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Highlights from the 11th ISCB Student Council Symposium 2015. Dublin, Ireland. 10 July 2015

BMC bioinformatics 2016年第3期17 Suppl 3卷 95页

作者： Katie Wilkins Mehedi Hassan Margherita Francescatto Jakob Jespersen R. Gonzalo Parra Bart Cuypers Dan DeBlasio Alexander Junge Anupama Jigisha Farzana Rahman Griet Laenen Sander Willems Lieven Thorrez Yves Moreau Nagarajan Raju Sonia Pankaj Chothani C. Ramakrishnan Masakazu Sekijima M. Michael Gromiha Paddy J Slator Nigel J Burroughs Przemysław Szałaj Zhonghui Tang Paul Michalski Oskar Luo Xingwang Li Yijun Ruan Dariusz Plewczynski Giulia Fiscon Emanuel Weitschek Massimo Ciccozzi Paola Bertolazzi Giovanni Felici Pieter Meysman Manu Vanaerschot Maya Berg Hideo Imamura Jean-Claude Dujardin Kris Laukens Westa Domanova James R. Krycer Rima Chaudhuri Pengyi Yang Fatemeh Vafaee Daniel J. Fazakerley Sean J. Humphrey David E. James Zdenka Kuncic Plant Pathology and Plant-Microbe Biology Section School of Integrative Plant Science Cornell University Ithaca USA Graduate Field of Computational Biology Cornell University Ithaca USA School of Computing & Mathematics University of South Wales Cardiff UK Department of Genome Biology for Neurodegenerative Diseases German Center for Neurodegenerative Diseases (DZNE) within the Helmholtz Association ᅟ Germany Department of Surgery Massachusetts General Hospital The Broad Institute of MIT and Harvard Boston USA Department of Systems Biology Technical University of Denmark Kemitorvet Denmark Protein Physiology Lab Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires Buenos Aires Argentina Molecular Parasitology Unit (MPU) Institute of Tropical Medicine Antwerp Belgium Advanced Database Research and Modeling (ADReM) research group University of Antwerp Antwerpen Belgium Department of Computer Science University of Arizona Tucson USA Department of Veterinary Clinical and Animal Sciences Center for non-coding RNA in Technology and Health University of Copenhagen Copenhagen Denmark University College Dublin Dublin Ireland Department of Electrical Engineering (ESAT) STADIUS Center for Dynamical Systems Signal Processing and Data Analytics KU Leuven Leuven Belgium Minds Medical IT Department Leuven Belgium Scientific Institute of Public Health (WIV-ISP) Platform of Biotechnology and Molecular Biology (PBB) Brussels Belgium Department of Development and Regeneration @ Kulak KU Leuven Kortrijk Belgium Department of Biotechnology Bhupat and Jyoti Metha School of Biosciences Indian Institute of Technology Madras Chennai India Philips Research North America Briarcliff Manor USA Global Scientific Information and Computing Center (GSIC) Tokyo Institute of Technology Tokyo Japan Systems Biology Centre University of Warwick Senate House Coventry UK Systems Biology Doctoral Training Centre University of Warwick Senate House Coventry UK Center for B

A1 Highlights from the eleventh ISCB Student Council Symposium 2015 Katie Wilkins, Mehedi Hassan, Margherita Francescatto, Jakob Jespersen, R. Gonzalo Parra, Bart Cuypers, Dan DeBlasio, Alexander Junge, Anupama Jigisha, Farzana Rahman O1 Prioritizing a drug’s targets using both gene expression and structural similarity Griet Laenen, Sander Willems, Lieven Thorrez, Yves Moreau O2 Organism specific protein-RNA recognition: A computational analysis of protein-RNA complex structures from different organisms Nagarajan Raju, Sonia Pankaj Chothani, C. Ramakrishnan, Masakazu Sekijima; M. Michael Gromiha O3 Detection of Heterogeneity in Single Particle Tracking Trajectories Paddy J Slator, Nigel J Burroughs O4 3D-NOME: 3D NucleOme Multiscale Engine for data-driven modeling of three-dimensional genome architecture Przemysław Szałaj, Zhonghui Tang, Paul Michalski, Oskar Luo, Xingwang Li, Yijun Ruan, Dariusz Plewczynski O5 A novel feature selection method to extract multiple adjacent solutions for viral genomic sequences classification Giulia Fiscon, Emanuel Weitschek, Massimo Ciccozzi, Paola Bertolazzi, Giovanni Felici O6 A Systems Biology Compendium for Leishmania donovani Bart Cuypers, Pieter Meysman, Manu Vanaerschot, Maya Berg, Hideo Imamura, Jean-Claude Dujardin, Kris Laukens O7 Unravelling signal coordination from large scale phosphorylation kinetic data Westa Domanova, James R. Krycer, Rima Chaudhuri, Pengyi Yang, Fatemeh Vafaee, Daniel J. Fazakerley, Sean J. Humphrey, David E. James, Zdenka Kuncic

