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Agile parallel bioinformatics workflow management using Pwrake

BMC Research Notes 2011年第1期4卷 1-8页

作者： Mishima, Hiroyuki Sasaki, Kensaku Tanaka, Masahiro Tatebe, Osamu Yoshiura, Koh-Ichiro Department of Human Genetics Nagasaki University Graduate School of Biomedical Sciences Nagasaki Nagasaki 1-12-4 Sakamoto Japan Nagasaki University Global Center of Excellence Program Nagasaki Nagasaki 1-12-4 Sakamoto Japan Center for Computational Sciences University of Tsukuba Tsukuba Ibaraki 1-1-1 Tennodai Japan Core Research for Evolutional Science and Technology Japan Science and Technology Agency Kawaguchi Saitama 4-1-8 Honcho Japan Departmentent of Computer Science Graduate School of Systems and Information Engineering University of Tsukuba Tsukuba Ibaraki 1-1-1 Tennodai Japan

Background: In bioinformatics projects, scientific workflow systems are widely used to manage computational procedures. Full-featured workflow systems have been proposed to fulfil the demand for workflow management. However, such systems tend to be over-weighted for actual bioinformatics practices. We realize that quick deployment of cutting-edge software implementing advanced algorithms and data formats, and continuous adaptation to changes in computational resources and the environment are often prioritized in scientific workflow management. These features have a greater affinity with the agile software development method through iterative development phases after trial and error. Here, we show the application of a scientific workflow system Pwrake to bioinformatics workflows. Pwrake is a parallel workflow extension of Ruby's standard build tool Rake, the flexibility of which has been demonstrated in the astronomy domain. Therefore, we hypothesize that Pwrake also has advantages in actual bioinformatics workflows. Findings. We implemented the Pwrake workflows to process next generation sequencing data using the Genomic Analysis Toolkit (GATK) and Dindel. GATK and Dindel workflows are typical examples of sequential and parallel workflows, respectively. We found that in practice, actual scientific workflow development iterates over two phases, the workflow definition phase and the parameter adjustment phase. We introduced separate workflow definitions to help focus on each of the two developmental phases, as well as helper methods to simplify the descriptions. This approach increased iterative development efficiency. Moreover, we implemented combined workflows to demonstrate modularity of the GATK and Dindel workflows. Conclusions: Pwrake enables agile management of scientific workflows in the bioinformatics domain. The internal domain specific language design built on Ruby gives the flexibility of rakefiles for writing scientific workflows. Furthermore, readability

关键词： Ruby Iterative Development Agile Software Development Host Language Bioinformatics Domain

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Persistent Ocean Monitoring with Underwater Gliders: Towards Accurate Reconstruction of Dynamic Ocean Processes

Persistent Ocean Monitoring with Underwater Gliders: Towards...

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2011 IEEE International Conference on robotics and Automation(2011年IEEE世界机器人与自动化大会 ICRA 2011)

作者： Ryan N. Smith Mac Schwager Daniela Rus Stephen L. Smith Gaurav S. Sukhatme School of Engineering Systems at the Queensland University of Technology BrisbaneQLD4000 Australia GRASP Lab University of PennsylvaniaPhiladelphiaPA 19104USA Distributed Robotics Lab Computer Science and Artificial Intelligence LaboratoryMassachusetts Insti Robotic Embedded Systems Laboratory Department of Computer ScienceUniversity of Southern California

This paper proposes a path planning algorithm and a velocity control algorithm for underwater gliders to persistently monitor a patch of ocean. The algorithms address a pressing need among ocean scientists to collect high-value data for studying ocean events of scientific and environmental interest, such as the occurrence of harmful algal blooms. The path planner optimizes a cost function that blends two competing factors: it maximizes the information value of the path, while minimizing the deviation from the path due to ocean currents. The speed control algorithm then optimizes the speed along the planned path so that higher resolution samples are collected in areas of higher information value. The resulting paths are closed circuits that can be repeatedly traversed to collect long term ocean data in dynamic environments. The algorithms were tested during sea trials on an underwater glider operating off the coast of southern California over the course of several weeks. The results show significant improvements in data resolution and path reliability compared to a sampling path that is typically used in the region.

关键词： Oceans Heuristic algorithms Vehicles Monitoring Sea measurements Vehicle dynamics Read only memory

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Publisher’s Note: “Guided-mode-resonance-coupled plasmonic-active SiO2 nanotubes for surface enhanced Raman spectroscopy” [Appl. Phys. Lett. 100, 191114 (2012)]

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Applied Physics Letters 2012年第5期101卷

作者： Xiaobin Xu Dihan Hasan Lei Wang Swapnajit Chakravarty Ray T. Chen D. L. Fan Alan X. Wang 1Materials Science and Engineering Program Texas Materials Institute University of Texas at Austin Austin Texas 78712 USA 2School of Electrical Engineering and Computer Science Oregon State University Corvallis Oregon 97331 USA 3Wuhan National Laboratory for Optoelectronics Huazhong University of Science and Technology 430074 Wuhan China 4Microelectronic Research Center University of Texas at Austin Austin Texas 78758 USA 5Omega Optics Inc. Austin Texas 78759 USA 6Department of Mechanical Engineering University of Texas at Austin Austin Texas 78712 USA

This article was originally published online on 10 May 2012 with an incorrect affiliation for co-author D. L. Fan and an incorrect footnote designation for co-a

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Study of classification of failure states for Small Unmanned Ground Vehicle by response surface methodology

Study of classification of failure states for Small Unmanned...

