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BioVLAB-MMIA: A Reconfigurable Cloud Computing Environment for microRNA and mRNA Integrated Analysis

BioVLAB-MMIA: A Reconfigurable Cloud Computing Environment f...

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IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

作者： Hyungro Lee Youngik Yang Heejoon Chae Seungyoon Nam Donghoon Choi Patanachai Tangchaisin Chathura Herath Suresh Marru Kenneth P. Nephew Sun Kim School of Informatics and Computing Indiana University Bloomington IN USA J Craig Venter Institute San Diego CA USA National Cancer Center Goyang South Korea Supercomputing Center Korea Institute of Science and Technology Information South Korea Medical Sciences Program Indiana University School of Medicine Indiana University Bloomington IN USA School of Computer Science and Engineering Seoul National University Seoul South Korea

MicroRNAs, by regulating the expression of hundreds of target genes, play critical roles in developmental biology and the etiology of numerous diseases, including cancer. As vast amounts of microRNA expression profile data are now publicly available, the integration of those data sets with gene expression profiles represents an extremely active area of life science research. However, the ability to conduct genome wide microRNA-mRNA (gene) integration currently requires sophisticated, high-end informatics tools, significant expertise in bioinformatics and computer science to carry out the complex integration analysis. In addition, increased computing infrastructure capabilities are essential in order to accommodate large data sets. In this study, we have extending BioVLAB cloud workbench to develop an environment for the integrated analysis of microRNA and mRNA expression data, named BioVLAB-MMIA. The workbench facilitates computations on the Amazon EC2 and S3 resources orchestrated by XBaya Workflow Suite. The advantages of BioVLAB-MMIA over the web-based MMIA system include: 1) readily expanded as new computational tools become available; 2) easily modifiable by re-configuring graphic icons in the workflow; 3) on-demand cloud computing resources can be used on an as needed basis; 4) distributed orchestration supports complex and long running workflows asynchronously.

关键词： Bioinformatics Cloud computing Cancer Genomics Educational institutions Diseases computer architecture

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A robotics engineering M.S. degree

A robotics engineering M.S. degree

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2010 ASEE Annual Conference and Exposition

作者： Gennert, Michael Michalson, William Demetriou, Michael Computer Science Department Robotics Engineering Program Worcester Polytechnic Institute United States Worcester Polytechnic Institute United States

There is an increasing demand for creative scientific, engineering, and management talent to meet national needs. We believe that the best way to educate professionals for leadership roles is in a unified multi-disciplinary curriculum. This paper describes one such program, a Master of science degree in robotics engineering at Worcester Polytechnic Institute, whose goal is to prepare men and women for technical leadership in the robotics industry and research in robotics. The program, launched in fall 2009, develops competence in electro-mechanical-computational systems and an awareness of management systems. It constitutes a multi-disciplinary effort by faculty in Arts & sciences (Mathematics and computer science), engineering (Electrical & computer engineering and Mechanical engineering), and Management. The program is organized around a technical coursework core with select science and engineering electives. Technical strength is supplemented by organizational and management principles embodied in context courses in Systems engineering and Management. The program culminates in individual capstone projects that take the form of a thesis, directed research, or practicum with written report. In all cases, a public oral presentation is required. A B.S./M.S. option allows the program to be completed in a single additional year of work past the Bachelor's degree. By using existing courses where appropriate, we were able to start the program by developing only two new courses, Foundations of robotics and Robot Dynamics, supplemented by special topics, independent study, and other project work. We anticipate adding new courses as the program grows, additional faculty join the program, and as we introduce a Ph.D. in robotics engineering. Initial response to the program by students and industry has been very positive, and the program shows great promise to contribute significantly to meeting future engineering workforce needs. © American Society for engineering Education,

关键词： Curricula

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Consensus of multi-agent systems under periodic time-varying network

Consensus of multi-agent systems under periodic time-varying...

