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An Efficient Hardware-Based Approach for Molecular Folding Calculations via System-on-Chip

An Efficient Hardware-Based Approach for Molecular Folding C...

The 3rd International conference on Bioinformatics and biomedical Engineering(iCBBE 2009)(第三届生物信息与生物医学工程国际会议)

作者： Wen-Tsai Sung Department of Electrical Engineering National Chin-Yi University of TechnologyTaiwan No.35Lane 215Section 1Chung-Shan RoadTaiping CityTaichung County411 Taiwan

This paper presents a methodology for the design of a reconfigurable computing system applied to a complex problem in molecular Biology: the protein folding problem. This paper employed VMD tool and force field simulation theorem based on FPGA for protein folding solution. This technique consists of two components: finished protein folding process and found out active sites for drug docking. The goal of protein folding simulation is to search the global energy minimum location with stability state and the when the protein is finished the folding task, we can find out the active sites for pre-process of ligand protein docking. An efficient hardware-based approach was devised to achieve a significant reduction of the search space of possible foldings. Several simulations were done to evaluate the performance of the system as well as the demand for FPGA's resources.

关键词： Drug Docking Minimum Energy Protein Folding Molecular visualization FPGA

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High-performance tomographic reconstruction using graphics processing units 18

High-performance tomographic reconstruction using graphics p...

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IMACS World Congress/Modelling and Simulation Society-of-Australia-and-New-Zealand (MSSANZ)/18th MODSIM09 Biennial conference on Modelling and Simulation

作者： Nesterets, Ya I. Gureyev, T. E. CSIRO Mat Sci & Engn Clayton Vic Australia

ISBN: (纸本)9780975840078

Computed Tomography (CT) has become a routine tool for three-dimensional (3D) visualization of the internal structure of objects which are opaque to visible light. X-ray CT is widely used in materials science, biomedical applications and elsewhere. Different CT reconstruction algorithms have been developed including the well-known Filtered-Back-Projection (FBP) algorithm in the parallel beam geometry and the Feldkamp-Davis-Kress (FDK) algorithm applicable to cone-beam geometry with a circular trajectory of a small X-ray source and a flat two-dimensional (2D) detector. Recent progress in detector technology resulted in the availability of commercial 2D Charge-Coupled-Devices (CCDs) with linear dimensions of the order of 4k pixels or more. The amount of memory required for storing a 3D volume of floating-point data of such linear size is 256GB or more, which significantly exceeds the typical amount of RAM found not only in high-end desktop computers but also in small computer clusters. The most computationally intensive step in the FBP and FDK CT reconstruction algorithms is the so-called back-projection operation that takes up to 99% of the total reconstruction time in a typical CPU-based implementation. The 3D computer graphics capabilities of general-purpose graphics processing units (GP-GPUs) utilized e. g. via OpenGL or DirectX have been used for the back-projection operation for the last ten to fifteen years. With the recent increase in the size of reconstructed volumes as mentioned above, standard approaches which usually store the whole reconstructed volume in GPU memory have become problematic. Different algorithmic approaches are required for the effective use of GPUs for CT reconstruction of large data volumes. We have developed new CPU-based and GPU-based implementations of the FBP and FDK algorithms for Xray CT. These implementations take into account the following principles: Use as little RAM and/or GPU memory for the reconstruction of each axial slice

关键词： Computed Tomography (CT) High-Performance computing (HPC) Graphics Processing Unit (GPU)

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Patient motion tracking in the presence of measurement errors

Patient motion tracking in the presence of measurement error...

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Annual International conference of the IEEE Engineering in Medicine and Biology Society (EMBC)

作者： Tamas Haidegger Zoltan Benyo Peter Kazanzides Department of Control Engineering and Information Technology-Laboratory of Biomedical Engineering Budapest University슠of슠Technology슠and슠Economics Budapest Hungary Center of Computer Integrated Surgical Systems and Technology Johns Hopkins University Baltimore MD USA

The primary aim of computer-integrated surgical systems is to provide physicians with superior surgical tools for better patient outcome. Robotic technology is capable of both minimally invasive surgery and microsurgery, offering remarkable advantages for the surgeon and the patient. Current systems allow for sub-millimeter intraoperative spatial positioning, however certain limitations still remain. Measurement noise and unintended changes in the operating room environment can result in major errors. Positioning errors are a significant danger to patients in procedures involving robots and other automated devices. We have developed a new robotic system at the Johns Hopkins University to support cranial drilling in neurosurgery procedures. The robot provides advanced visualization and safety features. The generic algorithm described in this paper allows for automated compensation of patient motion through optical tracking and Kalman filtering. When applied to the neurosurgery setup, preliminary results show that it is possible to identify patient motion within 700 ms, and apply the appropriate compensation with an average of 1.24 mm positioning error after 2 s of setup time.