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International Conference on Ubiquitous Robots and Ambient Intelligence (URAI)

作者： Young Kook Kim Dooyeol Koh Sang Hoon Lee Soohyun Kim Robotics Program Korea Advanced Institute of Science and Technology Daejeon South Korea Division of Mechanical Engineering School of Mechanical AeroSpace and Systems Engineering Korea Advanced Institute of Science and Technology Daejeon South Korea 5th Research and Development Institute-2 Agency for Defense Development Daejeon South Korea

ISBN: (纸本)9781457707223

SUGV(Small Unmanned Ground Vehicle) used for human rescue and military operation is need to overcome the environment that tough terrains such as a hole or high obstacles. As far as the survival of the vehicle and the preserving ability of the information in the vehicle are concerned, it is essential to have an approach for recognizing unattainable driving states. However, despite the fact that the study of obstacle avoidance and stabilization of SUGV is focused on, it is hardly found out ways of classifying unattainable driving states with the sensors mounted on the SUGV unit. In order to overcome the problem, this paper proposes a practical way for classifying SUGV Failure State(SFS) with the meaningful parameters by statistical method, response surface methodology(RSM).

关键词： Response surface methodology Equations Vehicles Mathematical model Robot sensing systems

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Sensor suites for assistive arm prosthetics

Sensor suites for assistive arm prosthetics

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Annual IEEE Symposium on computer-Based Medical Systems

作者： Martin Buckley Ravi Vaidyanathan Walterio Mayol-Cuevas Bristol Robotics Laboratory University of Bristol UK University of West of England UK Department of Systems Engineering US Naval Postgraduate School Monterrey CA USA Department of Mechanical Engineering Imperial College London London UK Department of Computer Science University of Bristol UK

This paper introduces a sensor suite framework for the partial automation of prosthetic arm control allowing high level control with a reduction of cognitive burden placed upon the user. Automation aims to replicate the hand eye co-ordination through the synergy of a virtual 7DOF arm prosthesis together with the development of a gaze tracking system. The interactions between elements of the suite are detailed and a selection of sensors implemented to control a simple simulation. Use of the novel tongue control system is used to provide discrete input to the system. Initial tests are made of of the system together with a users ability to learn to use the system with promising user feedback on ease of interaction and potential for reduced cognitive burden.

关键词： Cameras Prosthetics Tongue Games Joints Elbow Control systems

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Crane control via parallel distributed fuzzy LQR controller using genetic fuzzy rule selection

Crane control via parallel distributed fuzzy LQR controller ...

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International Conference on Control, Instrumentation, and Automation

作者： M. Adeli H. Zarabadipour M. Aliyari Shoorehdeli Department of robotics and mechatronics School of Science and Technology Nazarbayev University Astana Kazakhstan Department of Electrical Engineering Shahid Rajaee University Tehran Iran DORA S.p.A. STMicroelectronics group Aosta — Italy Agrate Brianza MI Italy Department of mechanical engineering School of Engineering Nazarbayev University Astana Kazakhstan Department of Electrical and Computer Engineering University of Stavanger Stavanger Norway

Overhead crane is an industrial structure that is widely used in many harbors and factories. It is usually operated manually or by some conventional control methods. In this paper, we propose a hybrid controller includes both position regulation and anti-swing control. According to Takagi-Sugeno fuzzy model of an overhead crane and genetic algorithm, a fuzzy controller is designed with parallel distributed compensation and Linear Quadratic Regulation. Using genetic algorithm, important fuzzy rules are selected and so the number of rules decreased and design procedure need less computation and its computation needs less time. Further, the stability of the overhead crane with the parallel distributed fuzzy LQR controller is discussed. The stability analysis and control design problems is reduced to linear matrix inequality (LMI) problems. Simulation results illustrated the validity of the proposed parallel distributed fuzzy LQR control method and it was compared with a similar method parallel distributed fuzzy controller with same fuzzy rule set.