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作者： Kim, Hongkeun Shim, Hyungbo Back, Juhoon Seo, Jin Heon ASRI School of Electrical Engineering and Computer Science Seoul National University Seoul Korea Republic of School of Robotics Kwangwoon University Seoul Korea Republic of

ISBN: (纸本)9783902661807

In this paper, we address the consensus problem for a class of feedback linearizable nonlinear multi-agent systems under a dynamically changing and periodic network communication. The information delivered throughout the communication network is the output of each identical MIMO autonomous agent which can be of any order. First of all, with a local-level control strategy, we show that the consensus is reached by only using a linear time-invariant compensator if the network changes sufficiently fast in time and the compensator is designed so that the multi-agent system achieves the consensus for the average of the communication network. In this case, it is also shown that the state trajectories are close to those of average system if one of the agents is. Finally, in the case of integrator chains, we relax the fast switching condition of the network and give an example that verifies the result. © 2010 IFAC.

关键词： Time varying networks

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Reduced-order dynamic observer error linearization

Reduced-order dynamic observer error linearization

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作者： Yang, Jongwook Back, Juhoon Seo, Jin H. Shim, Hyungbo ASRI School of Electrical Engineering and Computer Science Seoul National University Seoul Korea Republic of School of Robotics Kwangwoon University Seoul Korea Republic of

ISBN: (纸本)9783902661807

For an unforced nonlinear single output system, we propose a new approach to observer error linearization called reduced-order dynamic observer error linearization (RDOEL), which is a modified version of dynamic observer error linearization (DOEL). While RDOEL also has an auxiliary dynamics and a generalized output injection like DOEL, it offers a lower dimensional observer than DOEL, and allows a complete constructive algorithm in contrast to DOEL when the auxiliary dynamics is a chain of integrators. For RDOEL whose auxiliary dynamics is a chain of integrators (RDOELI), we provide a complete constructive algorithm which presents not only a coordinate transformation between the original system and a nonlinear observer canonical form, but also the minimum number of integrators needed to perform RDOELI. Moreover, we show that if the original system is of dimension n, then the minimum number of integrators is less than or equal to n - 2. In order to describe our algorithm well, we present an example that the auxiliary dynamics is a chain of two integrators. © 2010 IFAC.

关键词： Linearization

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Fuzzy rule based neuro-dynamic programming for mobile robot skill acquisition on the basis of a nested multi-agent architecture

Fuzzy rule based neuro-dynamic programming for mobile robot ...

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IEEE International Conference on robotics and Biomimetics

作者： Karigiannis, John N. Rekatsinas, Theodoros I. Tzafestas, Costas S. School of Electrical and Computer Engineering Division of Signals Control and Robotics National Technical University of Athens Zographou Athens Greece School of Computer Science University of Maryland College Park MD 20742 United States

ISBN: (纸本)9781424493173

Biologically inspired architectures that mimic the organizational structure of living organisms and in general frameworks that will improve the design of intelligent robots attract significant attention from the research community. Self-organization problems, intrinsic behaviors as well as effective learning and skill transfer processes in the context of robotic systems have been significantly investigated by researchers. Our work presents a new framework of developmental skill learning process by introducing a hierarchical nested multi-agent architecture. A neuro-dynamic learning mechanism employing function approximators in a fuzzified state-space is utilized, leading to a collaborative control scheme among the distributed agents engaged in a continuous space, which enables the multi-agent system to learn, over a period of time, how to perform sequences of continuous actions in a cooperative manner without any prior task model. The agents comprising the system manage to gain experience over the task that they collaboratively perform by continuously exploring and exploiting their state-to-action mapping space. For the specific problem setting, the proposed theoretical framework is employed in the case of two simulated e-Puck robots performing a collaborative box-pushing task. This task involves active cooperation between the robots in order to jointly push an object on a plane to a specified goal location. We should note that 1) there are no contact points specified for the two e-Pucks and 2) the shape of the object is indifferent. The actuated wheels of the mobile robots are considered as the independent agents that have to build up cooperative skills over time, in order for the robot to demonstrate intelligent behavior. Our goal in this experimental study is to evaluate both the proposed hierarchical multi-agent architecture, as well as the methodological control framework. Such a hierarchical multi-agent approach is envisioned to be highly scalable for the contr

关键词： Memory architecture

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Combining wireless neural recording and video capture for the analysis of natural gait

Combining wireless neural recording and video capture for th...

