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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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Towards a methodological approach to identify future M&S standard needs

Towards a methodological approach to identify future M&S sta...

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2011 Winter simulation Conference, WSC 2011

作者： Tolk, Andreas Balci, Osman Diallo, Saikou Y. Fishwick, Paul A. Hu, Xiaolin Loper, Margaret Petty, Mikel D. Reynolds Jr., Paul F. Sarjoughian, Hessam Zeigler, Bernard P. Old Dominion University Engineering Management and Systems Engineering 241 Kaufman Hall Norfolk VA 23529 United States Virginia Tech. Department of Computer Science 3160B Torgersen Hall Blacksburg VA 24061 United States Virginia Modeling Analysis and Simulation Center Old Dominion University 1030 University Blvd Suffolk VA 23435 United States University of Florida Digital Arts and Sciences CISE Department Gainesville FL 32611 United States Georgia State University Computer Science Department Atlanta GA 30303 United States Georgia Tech. Research Institute Information and Communications Laboratory Atlanta GA 30318 United States University of Alabama in Huntsville Shelby Center 144 301 Sparkman Drive Huntsville AL 35899 United States University of Virginia 151 Engineer's Way Charlottesville VA 22901 United States Arizona State University Center for Integrative Modeling and Simulation Tempe AZ 85271 United States RTSync Corp. 11900 Parklawn Dr. Rockville MD 20852 United States

ISBN: (纸本)9781457721083

Although modeling and simulation is successfully applied for several decades, the community only established a handful of M&S specific standards. Although the standards were applied enabling worldwide distributed simulation applications, in particular in the training application domain of military simulation systems, the general success of M&S standard efforts and their potential for general applicability has been debated repeatedly during several conferences and workshop. This collection of position statements discusses related questions, such as, "What makes M&S special that we need M&S standards," "Are M&S standards truly different from Software engineering Standards," and "What metrics can be used to measure M&S standard success," and tries to contribute to establishing a methodological approach to identify future M&S standard needs. These position statements have been contributed in preparation of a panel discussion and edited for the supporting proceedings. © 2011 IEEE.

关键词： Military applications

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Comprehensive on-chip traffic generator model for SoC design and synthesis 10

Comprehensive on-chip traffic generator model for SoC design...

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Symposium on Theory of modeling and simulation: DEVS integrative M and S Symposium, DEVS 2010, Part of the 2010 Spring simulation Multiconference, SpringSim 2010

作者： Jarrah, Moath Jarrah, Ameen Zeigler, Bernard Department of Computer Engineering Jordan University of Science and Technology Jordan Arizona Center for Integrative Modeling and Simulation Department of Electrical and Computer Engineering University of Arizona United States

ISBN: (纸本)9781617382048

On-Chip traffic modeling is a new research topic that came along with Network on Chip (NoC) design. On-chip traffic varies in rate and nature depending on the running application and the System on Chip components. Different traffic models have been proposed as an attempt to capture the various transactions that occur inside the NoC, which connects different Intellectual Properties (IPs) on the same chip. In this research paper, recent traffic modeling paradigms will be reviewed and discussed. These models have been developed into traffic generator entities to emulate the traffic patterns on chip. However, none of these models (and hence traffic generators) completely capture the behavior of different applications and the interactions between different IPs components on chip, which can alter the traffic state and rate. In this paper, we will propose a comprehensive and flexible model that is based on Discrete EVent System Specification formalisms (DEVS) for modeling and simulation. Our model could be implemented as a traffic generator that has three internal functions, and input and output ports for the interactions with other IPs components such as caches, DSP units, etc.

关键词： Network-on-chip

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Towards a methodological approach to identify future M&S standard needs 11

Towards a methodological approach to identify future M&S sta...