关键词： Tracking Measurement errors Robotics and automation Minimally invasive surgery Neurosurgery Optical filters Physics computing Robots Microsurgery Surges

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Surface Reconstruction of Locust Chest Based on Serial Section Images

Surface Reconstruction of Locust Chest Based on Serial Secti...

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第三届国际计算机及计算技术农业应用学术会议

作者： Junzhou Wu,Limin Zheng,Hong Zhu,Ping Wu College of Information and Electric Engineering,China Agricultural University,Beijing,100083

The abstract is to be in fully-justified italicized text, at the top of the left-hand column as it is here,below the author *** the word"Abstract"as the title,in 12-point Times,boldface type,centered relative to the column,initially *** abstract is to be in 10-point,single-spaced type,and up to 150 words in *** two blank lines after the abstract,then begin the main text. ViSC(visualization in scientific computing) is an important research topic in computer *** application almost covers all areas of natural sciences and engineering technology and is particularly prominent in the field of biomedical *** reconstruction is one of the most critical technologies in biomedical *** process is described as following:extracting information from serial two-dimensional images of tissues and organs generated from medical imaging equipments (computed tomography CT,magnetic resonance imaging MRI,etc.),building a three dimensional geometric model using computer three-dimensional image technology,rendering and displaying the"real"image on the computer *** representation of three-dimensional structures of biological tissues and organs is immensely valuable to study the structure, functions and the relationship between *** reconstruction technology includes two methods:volume rendering and surface reconstruction, the later was adopted in this *** lines and marching cube are common algorithms in surface *** paper aimed at reconstructing a locust chest based on serial section *** reconstructed 3D image could be saved on the hard drive as a STL file.

关键词： Locust serial section micro-images Three-dimensional reconstruction Contour lines Marching cube STL files

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Comparison of visualization methods of genome-wide SNP profiles in childhood acute lymphoblastic leukaemia

Conferences in Research and Practice in Information Technolo...

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conferences in Research and Practice in Information Technology Series 2008年 87卷 111-121页

作者： Al-Oqaily, Ahmad Kennedy, Paul J. Catchpoole, Daniel Simoff, Simeon Faculty of Engineering and IT University of Technology Sydney PO Box 123 Broadway NSW 2007 Australia The Oncology Research Unit The Children's Hospital at Westmead Locked Bag 4001 Westmead NSW 2145 Australia School of Computing and Mathematics University of Western Sydney Locked Bag 1797 Parammata Australia

ISBN: (纸本)9781920682682

Data mining and knowledge discovery have been applied to datasets in various industries including biomedical data. Modelling, data mining and visualization in biomedical data address the problem of extracting knowledge from large and complex biomedical data. The current challenge of dealing with such data is to develop statistical-based and data mining methods that search and browse the underlying patterns within the data. In this paper, we employ several data reduction methods for visualizing genome- wide Single Nucleotide Polymorphism (SNP) datasets based on state-of-art data reduction techniques. visualization approach has been selected based on the trustworthiness of the resultant visualizations. To deal with large amounts of genetic variation data, we have chosen to apply different data reduction methods to deal with the problem induced by high dimensionality. Based on the trustworthiness metric we found that neighbour Retrieval Visualizer (NeRV) outperformed other methods. This method optimizes the retrieval quality of Stochastic neighbour Embedding. The quality measure of the visualization (i.e. NeRV) showed excellent results, even though the dataset was reduced from 13917 to 2 dimensions. The visualization results will assist clinicians and biomedical researchers in understanding the systems biology of patients and how to compare different groups of clusters in visualizations. © 2008, Australian Computer Society, Inc.

关键词： visualization

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An efficient method for sampling and computing molecular surface

An efficient method for sampling and computing molecular sur...

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1st International conference on biomedical Engineering and Informatics

作者： Xiang, Junping Hu, Maolin Anhui Univ Minist Educ Key Lab Intelligent Comp & Signal Proc Hefei 230039 Anhui Peoples R China

ISBN: (纸本)9780769531182

An atom-centered protocol based method for surface sampling in grid space is proposed. Van der Waals, solvent-accessible and solvent-excluded surface can be generated in a unified framework. A spherical hash function is used to mark whether the points are inside a sphere, and the hash tables are used to record which spheres the surface points locate on. The proposed method can be modified to apply in the parallel computation directly, which is useful for molecular dynamics simulation, docking and surface comparison and so on. Our tests indicate that the proposed method is efficient and the generated surfaces are suitable for quantitative analysis and visualization.

关键词： Spheres

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Faster, higher quality volume visualization for 3D medical imaging

Faster, higher quality volume visualization for 3D medical i...