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International IEEE/EMBS Conference on Neural engineering, CNE

作者： Justin D. Foster Oren Freifeld Paul Nuyujukian Stephen I. Ryu Michael J. Black Krishna V. Shenoy Department of Electrical Engineering University of Stanford Stanford CA USA Division of Applied Mathematics Brown University Providence RI USA Bioengineering and Stanford Medical School University of Stanford Stanford CA USA Department of Neurosurgery Palo Alto Medical Foundation Palo Alto CA USA Department of Computer Science Brown University Providence RI USA Max-Planck Institute Tubingen Germany Departments of Electrical Engineering Bioengineering and Neurobiology and the Neurosciences Program University of Stanford Stanford CA USA

Neural control of movement is typically studied in constrained environments where there is a reduced set of possible behaviors. This constraint may unintentionally limit the applicability of findings to the generalized case of unconstrained behavior. We hypothesize that examining the unconstrained state across multiple behavioral contexts will lead to new insights into the neural control of movement and help advance the design of neural prosthetic decode algorithms. However, to pursue electrophysiological studies in such a manner requires a more flexible framework for experimentation. We propose that head-mounted neural recording systems with wireless data transmission, combined with markerless computer-vision based motion tracking, will enable new, less constrained experiments. As a proof-of-concept, we recorded and wirelessly transmitted broadband neural data from 32 electrodes in premotor cortex while acquiring single-camera video of a rhesus macaque walking on a treadmill. We demonstrate the ability to extract behavioral kinematics using an automated computer vision algorithm without use of markers and to predict kinematics from the neural data. Together these advances suggest that a new class of “freely moving monkey” experiments should be possible and should help broaden our understanding of the neural control of movement.

关键词： Animals Kinematics Decoding Neuroscience Synchronization Image segmentation Wireless communication

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SURF and spatial association correspondence applied in extraction and matching of feature points from MR images of deformed tissues

SURF and spatial association correspondence applied in extra...

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2010 IEEE International Conference on robotics and Biomimetics, ROBIO 2010

作者： Zhang, Xubing Hirai, Shinichi Zhang, Penglin Dept. of Robotics Faculty of Science and Engineering Ritsumeikan University Kusatsu Shiga 525-8577 Japan School of Computer Science Wuhan Textile University Wuhan 430073 China School of Remote Sensing and Information Engineering Wuhan University Wuhan 430079 China

ISBN: (纸本)9781424493173

The extraction and matching of feature points is very important for measuring deformation fields of MR images. Current methods cannot extract and match enough feature points correctly when non-rigid soft biological tissues are deformed in MR images. The authors have therefore used SURF to extract feature points from initial MR images, utilizing every point in deformed MR images as feature points. Subsequently, SURF descriptors and Spatial Association Correspondence (SAC) of neighboring pixels are utilized to match the corresponding feature points of the initial and deformed MR images. Finally, by clustering the differences between deformed points matched by SURF-SAC with the corresponding points calculated by affine transformation, most incorrect match points can be eliminated. Our experimental results show that the proposed method can extract and match more correct corresponding feature point pairs than SURF and SIFT methods. © 2010 IEEE.

关键词： Extraction

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Magnetic resonance imaging of irreversible electroporation in tubers

Magnetic resonance imaging of irreversible electroporation i...

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12th Mediterranean Conference on Medical and Biological engineering and Computing, MEDICON 2010

作者： Hjouj, Mohammad Rubinsky, Boris Center for Bioengineering School of Computer Science Engineering Hebrew University of Jerusalem Israel Department of Mechanical Engineering Graduate Program in Biophysics University of California Berkeley United States