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simulation Winter Conference

作者： Andreas Tolk Osman Balci Saikou Y. Diallo Paul A. Fishwick Xiaolin Hu Margaret Loper Mikel D. Petty Paul F. Reynolds Hessam Sarjoughian Bernard P. Zeigler Engineering Management & Systems Engineering Old Dominion University Norfolk VA USA Department of Computer Science Virginia Polytechnic Institute and State University Blacksburg VA USA Virginia Modeling Analysis & Simulation Center Old Dominion University Suffolk VA USA Digital Arts and Sciences CISE Department University of Florida Gainesville FL USA Computer Science Department Georgia State University Atlanta GA USA Information & Communications Laboratory Georgia Tech Research Institute Georgia Institute of Technology Atlanta GA USA University of Alabama-Huntsville Huntsville AL USA University of Virginia Charlottesville VA USA Center for Integrative Modeling and Simulation Arizona State University Tempe AZ USA RTSync Corp. Rockville MD USA

Although modeling and simulation is successfully applied for several decades, the community only established a handful of M&S specific standards. Although the standards were applied enabling worldwide distributed simulation applications, in particular in the training application domain of military simulation systems, the general success of M&S standard efforts and their potential for general applicability has been debated repeatedly during several conferences and workshop. This collection of position statements discusses related questions, such as, “What makes M&S special that we need M&S standards,” “Are M&S standards truly different from Software engineering Standards,” and “What metrics can be used to measure M&S standard success,” and tries to contribute to establishing a methodological approach to identify future M&S standard needs. These position statements have been contributed in preparation of a panel discussion and edited for the supporting proceedings.

关键词： Standards USA Councils Biological system modeling Educational institutions Computational modeling

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Implementation of Cloud Computing Environment for discrete event system simulation using service oriented architecture

Implementation of Cloud Computing Environment for discrete e...

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International Workshop on Wireless Network Algorithm and Theory

作者： Seo, Chungman Han, Youngshin Lee, Haeyoung Jung, Jason J. Lee, Chilgee Arizona Center for Integrative Modeling and Simulation Electrical and Computer Engineering Department University of Arizona Tucson AZ. 85721 United States School of Information and Communication Engineering Sungkyunkwan University Suwon 440-740 Korea Republic of CPS Research Team ETRI Daejeon 305-700 Korea Republic of Yeungnam University Gyeungsan Korea Republic of

ISBN: (纸本)9780769543222

This paper presents a cloud computing architecture for discrete event system modeling and simulation. Simulators with models used in the cloud computing are considered as web services which are accessed via web browser. This environment supports the simulation of homogeneous or heterogeneous models without much knowledge of discrete event modeling and simulation. © 2010 IEEE.

关键词： Cloud computing

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Implementation of Cloud Computing Environment for Discrete Event System simulation using Service Oriented Architecture

Implementation of Cloud Computing Environment for Discrete E...

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IEEE/IFIP International Conference on Embedded and Ubiquitous Computing, EUC

作者： Chungman Seo Youngshin Han Haeyoung Lee Jason J. Jung Chilgee Lee Arizona Center for Integrative Modeling and Simulation Electrical and Computer Engineering Department University of Arizona Tucson Tucson AZ USA School of Information and Communication Engineering Sungkyunkwan University Suwon South Korea CPS Research Team Electronics and Telecommunications Research Institute Daejeon South Korea Yeungnam University Gyeongsan South Korea

关键词： Computational modeling XML Cloud computing Service oriented architecture Data models Servers

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DEVS-suite: A simulator supporting visual experimentation design and behavior monitoring

DEVS-suite: A simulator supporting visual experimentation de...

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DEVS integrative M and S Symposium, DEVS 2009, Part of the 2009 Spring simulation Multiconference, SpringSim 2009

作者： Kim, Sungung Sarjoughian, Hessam S. Elamvazhuthi, Vignesh Dept. of Computer Science and Engineering Arizona Center for Integrative Modeling and Simulation Arizona State University Tempe AZ 85281 United States

Complexity associated with the design of experiments for simulation models can be reduced through visualization. DEVS-Suite, a new generation of the DEVS Tracking Envi-ronment which itself was extended from DEVSJAVA, sup-ports visual design of experiments and introduces simula-tion data visualization. Data generated by the selected models can be collected dynamically and displayed as time-based trajectories. These capabilities complement animation of DEVS model components and their interactions. A ser-vice-oriented software system is modeled to illustrate the novel modeling features for DEVS simulations. Another ex-ample is developed in Ptolemy II and SimEvents to show the reduced visual complexity afforded by DEVS-Suite.

