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Analysis of DNA sequence transformations on grids

JOURNAL OF PARALLEL AND distributed COMPUTING 2009年第1期69卷 80-90页

作者： Joshi, Yadnyesh Vadhiyar, Sathish Indian Inst Sci Supercomp Educ & Res Ctr Bangalore 560012 Karnataka India

Study of the evolution of species or organisms is essential for various biological applications. Evolution is typically studied at the molecular level by analyzing the mutations of DNA sequences of organisms. Techniques have been developed for building phylogenetic or evolutionary trees for a set of sequences. Though phylogenetic trees capture the overall evolutionary relationships among the sequences, they do not reveal fine-level details of the evolution. In this work, we attempt to resolve various fine-level sequence transformation details associated with a phylogenetic tree using cellular automata. In particular, our work tries to determine the cellular automata rules for neighbor-dependent mutations of segments of DNA sequences. We also determine the number of time steps needed for evolution of a progeny from an ancestor and the unknown segments of the intermediate sequences in the phylogenetic tree. Due to the existence of vast number of cellular automata rules, we have developed a grid system that performs parallel guided explorations of the rules on grid resources. We demonstrate our techniques by conducting experiments on a grid comprising machines in three Countries and obtaining potentially useful statistics regarding evolutions in three HIV sequences. In particular, our work is able to verify the phenomenon of neighbor-dependent mutations and find that certain combinations of neighbor-dependent mutations, defined by a cellular automata rule, occur with greater than 90% probability. We also find the average number of time steps for mutations for some branches of phylogenetic tree over a large number of possible transformations with standard deviations less than 2. (C) 2008 Elsevier Inc. All rights reserved.

关键词： Bioinformatics Biology and genetics Grid computing Grids Grid applications distributed systems Client/Server distributed applications

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First experiences with the Polish Optical Internet

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COMPUTER NETWORKS-THE INTERNATIONAL JOURNAL OF COMPUTER AND TELECOMMUNICATIONS NETWORKING 2001年第6期37卷 747-759页

作者： Binczewski, A Meyer, N Nabrzyski, J Starzak, S Stroinski, M Weglarz, J Poznan Supercomp & Networking Ctr PL-61704 Poznan Poland

The paper describes the new development programme of the Polish information infrastructure. The programme, called in Polish PIONIER: (English-PIONEER) Polish Optical Internet, Advanced applications, Services and Technologies for the Information Society, has been proposed to the Polish State Committee for Scientific Research and has been accepted. The aim of the programme is to create an advanced infrastructure together with tools, services and applications available to the entire scientific community and eventually to government and local administrations as well as society in general. Services and applications are expected to appear as selected pilot realizations in order to verify deployed technologies. Some of the pilot realizations and testbeds are also presented in the paper. (C) 2001 Elsevier Science B.V. All rights reserved.

关键词： optical networks DWDM QoS grids portals testbeds distributed applications

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Dynamic Resource Provisioning in Massively Multiplayer Online Games

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IEEE TRANSACTIONS ON PARALLEL AND distributed SYSTEMS 2011年第3期22卷 380-395页

作者： Nae, Vlad Iosup, Alexandru Prodan, Radu Univ Innsbruck Inst Comp Sci Distributed & Parallel Syst Grp A-6020 Innsbruck Austria Delft Univ Technol Parallel & Distributed Syst Grp NL-2628 CD Delft Netherlands

Today's Massively Multiplayer Online Games (MMOGs) can include millions of concurrent players spread across the world and interacting with each other within a single session. Faced with high resource demand variability and with misfit resource renting policies, the current industry practice is to overprovision for each game tens of self-owned data centers, making the market entry affordable only for big companies. Focusing on the reduction of entry and operational costs, we investigate a new dynamic resource provisioning method for MMOG operation using external data centers as low-cost resource providers. First, we identify in the various types of player interaction a source of short-term load variability, which complements the long-term load variability due to the size of the player population. Then, we introduce a combined MMOG processor, network, and memory load model that takes into account both the player interaction type and the population size. Our model is best used for estimating the MMOG resource demand dynamically, and thus, for dynamic resource provisioning based on the game world entity distribution. We evaluate several classes of online predictors for MMOG entity distribution and propose and tune a neural network-based predictor to deliver good accuracy consistently under real-time performance constraints. We assess using trace-based simulation the impact of the data center policies on the quality of resource provisioning. We find that the dynamic resource provisioning can be much more efficient than its static alternative even when the external data centers are busy, and that data centers with policies unsuitable for MMOGs are penalized by our dynamic resource provisioning method. Finally, we present experimental results showing the real-time parallelization and load balancing of a real game prototype using data center resources provisioned using our method and show its advantage against a rudimentary client threshold approach.

