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Meeting Report: BioSharing at ISMB 2010

Standards in genomic sciences 2010年第3期3卷 254-8页

作者： Dawn Field Susanna Sansone Edward F Delong Peter Sterk Iddo Friedberg Pascale Gaudet Susanna Lewis Renzo Kottmann Lynette Hirschman George Garrity Guy Cochrane John Wooley Folker Meyer Sarah Hunter Owen White Brian Bramlett Susan Gregurick Hilmar Lapp Sandra Orchard Philippe Rocca-Serra Alan Ruttenberg Nigam Shah Chris Taylor Anne Thessen Centre for Ecology & Hydrology Wallingford UK Oxford e-Research Centre University of Oxford Oxford UK Department of Biological Engineering Massachusetts Institue of Technology Cambridge USA Department of Microbiology Miami University Oxford USA Department of Computer Science and Software Engineering Miami University Oxford USA Swiss Institute of Bioinformatics Geneva 4 Switzerland Lawrence Berkeley National Laboratory Berkeley USA Microbial Genomics Group Max Planck Institute for Marine Microbiology & Jacobs University Bremen Bremen Germany Information Technology Center The MITRE Corporation Bedford USA Department of Microbiology and Molecular Genetics Michigan State University East Lansing USA European Molecular Biology Laboratory (EMBL) Outstation European Bioinformatics Institute (EBI) Cambridge UK University of California San Diego La Jolla USA Argonne National Laboratory Argonne USA Institute for Genome Sciences University of Maryland School of Medicine Baltimore USA Lux Bio Group Portland USA Biological Systems Science Division Department of Energy Washington DC USA National Evolutionary Synthesis Center (NESCent) Durham USA Science Commons c/o Massachusetts Institute of Technology Computer Science and Artificial Intelligence Laboratory Cambridge USA Stanford Center for Biomedical Informatics Research Stanford USA Marine Biological Laboratory USA

This report summarizes the proceedings of the one day BioSharing meeting held at the Intelligent systems for Molecular Biology (ISMB) 2010 conference in Boston, MA, USA This inaugural BioSharing event was hosted by the Genomic Standards Consortium as part of its M3 & BioSharing special interest group (SIG) workshop. The BioSharing event included invited talks from a range of community leaders and a panel discussion at the end of the day. The panel session led to the formal agreement among community leaders to join together to promote cross-community knowledge exchange and collaborations. A key focus of the newly formed Biosharing community will be linking up resources to promote real-world data sharing (virtuous cycle of data) and supporting compliance with data policies through the creation of a one-stop-portal of information. Further information about the newly established BioSharing effort can be found at http://***.

关键词： Community Leader Funding Agency Special Interest Group Panel Discussion Standardization Effort

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Important scene analysis model using result importance and situation importance

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International Journal of Wireless and Mobile Computing 2009年第4期3卷 225-235页

作者： Hashimoto, Takako Katooka, Takashi Iizawa, Atsushi Kitagawa, Hiroyuki Software RandD Group RICOH Company Ltd. Bukyo-ku Tokyo 112-0002 Japan Department of Computer Science Graduate School of Systems and Information Engineering University of Tsukuba Tsukuba Ibaraki 305-8573 Japan Chiba University of Commerce Japan Network Solution and Services Center Global Marketing Group RICOH Company Ltd. Japan Ricoh IT Solutions Co. Ltd. Japan

Functional improvements to mobile terminals have made possible the spread of multimedia information delivery services. Especially for sports, a service that extracts important scenes and reports them to users has become popular. We take the approach that situational changes in a game's progress can be presented as state transitions, and devise an important scene analysis model based on Result Importance (RI), which represents each situation's actual importance, and Situation Importance (SI), which shows the degree of a chance at the situation. With our model, significant scenes are extracted dynamically. Experimental results indicate that the proposed method is very promising. Copyright © 2009 Inderscience Enterprises Ltd.

关键词： Multimedia systems

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Outsourcing to an unknown workforce: Exploring opensourcing as a global sourcing strategy

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MIS Quarterly: Management Information systems 2008年第2期32卷 385-409页

作者： Ågerfalk, Pär J. Fitzgerald, Brian Department of Information Science Computer and Systems Science Uppsala University Uppsala Sweden Lero - The Irish Software Engineering Research Centre University of Limerick Limerick Ireland Lero - The Irish Software Engineering Research Centre