ISBN: (纸本)9783642130380

Purpose: A preliminary study on the magnetic resonance (MRI) characteristics of (vegetable) tissue NTIRE is an emerging minimally invasive surgery technique for tissue ablation in which, microsecond, high electrical field pulses form permanent nano-scale defects in the cell membrane. Materials and Methods: The potato is used as the simplest conceivable first order tissue model for studying the MRI characteristics of electroporation, because while made of structured cells it does not have blood flow, it is relatively homogeneous and cell damage is readily visible through a natural oxidation process of the intracellular enzymes.. Clinical NTIRE sequences were applied to potato tubers and MRI sequences of the treated area were compared with colorimetric photographs. Results: A comparison of T1 weighted, T2 weighted, fluid attenuation inversion recovery (FLAIR) and short TI inversion recovery (STIR) of NTIRE shows that T1 weighted signals, such as FLAIR, produce brighter images of the treated areas. In contrast the images of the treated areas are completely lost with liquids enhancing and fat eliminating sequences, such as STIR. Conclusion: MRI can image tissue treated by NTIRE. A possible explanation for the findings is that by producing nanoscale defects in the cell membrane lipid bilayer, NTIRE causes an enhanced signal from the cell membrane lipids that in the treated cells are not bound anymore in a restrictive liquidgel membrane structure and have more degrees of freedom. © 2010 International Federation for Medical and Biological engineering.

关键词： Magnetic resonance imaging

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High embedding reversible data hiding scheme for JPEG

High embedding reversible data hiding scheme for JPEG

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6th International Conference on Intelligent Information Hiding and Multimedia Signal Processing, IIHMSP 2010

作者： Kuo, Wen-Chung Kuo, Shao-Hung Wuu, Lih-Chyau Depart. of Computer Science and Information Engineering National Formusa University Yunlin 632 Taiwan Graduate School of Engineering Science Technology Doctoral Program National YunLin University of Science and Technology Yunlin 640 Taiwan

ISBN: (纸本)9780769542225

Both Data hiding and data compression are very important technologies in the field of image processing. It seems that there is no relationship between data hiding and data compression because most of the data hiding mechanisms focus on information security and the data compression mechanisms emphasize the compression ratio. In fact, they are closely related. Until now, there are many literatures to discuss the secret data how to be embedded into the media image. Unfortunately, the stego-image's size will be increased when the media image is hidden a lot of secret data. In order to overcome this disadvantage, a reversible data hiding scheme based on EMD data hiding and JPEG compression technology will be proposed in this paper. According to the experimental results, we can prove that our proposed scheme still keeps high embedding capacity, security and good compression ratio. © 2010 IEEE.

关键词： Steganography

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On challenges of robot assisted radiotherapy for lung tumors

On challenges of robot assisted radiotherapy for lung tumors

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2010 IEEE International Conference on robotics and Biomimetics, ROBIO 2010

作者： Ma, Lei Herrmann, Christian Schilling, Klaus School of Electrical Engineering Southwest Jiaotong University Chengdu 610031 China University of Würzburg Department of Computer Science VII: Robotics and Telematics D-97074 Würzburg Germany

ISBN: (纸本)9781424493173

This paper is concerned with recent development in robot assisted radiotherapy for lung tumors. The paper first analyzes technical challenges regarding tumor position determination and prediction, by invasive and non-invasive methods, correlation models of the tumor motion and the respiratory signals, as well as modeling and control of the robot manipulator. Several currently available solutions and concepts are then briefly introduced. Emphasis is placed on the ATTS (adaptive tumor tracking system) system developed at the University of Würzburg. Within the ATTS, information of the tumor motion is used to control a robotic treatment couch HexaPOD, which moves in six degrees of freedom and maintains the tumor in a certain fixed spatial position. With this new technology it is possible to avoid gating during the radiotherapy as well as active breathing control, such that duration and cost of the therapy as well as trauma of the patient can be reduced. The tumor position is obtained by data fusion from two sensing system. Correlation methods for data fusion were extensively investigated and a prediction model for tumor motion is found that can forecast the tumor position for up to one respiratory period. Modeling of the HexaPOD treatment couch is addressed. The most suitable model is found to be a low-order linear dynamic equation together with a saturation component. Three different control methods and comparative test results are then presented to show feasibility of the proposed model and control schemes. © 2010 IEEE.

关键词： Radiotherapy

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