关键词： distributed applications modeling techniques performance attributes real time games

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Reducing User Perceived Latency with a Proactive Prefetching Middleware for Mobile SOA Access

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INTERNATIONAL JOURNAL OF WEB SERVICES RESEARCH 2011年第1期8卷 68-85页

作者： Schreiber, Daniel Goeb, Andreas Aitenbichler, Erwin Muehlhaeuser, Max Tech Univ Darmstadt Darmstadt Germany

Network latency is one of the most critical factors for the usability of mobile SOA applications. This paper introduces prefetching and caching enhancements for an existing SOA framework for mobile applications to reduce the user perceived latency. Latency reduction is achieved by proactively sending data to the mobile device that could most likely be requested at a later time. This additional data is piggybacked onto responses to actual requests and injected into a client side cache, so that it can be used without an additional connection. The prefetching is done automatically using a sequence prediction algorithm. The benefit of prefetching and caching enhancements were evaluated for different network settings and a reduction of user perceived latency of up to 31% was found in a typical scenario. In contrast to other prefetching solutions, our piggybacking approach also allows to significantly increase battery lifetime of the mobile device.

关键词： Buffering distributed applications Human-Centered Computing Low-Bandwidth Operation Mobile Communication Systems Web-Based Services

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Prediction of Optimal Parallelism Level in Wide Area Data Transfers

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IEEE TRANSACTIONS ON PARALLEL AND distributed SYSTEMS 2011年第12期22卷 2033-2045页

作者： Yildirim, Esma Yin, Dengpan Kosar, Tevfik SUNY Buffalo Dept Comp Sci & Engn Buffalo NY 14260 USA Louisiana State Univ Dept Comp Sci Baton Rouge LA 70803 USA Louisiana State Univ Ctr Computat & Technol Baton Rouge LA 70803 USA

Wide area data transfer may be a major bottleneck for the end-to-end performance of distributed applications. A practical way of increasing the wide area throughput at the application layer is using multiple parallel streams. Although increased number of parallel streams may yield much better performance than using a single stream, overwhelming the network by opening too many streams may have an inverse effect. The congestion created by excess number of streams may cause a drop down in the throughput achieved. Hence, it is important to decide on the optimal number of streams without congesting the network. Predicting this "optimum" number is not straightforward, since it depends on many parameters specific to each individual transfer. Generic models that try to predict this number either rely too much on historical information or fail to achieve accurate predictions. In this paper, we present a set of new models which aim to approximate the optimal number with least history information and lowest prediction overhead. An algorithm is introduced to select the best combination of historic information to do the prediction for evaluation purposes as well as optimizing prediction by reducing error rate. We measure the feasibility and accuracy of the proposed prediction models by comparing to actual GridFTP data transfer by using little historical information and have seen that we could predict the throughput of parallel streams accurately and find a very close approximation of the optimal stream number.

关键词： distributed applications modeling and prediction parallelism and concurrency network protocols

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A survey of life sciences applications on the Grid

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NEW GENERATION COMPUTING 2004年第2期22卷 111-125页

作者： Krishnan, A BioInformat Inst Singapore 119613 Singapore

The availability of powerful microprocessors and improvements in the performance of networks has enabled high performance computing on wide-area, distributed systems. Computational grids, by integrating diverse, geographically distributed and essentially heterogeneous resources provide the infrastructure for solving large-scale problems. However, heterogeneity, on the one hand allows for scalability, but on the other hand makes application development and deployment for such an environment extremely difficult. The field of life sciences has seen an explosion in data over the past decade. The data acquired needs to be processed, interpreted and analyzed to be useful. The large resource needs of bioinformatics allied to the large number of data-parallel applications in this field and the availability of a powerful, high performance, computing grid environment lead naturally to opportunities for developing grid-enabled applications. This survey, done as part of the Life Sciences Research Group (a research group belonging to the Global Grid Forum) attempts to collate information regarding grid-enabled applications in this field.

