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8th Workshop on Workflows in Support of Large-Scale Science, WORKS 2013

作者： Gesing, Sandra Atkinson, Malcolm Klampanos, Iraklis Galea, Michelle Berthold, Michael R. Barbera, Roberto Scardaci, Diego Terstyanszky, Gabor Kiss, Tamas Kacsuk, Peter University of Notre Dame Ctr for Research Computing University of Edinburgh Informatics Forum 111 Information Technology Center Notre DameIN46556 United States University of Edinburgh Informatics Forum EdinburghEH8 9AB United Kingdom Universität Konstanz FB Informatik and Informationswissenschaft Box 712 Konstanz78457 Germany Italian National Institute of Nuclear Physics Catania95123 Italy University of Westminster 115 New Cavendish Street LondonW1W 6UW United Kingdom Laboratory of Parallel and Distributed Systems MTA SZTAKI Kende Street 13-17 Budapest1111 Hungary

ISBN: (纸本)9781450325028

This paper identifies the high value to researchers in many disciplines of having web-based graphical editors for scientific workflows and draws attention to two technological transitions: good quality editors can now run in a browser and workflow enactment systems are emerging that manage multiple workflow languages and support multi-lingual workflows. We contend that this provides a unique opportunity to introduce multi-lingual graphical workflow editors which in turn would yield substantial benefits: workflow users would find it easier to share and combine methods encoded in multiple workflow languages, the common framework would stimulate conceptual convergence and increased workflow component sharing, and the many workflow communities could share a substantial part of the effort of delivering good quality graphical workflow editors in browsers. The paper examines whether such a common framework is feasible and presents an initial design for a web-based editor, tested with a preliminary prototype. It is not a fait accompli but rather an urgent rallying cry to explore collaboratively a generic web-based framework before investing in many divergent individual implementations.

关键词： Interoperability

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Evaluation and comparison of cell nuclei detection algorithms

Evaluation and comparison of cell nuclei detection algorithm...

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IEEE 16th International Conference on Intelligent Engineering Systems, INES 2012

作者： Szénási, Sándor Vámossy, Zoltán Kozlovszky, Miklós Óbuda University Doctoral School of Applied Informatics Budapest Hungary Óbuda University John Von Neumann Faculty of Informatics Budapest Hungary MTA SZTAKI Laboratory of Parallel and Distributed Computing Budapest Hungary

ISBN: (纸本)9781467326957

The processing of microscopic tissue images and especially the detection of cell nuclei is nowadays done more and more using digital imagery and special immunodiagnostic software products. Since several methods (and applications) were developed for the same purpose, it is important to have a measuring number to determine which one is more efficient than the others. The purpose of the article is to develop a generally usable measurement number that is based on the "gold standard" tests used in the field of medicine and that can be used to perform an evaluation using any of image segmentation algorithms. Since interpreting the results themselves can be a pretty time consuming task, the article also contains a recommendation for the efficient implementation and a simple example to compare three algorithms used for cell nuclei detection. © 2012 IEEE.

关键词： Image segmentation

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Assessment of two pressure-velocity coupling strategies for local meshless numerical method

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9th International Conference on Advances in Fluid Mechanics - Advances in Fluid Mechanics IX, AFM 2012

作者： Kosec, G. Vertnik, R. Šarler, B. Jožef Stefan Institute Laboratory for Parallel and Distributed Computing Slovenia University of Nova Gorica Laboratory for Multiphase Processes Slovenia Štore steel d.o.o. Research Slovenia Centre of Excellence for Biosensors Automation and Process Control Laboratory for Advanced Materials Systems Slovenia

ISBN: (纸本)9781845646004

The performance of two pressure-velocity coupling strategies, associated with the primitive variable solution of incompressible Newtonian fluid with the meshless Local Radial Basis Function Collocation Method (LRBFCM), is compared with respect to computational efficiency, stability, accuracy and spatial convergence. The LRBFCM is structured with multiquadrics on five noded support domains. The explicit time stepping is used. The Backward- Facing Step problem (BFS) has been selected as a benchmark problem, previously tackled by several numerical methods. The semi-local fractional step method (FSM) and completely local pressure-velocity couplings (LPVC) are compared. The numerical results are validated against previously published data. The results are represented and compared in terms of a convergence plot of the reattachment position. We show that both approaches provide reasonable results;however, LVPC is less computationally complex and less stable in comparison to FSM. © 2012 WIT Press.

关键词： Computational efficiency

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Assessment of two pressure-velocity coupling strategies for local meshless numerical method

Assessment of two pressure-velocity coupling strategies for ...