This paper presents a psychological contract perspective on the use of the open source development model as a global sourcing strategy - opensourcing, as we term it here-where-by commercial companies and open source communities collaborate on development of software of commercial interest to the company. Building on previous research on information systems outsourcing, a theoretical framework for exploring the opensourcing phenomenon is derived. The first phase of the research concerned qualitative case studies involving three commercial organizations (IONA Technologies, Philips Medical systems, and Telefonica) that had "liberated" what had hitherto been proprietary software and sought to grow a global open source community around their product. We followed this with a large-scale survey involving additional exemplars of the phenomenon. The study identifies a number of symmetrical and complementary customer and community obligations that are associated with opensourcing success. We also identify a number of tension points on which customer and community perceptions tend to vary. Overall the key watchwords for opensourcing are openness, trust, tact, professionalism, transparency, and complementariness: The customer and community need to establish a trusted partnership of shared responsibility in building an overall opensourcing ecosystem. The study reveals an ongoing shift from OSS as a community of individual developers to OSS as a community of commercial organizations, primarily small to medium-sized enterprises. It also reveals that opensourcing provides ample opportunity for companies to headhunt top developers, hence moving from outsourcing to a largely unknown OSS workforce toward recruitment of developers from a global open source community whose talents have become known as a result of the opensourcing experience.

关键词： Outsourcing

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A framework to achieve reverse channel multicast in IEEE 802.16 based wireless broadband networks for interoperability with IP networks

A framework to achieve reverse channel multicast in IEEE 802...

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作者： Ansari, Abdul Qadir Rajput, Abdul Qadeer Khan Hashmani, Manzoor Department of Computer Systems and Software Engineering Mehran University of Engineering and Technology Jamshoro Pakistan

ISBN: (纸本)3540898522

The purpose of this paper is to present a framework design to achieve reverse channel multicast support in IEEE-802.16 networks. The unavailability of reverse channel multicast in IEEE 802.16 networks is one of the issues to be resolved in order to achieve its interoperability with IP networks. The interoperability of IEEE 802.16 networks and IP networks is not yet addressed. Forward channel multicast support is inherent in the IEEE-802.16 standard. Achieving reverse channel multicast support, we can enable IP services requiring native multicast support over IEEE-802.16 networks for seamless interoperation. IP network rudiments are mature enough and not likely to be redefined for any new network design;rather the reverse of this is more likely to be worked on. A framework design to achieve reverse channel multicast support is presented introducing a concentrator layer (Multi Node Access Layer) before Base Station (BS) and MARS (Multicast Address Resolution Server) to handle multicast requests. © 2008 Springer-Verlag.

关键词： Interoperability

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DEPCAS: an RFID middleware generalization. An example with tracking systems

DEPCAS: an RFID middleware generalization. An example with t...

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2008 International Conference on Wireless Networks, ICWN 2008

作者： Abad, I. Cerrada, C. Cerrada, J.A. Heradio, R. Software Engineering and Computer Systems Department UNED: Distance Learning University of Spain Madrid Spain

ISBN: (纸本)1601320914

Introduction of new standards that impose the use of labels and identification by radio frequency in supply management area has promoted a necessity to research alternatives to solve this question. The different solutions proposed from the software point of view to incorporate the RFID ubiquitous information have been characterized by two extreme positions: of a side the solutions ad-hoc for every specific system, and by another one the solutions based on software packages that give generic support to the established standards. In this article we present our development: DEPCAS (Data EPC Acquisition System) based in the architecture for control systems (SCADAs) applied to the collection of RFID information. An application of DEPCAS is the resolution of heterogeneous situations of items tracking like for example, the luggage tracking, the sport events with massive participation management, the track of goods or merchandising, etc.

关键词： Radio frequency identification (RFID)

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Two-stage offshoring: An investigation of the Irish bridge

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MIS Quarterly: Management Information systems 2008年第2期32卷 257-279页

作者： Olsson, Helena Holmström Conchúir, Eoin Ó. Ågerfalk, Par J. Fitzgerald, Brian Department of Applied Information Technology IT University of Gothenburg Gothenburg Sweden Lero - The Irish Software Engineering Research Centre University of Limerick Limerick Ireland Department of Information Science Computer and Systems Science Uppsala University Uppsala Sweden Lero - The Irish Software Engineering Research Centre

This paper investigates two-stage offshoring as experienced by the Irish sites of two large global companies, headquartered in the United States, with significant software development operations. As part of these companies, the Irish sites act as a bridge in their offshoring arrangements: While the U.S. sites offshore work to Ireland, the Irish sites offshore work further to India and, hence, have experience of being both customer and vendor in two-stage offshore sourcing relationships. Using a framework derived from relational exchange theory (RET), we conducted multiple case study research to investigate and develop an initial theoretical model of the implementation of this two-stage offshoring bridge model. Our study shows that while both companies act as bridges in two-stage offshoring arrangements, their approaches differ in relation to (1) team integration, (2) organizational level implementation, and (3) site hierarchy. Although, there are opportunities afforded by the bridge model at present, the extent to which these opportunities will be viable into the future is open to question. As revealed in our study, temporal location seems to favor a bridge location such as Ireland, certainly with United States-Asian partners. However, location alone will not be enough to maintain position in future two-stage offshoring arrangements. Furthermore, our research supports the view that offshoring tends to progress through a staged sequence of progressively lower cost destinations. Such a development suggests that two-stage offshoring, as described in this paper, will eventually become what we would term multistage offshoring.