关键词： Visceral Leishmaniasis Feature Selection Method Frequent Itemset Mining Leishmania Donovani Student Council

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A science cloud for data intensive sciences

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data Science Journal 2013年 12卷 WDS139-WDS146页

作者： Murata, Ken T. Watari, Shinichi Nagatsuma, Tsutomu Kunitake, Manabu Watanabe, Hidenobu Yamamoto, Kazunori Kubota, Yasufumi Kato, Hisao Tsugawa, Takuya Ukawa, Kentaro Muranaga, Kazuya Kimura, Eizen Tatebe, Osamu Fukazawa, Keiichiro Murayama, Yasuhiro 4-2-1 Nukui-kita Koganei Tokyo 184-8795 Japan Systems Engineering Consultants Co. Ltd. 4-10-1 Yoga Setagaya Tokyo 158-0097 Japan Dept. Medical Informatics of Medical School of Ehime Univ. Situkawa Toon City Ehime 791-0295 Japan Dept. Computer Science Univ. of Tsukuba Tenoudai 1-1-1 Tsukuba Science City Ibaraki 305-8573 Japan Research Institute for Information Technology Kyushu University 6-10-1 Hakozaki Higashi-Ku Fukuoka 812-8581 Japan Integrated Science Data System Research Lab NICT 4-2-1 Nukui-kita Koganei Tokyo 184-8795 Japan

It is often discussed that the fourth methodology for science research is "informatics". The first methodology is a theoretic approach, the second one is observation and/or experiment, and the third one is computer simulation. Informatics is a new methodology for data intensive science, which is a new concept based on the fact that most scientific data are digitalized and the amount of data is huge. The facilities to support informatics are cloud systems. Herein we propose a cloud system especially designed for science. The basic concepts, design, resources, implementation, and applications of the NICT science cloud are discussed.

关键词： Digital storage

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Practical privacy for value-added applications in vehicular ad hoc networks 5th

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5th International Conference on Internet and Distributed Computing Systems, IDCS 2012

作者： Zhang, Lei Wu, Qianhong Qin, Bo Domingo-Ferrer, Josep Shanghai Key Laboratory of Trustworthy Computing Software Engineering Institute East China Normal University Shanghai China UNESCO Chair in Data Privacy Dept. of Comp. Eng. and Maths Universitat Rovira i Virgili TarragonaCatalonia Spain Key Lab. of Aerospace Information Security and Trusted Computing Ministry of Education Wuhan University School of Computer China Department of Maths School of Science Xi’an University of Technology China

ISBN: (纸本)9783642348822

Advances in mobile networking and information processing technologies have triggered vehicular ad hoc networks (VANETs) for traffic safety and value-added applications. Most efforts have been made to address the security concerns while little work has been done to investigate security and privacy for value-added applications in VANETs. To fill this gap, we propose a value-added application, specifically, a security and privacy preserving location-based service (LBS) scheme for VANETs. For each LBS transaction, the scheme provides authentication, integrity and non-repudiation for both the service provider and the user. A user can obtain the service in an anonymous way and hence user privacy is well protected. However, a tracing procedure can be invoked to find malicious users, thereby efficiently preventing users from abusing the anonymity provided by the system. © Springer-Verlag Berlin Heidelberg 2012.