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作者： Kosec, G. Vertnik, R. Šarler, B. Jožef Stefan Institute Laboratory for Parallel and Distributed Computing Slovenia University of Nova Gorica Laboratory for Multiphase Processes Slovenia Štore Steel D.o.o. Research Slovenia Centre of Excellence for Biosensors Automation and Process Control Laboratory for Advanced Materials Systems Slovenia

The performance of two pressure-velocity coupling strategies, associated with the primitive variable solution of incompressible Newtonian fluid with the meshless Local Radial Basis Function Collocation Method (LRBFCM), is compared with respect to computational efficiency, stability, accuracy and spatial convergence. The LRBFCM is structured with multiquadrics on five noded support domains. The explicit time stepping is used. The Backward-Facing Step problem (BFS) has been selected as a benchmark problem, previously tackled by several numerical methods. The semi-local fractional step method (FSM) and completely local pressure-velocity couplings (LPVC) are compared. The numerical results are validated against previously published data. The results are represented and compared in terms of a convergence plot of the reattachment position. We show that both approaches provide reasonable results;however, LVPC is less computationally complex and less stable in comparison to FSM. © 2012 WIT Press.

关键词： Computational efficiency

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Detecting faults by tracing companion states in cloud computing systems

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Jisuanji Xuebao/Chinese Journal of Computers 2012年第5期35卷 856-870页

作者： Rao, Xiang Wang, Huai-Min Chen, Zhen-Bang Zhou, Yang-Fan Cai, Hua Zhou, Qi Sun, Ting-Tao National Key Laboratory for Parallel and Distributed Processing National University of Defense Technology Changsha 410073 China Shenzhen Research Institute The Chinese University of Hong Kong Shenzhen China Department of Computing Platform Alibaba Cloud Computing Company Hangzhou 310011 China

A common way to construct a fault model is injecting the fault into the system and observing the subsequent symptoms, e. g. event logs. However, fault features would vary during the propagation period, and present different symptoms at different stage of the fault propagation process. The exiting detection window based feature extraction methods can only identify the early symptoms of a fault, but fail to detect the latter symptoms and cause false alarms. To solve the problem, we present a fault feature extraction method, called Companion State Tracer (CSTracer), which consists of 3 integrated steps: (1) pre-process logs to remove the unrelated logs;(2) construct a general identifier for the early symptoms of a fault;(3) construct a finite state machine model for the fault to trace the latter symptoms. CSTracer can persistently monitor a fault after the fault has been identified. We have justified the effectiveness of CSTracer in an enterprise cloud system. Compared with the existing, the results show that CSTracer has a better detection accuracy.

关键词： Fault detection

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Short fragment sequence alignment on the HP-SEE infrastructure

Short fragment sequence alignment on the HP-SEE infrastructu...

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Proceedings of the International Convention MIPRO

作者： Miklos Kozlovszky Gergely Windisch Ákos Balaskó Laboratory of Parallel and Distributed Computing MTA SZTAKI Budapest Hungary John von Neumann Faculty of Informatics Óbuda University Budapest Hungary

The recently used deep sequencing techniques represent a new data processing challenge: mapping short fragment reads to open-access eukaryotic genomes at the scale of several hundred thousand. This problem is solvable by BLAST, BWA and similar sequence alignment tools. BLAST is one of the most frequently used tool in bioinformatics and BWA is a relative new fast light-weighted tool that aligns effectively short sequences. Local installations of these algorithms are typically not able to handle large problem size therefore the sequence alignment process runs slowly, while web based implementations cannot accept high number of queries. HP-SEE infrastructure allows accessing massively parallel supercomputing infrastructure. With gUSE/WS-PGRADE we have created successfully an online Bioinformatics eScience Gateway, which is capable to serve the short fragment sequence alignment demand of the regional bioinformatics communities within the SEE region. Using workflows we have ported algorithms (BLAST and BWA) to the massively parallel HP-SEE infrastructure. In this paper we describe the created Bioinformatics eScience Gateway, and show as case study how we have implemented the ported BLAST workflow using parameter study. With our online service, researchers can do high throughput sequence alignments against the eukaryotic genomes to search for regulatory mechanisms controlled by short fragments on HP-SEE's supercomputing infrastructure.

关键词： Bioinformatics Logic gates Europe Communities Portals Graphical user interfaces Educational institutions

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Campaign scheduling

Campaign scheduling

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International Conference on High Performance computing

作者： Vinicius Pinheiro Krzysztof Rzadca Denis Trystram Laboratory for Parallel and Distributed Computing University of São Paulo Brazil Institute of Informatics University of Warsaw Poland Institut Universitaire de France France