关键词： Design of experiments

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CoSMoS: A visual environment for component-based modeling, experimental design, and simulation 2

CoSMoS: A visual environment for component-based modeling, e...

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2nd International ICST Conference on simulation Tools and Techniques, SIMUTools 2009

作者： Sarjoughian, Hessam S. Elamvazhuthi, Vignesh Arizona Center for Integrative Modeling and Simulation Computer Science Engineering Department Arizona State University TempeAZ85281-8809 United States Content Management and Archiving EMC Corporation PleasantonCA94566 United States

ISBN: (纸本)9789639799455

An integrated modeling and simulation tool called Componentbased System Modeler and Simulator (CoSMoS) is developed. It supports visual development of families of models that have well-defined logical specifications. The logical componentbased models persist in relational databases and may be automatically translated into specific target simulation and markup programming languages. The underlying systemtheoretic modeling framework of CoSMoS lends itself for the well-known discrete-time, continuous, and discrete-event modeling approaches. Currently, CoSMoS supports developing parallel DEVS-compliant models which can be executed using the DEVS-Suite simulator. The underlying process lifecycle of the CoSMoS enables systematic transitioning from visual model development and design of experiments to simulation execution and experimentation. simulation data can be used for run-time animation and viewing of time-based trajectories or exported for post processing. This tool helps to simplify simulation-based system design, verification, and validation. The core capabilities of the CoSMoS are exemplified with a conceptual model of an anti-virus network software system.

关键词： Viruses

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Assessing the impact of a modeling tool and its support for verification and validation

Assessing the impact of a modeling tool and its support for ...

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International Symposium on Performance Evaluation of computer & Telecommunication Systems SPECTS

作者： Jonathan D. Gibbs Hessam S. Sarjoughian Arizona Center for Integrative Modeling and Simulation Computer Science and Engineering Department Arizona State University Tempe AZ USA

Domain-specific tools for modeling and simulation (M&S) of computer network systems are aimed at simplifying the tasks of model developers and simulationists. In determining the extent to which a particular domain-specific M&S tool fits their needs, the developers must consider both how the tool can assist in the model development process, and how the tool may prevent or hinder them from achieving their objectives. We have considered two M&S tools in the domain of computer networks, IT Guru and the INET framework, and some of the ways in which they affect various aspects of simulation model development, with emphasis on the verification and validation (V&V) process as applied to net-centric enterprise systems. We have developed a metric for evaluating a domain-specific M&S tool based on certain qualitative characteristics. We will demonstrate how this metric can be applied to evaluate IT Guru and INET, and also offer some observations on how the metric can be applied to other domains besides computer networking.

关键词： computer simulation Computational modeling computer networks Hardware computer science Collaborative software Software testing Knowledge engineering Logic Access protocols

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Teaching and training of network protocols with DEVS-suite

Teaching and training of network protocols with DEVS-suite

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International Symposium on Performance Evaluation of computer & Telecommunication Systems SPECTS

作者： Ahmet Zengin Hessam Sarjoughian Department of Computer Science Education Sakarya University Serdivan Sakarya Turkey Arizona Center for Integrative Modeling and Simulation Department of Computer Science and Engineering Arizona State University Tempe AZ USA

This paper presents a robust simulation environment targeted for teaching and learning the complex dynamics of computer networks. The general-purpose DEVS-suite simulator supports animation with I/O and state trajectories of computer network models developed using parallel DEVS modeling approach. The simulator offers high-level model abstraction as compared with simulators such as NS-2. The combined capabilities afforded by the robust DEVS-suite simulator assists in understanding the fundamentals of computer network topologies and the logics of communication protocols. This newly developed DEVS-Suite offers an expressive, yet relatively simple to use, simulation environment for students and educators to develop and experiment with computer network models.

关键词： Protocols Computational modeling computer simulation computer networks computer science education Robustness Network topology Discrete event simulation Routing Animation

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