关键词： Location based services

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Large scale report generation in data consolidation environments of banks

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Huazhong Keji Daxue Xuebao (Ziran Kexue Ban)/Journal of Huazhong University of Science and Technology (Natural Science Edition) 2012年第SUPPL.1期40卷 5-8页

作者： Qin, Xiongpai Zhou, Xiaoyun Wu, Zhongxin Yang, Hongzhi Wang, Wei Ministry of Education Key Lab of Data Engineering and Knowledge Engineering Renmin University of China Beijing 100872 China Information School Renmin University of China Beijing 100872 China Computer Science Department Jiangsu Normal University Xuzhou 221116 Jiangsu China Beijing Nantian Software Co. Ltd. Beijing 100085 China

To generate large number of reports in a limited time window, four techniques were proposed, including ROLAP&SQL, Shared Scanning, Hadoop based Solution, and MOLAP&Cube Sharding, an algorithm that performs in memory aggregation was designed for the second solution. The experiment results show that all techniques except ROLAP&SQL can meet the time window constraint, the Hadoop based solution is a promising technique owe to its highly scalability. Considering maturity of the techniques and their performance, we put MOLAP&Cube Sharding into practice while keeping an eye on Hadoop for future adoption.

关键词： Custom report data consolidation Hadoop Large bank MOLAP ROLAP

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Q&A

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Design Management Review 2014年第3期25卷

作者： John Maeda Steven Heller Tim Hoover Has been a design partner at Kleiner Perkins Caufield & Byers since January 2014 helping entrepreneurs and portfolio companies to build design into their company cultures. He served as the president of Rhode Island School of Design for six years through 2013 and also served as an associate director of research at the MIT Media Lab. Maeda has been a practicing designer since 1990 and his work is in the permanent collections of the Museum of Modern Art San Francisco Museum of Modern Art and the Cartier Foundation. He serves on the boards of several corporations including Sonos and Wieden + Kennedy and is chair of eBay's Design Advisory Board. His four published books include The Laws of Simplicity and Redesigning Leadership. Maeda is the recipient of a variety of international awards for his creative work including induction into the Art Director's Club Hall of Fame. In 2001 he received the White House National Design Award in 2002 he received the Mainichi Design Prize in Japan and in 2005 he was awarded the Raymond Loewy Foundation Prize in Germany. Maeda earned a BS and an MS from MIT in computer science and electrical engineering. He received a PhD in design science from the University of Tsukuba Institute of Art and Design in Japan as well as an MBA from Arizona State University. Co‐chair and co‐founder of the MFA Designer as Author and Entrepreneur program at the School of Visual Arts in New York. He was the art director of The New York Times Book Review and now writes the VISUALS column for the NYTBR. He also writes “The Daily Heller” at *** a weekly online design column for Atlantic magazine. He is author co‐author and editor of more than 165 books on the history and practice of graphic design illustration and satiric art. His forthcoming books include 100 Classic Graphic Design Magazines (Laurence King Publishers) and Raw Data: The Process Behind Information Graphics (Thames + Hudson). Heller was the 2011 recipient of the Smithsonian National Design Award for Design Mind. He has also writ

John Maeda is a past president of Rhode Island school of Design and an internationally known designer. He's now involved in helping entrepreneurs build design into their company cultures. Writer and educator Steven Heller pairs up with Tim Hoover, head of product and design at Canary, to talk about designer CEOs, start‐ups, and cutting out the middleman.

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Updating in XML Using Semantic Constraints

International Journal of Database Theory and Application

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International Journal of database Theory and Application 2011年第2期4卷 1-12页

作者： Shahriar, Md. Sumon Liu, Jixue Tasmanian ICT Centre CSIRO Hobart 7001 Tasmania Australia Data and Web Engineering Lab School of Computer and Information Science University of South Australia Adelaide SA-5095 Australia

A novel technique for updating in XML using semantic constraints is proposed. In the proposed technique for XML updating, we consider close value pair semantics in ordered XML documents. Further, how semantic constraints can be incorporated with integrity constraints for XML updat-ing and how to update XML views using semantic constraints are discussed.