关键词： Cranes Mathematical model Genetic algorithms Nonlinear systems Stability analysis Control design Linear matrix inequalities

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Reports of the AAAI 2010 spring symposia

Reports of the AAAI 2010 spring symposia

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作者： Barkowsky, Thomas Bertel, Sven Broz, Frank Chaudhri, Vinay K. Eagle, Nathan Genesereth, Michael Halpin, Harry Hamner, Emily Hoffmann, Gabe Hölscher, Christoph Horvitz, Eric Lauwers, Tom McGuinness, Deborah L. Michalowski, Marek Mower, Emily Shipley, Thomas F. Stubbs, Kristen Vogl, Roland Williams, Mary-Anne Cognitive Systems Group University of Bremen Research Center SFB/TR 8 Spatial Cognition Germany Human Factors Division Beckman Institute for Advanced Science and Technology University of Illinois Urbana-Champaign IL United States Adaptive Systems Research Group Computer Science Department University of Hertfordshire United Kingdom Artificial Intelligence Center at SRI International United States Txteagle Inc. MIT Media Laboratory United States Computer Science Department Stanford University United States University of Edinburgh United Kingdom Robotics Institute Carnegie Mellon University United States Palo Alto Research Center United States Center for Cognitive Science University of Freiburg Germany CREATE lab Carnegie Mellon Robotics Institute United States Rensselaer Polytechnic Institute United States University of Southern California United States Department of Psychology Temple University Spatial Intelligence and Learning Center United States IRobot Corporation United States Stanford Program in Law Science and Technology Stanford University Law School United States Innovation and Enterprise Research Laboratory University of Technology Sydney Australia

The Association for the Advancement of Artificial Intelligence, in cooperation with Stanford University's Department of computer science, presented the 2010 Spring Symposium Series Monday through Wednesday, March 22-24, 2010, at Stanford University. The titles of the seven symposia were Artificial Intelligence for Development;Cognitive Shape Processing;Educational robotics and Beyond: Design and Evaluation;Embedded Reasoning: Intelligence in Embedded Systems;Intelligent Information Privacy Management;It's All in the Timing: Representing and Reasoning about Time in Interactive Behavior;and Linked Data Meets Artificial Intelligence. Copyright © 2010.

关键词： Embedded systems

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Comparison of disturbance rejection performance between sliding-mode control and equivalent-input-disturbance approach

Comparison of disturbance rejection performance between slid...

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International Conference on Mechatronics (ICM)

作者： Jinhua She Yaodong Pan Hiroshi Hashimoto Min Wu School of Computer Science Tokyo University of Technology Hachioji Tokyo Japan Control Systems Eng Honeywell Canada Mississauga ONT Canada Master Program of Innovation for Design and Eng Advanced Institute of Industrial Technology Tokyo Japan School of Information Science and Engineering Central South University Changsha China

Sliding mode control (SMC) has been considered as a powerful method for disturbances rejection. On the other hand, we have presented an equivalent-input disturbance (EID) approach to reject disturbances. This paper takes a dual-stage feed drive as an example to compare these two methods. The example shows that, while the EID approach obtains almost the same disturbance rejection performance for matched disturbances as that of the SMC does, it can reject unmatched disturbances. This shows the superiority of the EID approach over SMC method.

关键词： Equations Observers Manganese Frequency control

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Microfluidic flow cytometer utilizing optical space-time coding technique

Microfluidic flow cytometer utilizing optical space-time cod...

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IEEE Photonics Conference (IPC)

作者： Tsung-Feng Wu Zhe Mei Luca Pion-Tonachini Yu-Hwa Lo Materials Science and Engineering Program University of California at San Diego La Jolla CA USA School of Information and Electronics Beijing Institute of Technology Beijing China Department of Electrical and Computer Engineering University of California at San Diego La Jolla CA USA

An optical-coding technique for microfluidic flow cytometers to detect forward scattering and large angle scattering signals that can be used to differentiate beads and cells.

关键词： Optical scattering Microfluidics Optical sensors Optical signal processing Optical device fabrication Biomedical optical imaging

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WORKSHOP: The role of expectations in intuitive human-robot interaction

WORKSHOP: The role of expectations in intuitive human-robot ...

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ACM/IEEE International Conference on Human-Robot Interaction (HRI)

作者： Verena Hafner Manja Lohse Joachim Meyer Yukie Nagai Britta Wrede Department of Computer Science Cognitive Robotics Berlin Germany CoR-Laboratory and Applied Informatics Technical Faculty Bielefeld University Germany Department of Industrial Engineering and Management University of Negev Israel Department of Adaptive Machine Systems Graduate School of Engineering Osaka University Japan Head of CoR-Laboratory research group Hybrid Society Technical Faculty Bielefeld University Germany

Human interaction is highly intuitive: we infer reactions of our opponents mainly from what we have learned in years of experience and often assume that other people have the same knowledge about certain situations, abilities, and expectations as we do. In human-robot interaction (HRI) we cannot take for granted that this is equally true since HRI is asymmetrical. In other words, robots have different abilities, knowledge, and expectations than humans. They need to react appropriately to human expectations and behaviour. With this respect, scientific advances have been made to date for applications in entertainment and service robotics that largely depend on intuitive interaction. However, HRI today is often still unnatural, slow, and unsatisfactory for the human interlocutor. Both the sensorimotor interaction with environment and interlocutor, and the social aspects of the interaction still need to be researched and improved. Therefore, this full-day workshop aims to bring together researchers from different scientific fields to discuss these crosscutting issues and to exchange views on what are the preconditions and principles of intuitive interaction.

关键词： Educational institutions computer science Robot sensing systems Electronic mail Humans Industrial engineering

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