关键词： software engineering

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A distributed system for continuous integration with JINI 14

A distributed system for continuous integration with JINI

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14th International Conference on Distributed Multimedia systems, DMS 2008

作者： Cheng, Y.C. Ou, P.-H. Chen, C.-T. Hsu, T.-S. Software Systems Lab Department of Computer Science and Information Engineering National Taipei University of Technology Taiwan

ISBN: (纸本)1891706233

The present work extends a previously developed continuous integration system to support platform dependent builds and to reduce turnaround time by incorporating distributed computing capabilities. The two objectives are achieved by adopting the Replicated-Worker Pattern as the distributed architecture and using JINI distributed technology as the means of implementation. Experimental results in support of the claims are presented. © 2008 by Knowledge systems Institute Graduate School. All rights reserved.

关键词： Distributed computer systems

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Comprehension of visualization systems - Towards quantitative assessment

Comprehension of visualization systems - Towards quantitativ...

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1st International Conference on Advances in computer-Human Interaction, ACHI 2008

作者： Padda, Harkirat Mudur, Sudhir Seffah, Ahmed Joshi, Yojana Department of Computer Science and Software Engineering Concordia University Montreal Canada Cimmetry Systems Corporation Montreal Canada

ISBN: (纸本)0769530869

Visual comprehension is the characteristic that deals with how efficiently and effectively users are able to grasp the underlying design intent along with the interactions to explore the visually represented information. To assess comprehension i.e. to measure this seemingly immeasurable factor of visualization systems, we are proposing a set of criteria based on a detailed analysis of information flow from the raw data to the cognition of information in human mind. Our comprehension criteria are adapted from the pioneering work of two eminent researchers - Donald A. Norman and Aaron Marcus, who have investigated the issues of human perception and cognition, and visual effectiveness respectively. These proposed criteria are refined by experts' opinion in order to compose a minimal evaluation set that is then applied to a bioinformatics visualization study tool to show the efficacy of criteria in assessing comprehension in a more quantitative manner. © 2008 IEEE.

关键词： Data visualization

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Verifying and analyzing adaptive logic through UML state models

Verifying and analyzing adaptive logic through UML state mod...

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1st International Conference on software Testing, Verification and Validation, ICST 2008

作者： Ramirez, Andres J. Cheng, Betty H. C. Software Engineering and Network Systems Laboratory Department of Computer Science and Engineering Michigan State University East Lansing MI 48824 United States

ISBN: (纸本)076953127X

It is becoming increasingly important to be able to adapt an application's behavior at run time in response to changing requirements and environmental conditions. Adaptive programs are typically difficult to specify, design, and verify. A variety of conditions may trigger an adaptation, each of which may involve different types of adaptation mechanisms. In many cases, adaptive systems are concurrent, thus further exacerbating the complexity. Furthermore, it is important that adaptations do not put the system into an inconsistent state during or after adaptation. This paper presents an iterative approach to modeling and analyzing UML behavioral design models of adaptive systems, where the UML state diagrams are automatically translated into Promela code for analysis with the Spin model checker. The adaptive models are analyzed for adherence to both system invariants and properties that should hold during adaptation. We demonstrate this approach on applications for the mobile computing domain where we verify the design models against formally-specified properties. © 2008 IEEE.

关键词： Adaptive systems

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Human motion recognition using Gaussian Processes classification

Human motion recognition using Gaussian Processes classifica...

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作者： Zhou, Hang Wang, Liang Suter, David Department of Electrical and Computer Systems Engineering Monash University VIC 3800 Australia Department of Computer Science and Software Engineering University of Melbourne VIC 3010 Australia

ISBN: (纸本)9781424421756

This paper investigates the applicability of Gaussian Processes (GP) classification for recognition of articulated and deformable human motions from image sequences. Using Tensor Subspace Analysis (TSA), space-time human silhouettes (extracted from motion videos) are transformed to low-dimensional multivariate time series, based on which structure-based statistical features are calculated to summarize the motion properties. GP classification is then used to learn and predict motion categories. Experimental results on two real-world state-of-the-art datasets show that the proposed approach is effective, and outperforms Support Vector Machine (SVM). © 2008 IEEE.

关键词： Support vector machines

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