关键词： XML

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Towards the preservation of functional dependency in XML data transformation

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International Journal of Intelligent information and database Systems 2010年第5期4卷 431-461页

作者： Shahriar, Md. Sumon Liu, Jixue Data and Web Engineering Lab. School of Computer and Information Science University of South Australia Mawson Lakes SA-5095 Australia

With the advent of XML as a data representation and exchange format over the web, a massive amount of data is being stored in XML. As the use of XML grows rapidly, the task of data transformation for integration purposes in XML is getting much importance to the research community. In XML data transformation, a source schema and its conforming data are transformed to a target schema and its conforming data respectively. The source schema often has integrity constraints to enforce semantics. One type of constraints is XML functional dependency (XFD). When a source schema is transformed to a target schema, XFDs can also be transformed. Thus, the problem how schema and data transformation should cause XFD transformation becomes important. In this paper, we study the transformation of XFDs. Towards this problem, we first define the XFDs over the XML document type definition (DTD) and the satisfactions of XFDs. We then show how XFDs are transformed and whether XFDs are valid when the DTDs are transformed. We further investigate whether the transformed XFDs are preserved by the transformed data. © 2010 Inderscience Enterprises Ltd.

关键词： XML

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Towards the Preservation of Referential Constraints in XML data Transformation for Integration*

International Journal of Database Theory and Application

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International Journal of database Theory and Application 2010年第2期3卷 1-10页

作者： Shahriar, Sumon Liu, Jixue Data and Web Engineering Lab School of Computer and Information Science University of South Australia Adelaide SA-5095 Australia

We investigate the transformation and the preservation of XML referential constraints in XML data transformation for integration purposes in this paper. In the transformation and the preservation, we consider XML inclusion dependencies and XML foreign keys. We show how XML referential constraints should be transformed and preserved using important transformation operators with sufficient conditions.

关键词： XML

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Constraint-Based data Transformation for Integration: An information System Approach*

International Journal of Database Theory and Application

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International Journal of database Theory and Application 2010年第1期3卷 53-61页

作者： Shahriar, Sumon Liu, Jixue Data and Web Engineering Lab School of Computer and Information Science University of South Australia Adelaide SA-5095 Australia

Transforming data from different information systems is important and challenging for integration purposes as data can be stored and represented in different data models in different information systems. In addition, when modeling data in the information systems, integrity constraints on the schemas are necessary for semantics and to maintain consistency purposes. Thus when schemas with conforming data are transformed from heterogeneous information systems, there is a need to transform and preserve semantics of data using constraints. Addressing this problem, we propose how data from different source information systems can be transformed to a global information system. We also review how constraints in data transformation are used in data integration for the purpose of integrating information systems. Our research is towards the handling of semantics using integrity constraints in data integration from heterogeneous information systems.

关键词： information systems

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Hierarchical certificateless signatures

Hierarchical certificateless signatures

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International Workshop on Wireless Network Algorithm and Theory

作者： Zhang, Lei Wu, Qianhong Domingo-Ferrer, Josep Qin, Bo UNESCO in Data Privacy Department of Computer Engineering and Mathematics Universitat Rovira i Virgili Catalonia Spain Wuhan University School of Computer Key Lab. of Aerospace Information Security and Trusted Computing China Xi'an University of Technology School of Science Department of Maths China

ISBN: (纸本)9780769543222

Certificateless cryptography eliminates the key escrow problem in identity-based cryptography. Hierarchical cryptography exploits a practical security model to mirror the organizational hierarchy in the real world. In this paper, to incorporate the advantages of both types of cryptosystems, we instantiate hierarchical certificateless cryptography by formalizing the notion of hierarchical certificateless signatures. Furthermore, we propose an HCLS scheme which, under the hardness of the computational Diffie-Hellman (CDH) problem, is proven to be existentially unforgeable against adaptive chosen-message attacks in the random oracle model. As to efficiency, our scheme has constant complexity, regardless of the depth of the hierarchy. Hence, the proposal is secure and scalable for practical applications. © 2010 IEEE.

关键词： Network security

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