12554
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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Trevor DeVore
Many modern-day Bioinformatics algorithms rely heavily on statistical models to analyze their biological data. Some of these statistical models lend themselves nicely to standard high performance computing optimizations such as parallelism, while others do not. One such algorithm is Markov Chain Monte Carlo (MCMC). In this thesis, we present a heterogeneous compute solution for optimizing […]
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Kedhar M, DR. M. Rajasekhara Babu, Mayank G, Abhinivesh M
Sequence alignment of two or more than two biological sequences such as protein, DNA (Deoxyribonucleic acid) or RNA (Ribonucleic acid) is called MSA (Multiple Sequence Alignment). Sequence homology can be inferred from the resulting MSA. Existing System uses dynamic programming technique which suffers from exponential growth of time as the sequence grows. A Hierarchical Expected […]
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Eric Wait, Mark Winter, Chris Bjornsson, Erzsebet Kokovay, Yue Wang, Susan Goderie, Sally Temple, Andrew Cohen
RESULTS: We present an application that enables the quantitative analysis of multichannel 5-D (x, y, z, t, channel) and large montage confocal fluorescence microscopy images. The image sequences show stem cells together with blood vessels, enabling quantification of the dynamic behaviors of stem cells in relation to their vascular niche, with applications in developmental and […]
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Anirban Mukhopadhyay, Chul Woo Lim, Suchendra M. Bhandarkar, Hanbo Chen, Austin New, Tianming Liu, Khaled Rasheed, Thiab Taha
Localization of cortical regions of interests (ROIs) in the human brain via analysis of Diffusion Tensor Imaging (DTI) data plays a pivotal role in basic and clinical neuroscience. In recent studies, 358 common cortical landmarks in the human brain, termed as Dense Individualized and Common Connectivity-based Cortical Landmarks (DICCCOLs), have been identified. Each of these […]
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Styliani Loukatou, Louis Papageorgiou, Paraskevas Fakourelis, Arianna Filntisi, Eleftheria Polychronidou, Ioannis Bassis, Vasileios Megalooikonomou, Wojciech Makalowski, Dimitrios Vlachakis, Sophia Kossida
Bioinformatics is the scientific field that focuses on the application of computer technology to the management of biological information. Over the years, bioinformatics applications have been used to store, process and integrate biological and genetic information, using a wide range of methodologies. One of the most de novo techniques used to understand the physical movements […]
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Guillaume Chapuis
The exponential growth in bioinformatics data generation and the stagnation of processor frequencies in modern processors stress the need for efficient implementations that fully exploit the parallel capabilities offered by modern computers. This thesis focuses on parallel algorithms and implementations for bioinformatics problems. Various types of parallelism are described and exploited. This thesis presents applications […]
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Chao Yu, Bo Yang
In this paper, we present the analysis and development of a cross-platform OpenCL parallelization of the Cellular Potts Model (CPM). In general, the evolution of the CPM is time-consuming. Using data-parallel programming model such as CUDA can accelerate the process, but it is highly dependent on the hardware type and manufacturer. Recently, OpenCL has attracted […]
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Nagaveni V, G T Raju
The main aim of string matching algorithm is to locate the appearance of a specific pattern in an array of larger size text. String matching algorithms has been used in many applications such as DNA analysis. This report introduces a new approach of string matching algorithm to detect the occurrence of several gene patterns in […]
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Yichao Zhou, Wei Xu, Bruce R. Donald, Jianyang Zeng
MOTIVATION: Structure-based computational protein design (SCPR) is an important topic in protein engineering. Under the assumption of a rigid backbone and a finite set of discrete conformations of side-chains, various methods have been proposed to address this problem. A popular method is to combine the dead-end elimination (DEE) and A* tree search algorithms, which provably […]
Yeim-Kuan Chang, De-Yu Chen
Sequence alignment is a task that calculates the degree of similarity between two sequences. Given a query sequence, finding a database sequence which is most similar to the query by sequence alignment is the first step in bioinformatics research. The first sequence alignment algorithm was proposed by Needle-man and Wunsch. They got the optimal global […]
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