关键词： grid computing distributed applications life sciences

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distributed and collaborative visualization of large data sets using high-speed networks

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FUTURE GENERATION COMPUTER SYSTEMS-THE INTERNATIONAL JOURNAL OF ESCIENCE 2006年第8期22卷 1004-1010页

作者： Hutanu, Andrei Allen, Gabrielle Beck, Stephen D. Holub, Petr Kaiser, Hartmut Kulshrestha, Archit Liska, Milos MacLaren, Jon Matyska, Ludek Paruchuri, Ravi Pkohaska, Steffen Seidel, Ed Ullmer, Brygg Venkataraman, Shalini Louisiana State Univ Ctr Computat & Technol Baton Rouge LA 70803 USA CESNET Prague 16200 Czech Republic Masaryk Univ Brno 62100 Czech Republic Zuse Inst Berlin D-14195 Berlin Germany

We describe an architecture for distributed collaborative visualization that integrates video conferencing, distributed data management and grid technologies as well as tangible interaction devices for visualization. High-speed, low-latency optical networks support high-quality collaborative interaction and remote visualization of large data. (c) 2006 Elsevier B.V. All rights reserved.

关键词： collaborative visualization distributed applications co-scheduling interaction devices video conferencing

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WhiteWater: distributed processing of fast streams

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IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING 2007年第9期19卷 1214-1226页

作者： Stanoi, Ioana Mihaila, George A. Palpanas, Themis Lang, Christian A. IBM Corp Almaden Res Ctr San Jose CA 95120 USA IBM TJ Watson Res Ctr Hawthorne NY 10532 USA Univ Trent Dept Informat & Telecommun I-38050 Povo TN Italy

Monitoring systems today often involve continuous queries over streaming data in a distributed collaborative fashion. The distribution of query operators over a network of processors, as well as their processing sequence, form a query configuration with inherent constraints on the throughput that it can support. In this paper, we discuss the implications of measuring and optimizing for output throughput, as well as its limitations. We propose to use instead the more granular input throughput and a version of throughput measure, the profiled input throughput, that is focused on matching the expected behavior of the input streams. We show how we can evaluate a query configuration based on profiled input throughput and that the problem of finding the optimal configuration is NP-hard. Furthermore, we describe how we can overcome the complexity limitation by adapting hill-climbing heuristics to reduce the search space of configurations. We show experimentally that the approach used is not only efficient but also effective.

关键词： query processing optimization database architectures distributed applications

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A Survey of State Persistency in Peer-to-Peer Massively Multiplayer Online Games

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IEEE TRANSACTIONS ON PARALLEL AND distributed SYSTEMS 2012年第5期23卷 818-834页

作者： Gilmore, John S. Engelbrecht, Herman A. Univ Stellenbosch Dept Elect & Elect Engn MIH Media Lab ZA-7600 Stellenbosch South Africa

Recently, there has been significant research focus on Peer-to-Peer (P2P) Massively Multiplayer Online Games (MMOGs). A number of architectures have been presented in the literature to implement the P2P approach. One aspect that has not received sufficient attention in these architectures is state persistency in P2P MMOGs. This survey presents an overview of the current challenges present in P2P MMOGs, followed by an overview of classic state consistency models used in C/S MMOGs. The survey then classifies the state persistency techniques currently used in P2P MMOGs into super peer storage, overlay storage, hybrid storage, and distance-based storage. Key characteristics, namely scalability, fairness, reliability, responsiveness, and security are then defined. Each state persistency technique is evaluated according to these characteristics and recommendations are then made of possible future areas of research into the different storage types.

关键词： distributed systems distributed applications internet applications games

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Exposing and eliminating vulnerabilities to denial of service attacks in secure gossip-based multicast

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IEEE TRANSACTIONS ON DEPENDABLE AND SECURE COMPUTING 2006年第1期3卷 45-61页

作者： Badishi, G Keidar, I Sasson, A Technion Israel Inst Technol Dept Elect Engn IL-32000 Haifa Israel IBM Labs Haifa Israel

We propose a framework and methodology for quantifying the effect of denial of service (DoS) attacks on a distributed system. We present a systematic study of the resistance of gossip-based multicast protocols to DoS attacks. We show that even distributed and randomized gossip-based protocols, which eliminate single points of failure, do not necessarily eliminate vulnerabilities to DoS attacks. We propose Drum - a simple gossip-based multicast protocol that eliminates such vulnerabilities. Drum was implemented in Java and tested on a large cluster. We show, using closed-form mathematical analysis, simulations, and empirical tests, that Drum survives severe DoS attacks.

关键词： distributed applications reliability availability serviceability distributed programming

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