (NPs) play increasingly important roles in nanotechnology and nanomedicine in which nanoparticle surface chemistry allows for control over interactions with other nanoparticles and biomolecules. In particular, for applications in drug and gene delivery, a fundamental understanding of the NP-nucleic acid interface allows for development of more efficient and effective nanoparticle carriers. Computational modeling can provide insights of processes occurring at the inorganic NP-nucleic interface in detail that is difficult to access by experimental methods...
January 18, 2017: Bioconjugate Chemistry
Nan Qin, Pablo Botas, Drosoula Giantsoudi, Jan Schuemann, Zhen Tian, Steve B Jiang, Harald Paganetti, Xun Jia
Monte Carlo (MC) simulation is commonly considered as the most accurate dose calculation method for proton therapy. Aiming at achieving fast MC dose calculations for clinical applications, we have previously developed a graphics-processing unit (GPU)-based MC tool, gPMC. In this paper, we report our recent updates on gPMC in terms of its accuracy, portability, and functionality, as well as comprehensive tests on this tool. The new version, gPMC v2.0, was developed under the OpenCL environment to enable portability across different computational platforms...
October 3, 2016: Physics in Medicine and Biology
Jia Zhao, Paisa Seeluangsawat, Qi Wang
A multiphasic, hydrodynamic model for spatially heterogeneous biofilms based on the phase field formulation is developed and applied to analyze antimicrobial tolerance of biofilms by acknowledging the existence of persistent and susceptible cells in the total population of bacteria. The model implements a new conversion rate between persistent and susceptible cells and its homogeneous dynamics is bench-marked against a known experiment quantitatively. It is then discretized and solved on graphic processing units (GPUs) in 3-D space and time...
December 2016: Mathematical Biosciences
Christian Hundt, Andreas Hildebrandt, Bertil Schmidt
BACKGROUND: Gene Set Enrichment Analysis (GSEA) is a popular method to reveal significant dependencies between predefined sets of gene symbols and observed phenotypes by evaluating the deviation of gene expression values between cases and controls. An established measure of inter-class deviation, the enrichment score, is usually computed using a weighted running sum statistic over the whole set of gene symbols. Due to the lack of analytic expressions the significance of enrichment scores is determined using a non-parametric estimation of their null distribution by permuting the phenotype labels of the probed patients...
2016: BMC Bioinformatics
Preston J MacDougall, Christopher E Henze, Anatoliy Volkov
We present a unique platform for molecular visualization and design that uses novel subatomic feature detection software in tandem with 3D hyperwall visualization technology. We demonstrate the fleshing-out of pharmacophores in drug molecules, as well as reactive sites in catalysts, focusing on subatomic features. Topological analysis with picometer resolution, in conjunction with interactive volume-rendering of the Laplacian of the electronic charge density, leads to new insight into docking and catalysis...
November 2016: Journal of Molecular Graphics & Modelling
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