We study the problem of scheduling in parallel systems with many users. We analyze scenarios with many submissions issued over time by several users. These submissions contain one or more jobs; the set of submissions are organized in successive campaigns. Jobs belonging to a single campaign are sequential and independent, but any job from a campaign cannot start until all the jobs from the previous campaign are completed. Each user's goal is to minimize the sum of flow times of his campaigns. We define a theoretical model for Campaign scheduling and show that, in the general case, it is NP-hard. For the single-user case, we show that an ρ-approximation scheduling algorithm for the (classic) parallel job scheduling problem is also an ρ-approximation for the Campaign scheduling problem. For the general case with k users, we establish a fairness criterion inspired by time sharing. We propose FAIRCAMP, a scheduling algorithm which uses campaign deadlines to achieve fairness among users between consecutive campaigns. We prove that FAIRCAMP increases the flow time of each user by a factor of at most k ρ compared with a machine dedicated to the user. We also prove that FAIRCAMP is a ρ-approximation algorithm for the maximum stretch. By simulation, we compare FAIRCAMP to the First-Come-First-Served (FCFS). We show that, compared with FCFS, FAIRCAMP reduces the maximum stretch by up to 3.4 times. The difference is significant in systems used by many (k > 5) users. Our results show that, rather than just individual, independent jobs, campaigns of jobs can be handled by the scheduler efficiently and fairly.

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Evaluation and comparison of cell nuclei detection algorithms

Evaluation and comparison of cell nuclei detection algorithm...

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IEEE International Conference on Intelligent Engineering Systems (INES)

作者： Sándor Szénási Zoltán Vámossy Miklós Kozlovszky Doctoral School of Applied Informatics Óbuda University Budapest Hungary John von Neumann Faculty of Informatics Óbuda University Budapest Hungary Laboratory of Parallel and Distributed Computing MTA SZTAKI Budapest Hungary

The processing of microscopic tissue images and especially the detection of cell nuclei is nowadays done more and more using digital imagery and special immunodiagnostic software products. Since several methods (and applications) were developed for the same purpose, it is important to have a measuring number to determine which one is more efficient than the others. The purpose of the article is to develop a generally usable measurement number that is based on the “gold standard” tests used in the field of medicine and that can be used to perform an evaluation using any of image segmentation algorithms. Since interpreting the results themselves can be a pretty time consuming task, the article also contains a recommendation for the efficient implementation and a simple example to compare three algorithms used for cell nuclei detection.

关键词： Accuracy Algorithm design and analysis Image segmentation Time measurement Gold Standards Classification algorithms

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Preparing initial population of genetic algorithm for region growing parameter optimization

Preparing initial population of genetic algorithm for region...

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International Symposium on Logistics and Industrial Informatics, LINDI

The processing of microscopic tissue images is nowadays done more and more using special immunodiagnostic-evaluation software products. Often to evaluate the samples, the first step is determining the number and location of cell nuclei. To do this, one of the most promising methods is the region growing, but this algorithm is very sensitive to the appropriate setting of different parameters. Due to the large number of parameters and due to the big set of possible values setting those parameters manually is a quite hard task, so we developed a genetic algorithm to optimize these values. The first step of the development is the statistical analysis of the parameters, and the determination of the important features, to extract valuable information for a to-be-implemented genetic algorithm that will perform the optimization.

关键词： Optimization Genetic algorithms Gold Standards Medical services Shape Databases

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A science gateway getting ready for serving the international molecular simulation community 2

A science gateway getting ready for serving the internationa...

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2012 EGI Community Forum / EMI 2nd Technical Conference, EGICF-EMITC 2012

作者： Gesing, Sandra Herres-Pawlis, Sonja Birkenheuer, Georg Brinkmann, André Grunzke, Richard Kacsuk, Peter Kohlbacher, Oliver Kozlovszky, Miklos Krüger, Jens Müller-Pfefferkorn, Ralph Schäfer, Patrick Steinke, Thomas Center for Bioinformatics Department of Computer Science University of Tübingen Sand 14 Tübingen72076 Germany Department of Chemistry Ludwig-Maximilians-University Munich Butenandtstr. 5-13 München81377 Germany Paderborn Center for Parallel Computing University of Paderborn Warburger Str. 100 Paderborn33089 Germany Johannes Gutenberg-University Mainz Mainz55099 Germany Center for Information Services and High Performance Computing Technische Universität Dresden Zellescher Weg 12-14 Germany Laboratory of Parallel and Distributed Systems MTA SZTAKI Kende Street 13-17 Budapest1111 Hungary Zuse Institute Berlin Takustraße 7 Berlin14195 Germany

The project MoSGrid (Molecular Simulation Grid) has been developing a web-based science gateway supporting the community with various services for quantum chemistry, molecular modeling, and docking. Users gain access to distributed computing infrastructures (DCIs) via intuitive user interfaces for sophisticated tools, specialized workflows, and distributed repositories. Currently, the MoSGrid community consists of about 120 users from a number of fields related to chemistry and bioinformatics located in Germany. However, the underlying security infrastructure is generally applicable and can be deployed in arbitrary projects. MoSGrid intends to address the international community by participating in the EU-projects SCI-BUS (Scientific gateway Based User Support) and ER-flow (Building an European Research Community through Interoperable Workflows and Data), and collaborating with the EU-project EDGI (European Desktop Grid Initiative). © Copyright owned by the author(s) under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike Licence.

关键词： Quantum chemistry

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