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Medical Imaging 2008 conference

作者： Kalvin, Alan D. Laine, Andrew F. Song, Ting Akimbo Technol 36 Sunnyside Pl Irvington NY 10533 USA Columbia Univ Dept Biomed Engn New York NY 10027 USA

ISBN: (纸本)9780819471024

The two major volume visualization methods used in biomedical applications are Maximum Intensity Projection (MIP) and Volume Rendering (VR), both of which involve the process of creating sets of 2D projections from 3D images. We have developed a new method for very fast, high-quality volume visualization of 3D biomedical images, based on the fact that the inverse of this process (transforming 2D projections into a 3D image) is essentially equivalent to tomographic image reconstruction. This new method uses the 2D projections acquired by the scanner, thereby obviating the need for the two computationally expensive steps currently required in the complete process of biomedical visualization, that is, (i) reconstructing the 3D image from 2D projection data, and (ii) computing the set of 213 projections from the reconstructed 3D image As well as improvements in computation speed, this method also results in improvements in visualization quality, and in the case of x-ray CT we can exploit this quality improvement to reduce radiation dosage. In this paper, demonstrate the benefits of developing biomedical visualization techniques by directly processing the sensor data acquired by body scanners, rather than by processing the image data reconstructed from the sensor data. We show results of using this approach for volume visualization for tomographic modalities, like x-ray CT, and as well as for MRI.

关键词： volume visualization image reconstruction Radon space k-space computed tomography MRI

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Wavelet de-noising and gradient enhancement in biomedical image processing

Wavelet de-noising and gradient enhancement in biomedical im...

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8th IASTED International conference on visualization, Imaging, and Image Processing, VIIP 2008

作者： Procházka, Aleš Hošťálková, Eva Vyšata, Oldřich Department of Computing and Control Engineering Institute of Chemical Technology in Prague Technická 6 166 28 Prague 6 Czech Republic Neurocenter Caregroup Jiráskova 1389 516 01 Rychnov nad Kněžnou Czech Republic

ISBN: (纸本)9780889867598

Detection of specific image components, their visualization and classification belong to main topics of biomedical image processing. The paper is devoted to problems related to the use of discrete wavelet transform (DWT) and the dual-tree complex wavelet transform (DTCWT) for image denoising and to selected methods of its enhancement. The study presents the analysis of results achieved for different wavelet functions and the following application of gradient methods for specific image components detection. The information content of final images is followed both from the medical point of view using the previous experience and numerically through the analysis of image spectral components. The proposed methods indicate the efficiency of the dual-tree complex wavelet transform use in this area.

关键词： Image denoising

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3D lumbar visualization based on VTK with fusing sagital slices and aixal slices

3D lumbar visualization based on VTK with fusing sagital sli...

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2nd International conference on Bioinformatics and biomedical Engineering, iCBBE 2008

作者： Zhan, Shu Hao, Shijie Jiang, Jian-Guo Li, Hong Hefei University of Technology Hefei Anhui 230009 China Anhui Medical University Hefei Anhui 230022 China

ISBN: (纸本)9781424417483

Based on the anatomical consistency in two series MRI images of a patient in different postures, an algorithm computing a spatially intersectant line of two images from each series is proposed. Furthermore, the anatomical corresponding section of 3D datasets formed by these series can be located. Finally, the datasets are 3D visualized with VTK (visualization ToolKits). This would be of great help to physicians when they give diagnoses. Also, the algorithm has its application in image registration, image segmentation and 3D visualization. © 2008 IEEE.

关键词： Magnetic resonance imaging

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Introduction of the new Decrypthon biomedical data center

Introduction of the new Decrypthon biomedical data center

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5th conference on Information Retrieval and Applications, CORIA 2008

作者： Nguyen, Hoan Friedrich, Anne Berthommier, Guillaume Poidevin, Laetitia Moulinier, Luc Ripp, Raymond Poch, Olivier Laboratoire de BioInformatique et Génomique Intégrative Institut de Génétique et de Biologie Moléculaire et Cellulaire UMR 7104 1 rue Laurent Fries 67404 Illkirch Strasbourg France

This paper presents the design and the implementation of the new high performance biomedical data center of the Décrypthon computing grid which provides a strong potential for calculation and storage to high trhoughput biological applications and *** order to efficiently share the biological data required by the application, the Décrypthon data center is integrated in the computing grid to provide local databases of nucleotide, genomic and proteomic *** addition, the access to methods for heterogeneous and distributeddata, and treatment of joint queries, analysis and visualization are provided.A new system of data integration, called BIRD (for Biological Integration and Retrieval of Data), considered as the core of the Décrypthon data center, was developed to locally integrate very large genomic, proteomic and transcriptomic *** also provides an engine and a high level query language allowing the biologist to extract pertinent information.

关键词： Query languages

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