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作者： Ciocchetta, Federica Degasperi, Andrea Heath, John K. Hillston, Jane Microsoft Research - University of Trento Centre for Computational and Systems Biology Trento Italy Department of Computing Science University of Glasgow G12 8QQ United Kingdom School of Biosciences University of Birmingham B15 2TT United Kingdom Laboratory for Foundations of Computer Science University of Edinburgh EH8 9AB United Kingdom Edinburgh United Kingdom

ISBN: (纸本)3642117112

In this work we present a Bio-PEPA model describing the Nuclear Factor κB (NF-κB) signalling pathway. In particular our model focuses on the dynamic response of NF-κB to an external stimulus. Each biochemical species in the pathway is represented by a specific Bio-PEPA component and the external stimulus is abstracted by time-dependent Bio-PEPA events describing the start and the end of the signal. The Bio-PEPA model is a formal intermediate representation of the pathway on which various kinds of analysis can be performed. Both stochastic and deterministic simulations are carried out to validate our model against the experimental data and in-silico experiments in the literature and to verify some properties, such as, the impact of the duration of the external stimulus and of the total NF-κB initial amount on the behaviour of some species of interest. Furthermore we use stochastic simulation to compare the behaviour of the single cell against the average behaviour of a population of cells. Finally, sensitivity analysis is considered to investigate the most influential parameters of the model. Importantly, the approach taken suggests that the sensitivity of some parameters alters with the time evolution of the pathway. © 2010 Springer.

关键词： Sensitivity analysis

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Synchronizing the Timestamps of Concurrent Events in Traces of Hybrid MPI/OpenMP Applications

Synchronizing the Timestamps of Concurrent Events in Traces ...

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IEEE International Conference on Cluster computing

作者： Daniel Becker Markus Geimer Rolf Rabenseifner Felix Wolf Department of Computer Science RWTH Aachen University Aachen Germany German Research School for Simulation Sciences Laboratory for Parallel Programming Aachen Germany Forschungszentrum Jülich Jülich Supercomputing Centre Jülich Germany University of Stuttgart High Performance Computing-Center Stuttgart Germany

Event traces are helpful in understanding the performance behavior of parallel applications since they allow the in-depth analysis of communication and synchronization patterns. However, the absence of synchronized clocks on most cluster systems may render the analysis ineffective because inaccurate relative event timings may misrepresent the logical event order and lead to errors when quantifying the impact of certain behaviors or confuse the users of time-line visualization tools by showing messages flowing backward in time. In our earlier work, we have developed a scalable algorithm that eliminates inconsistent inter-process timings postmortem in traces of pure MPI applications. Since hybrid programming, the combination of MPI and OpenMP in a single application, is becoming more popular on clusters in response to rising numbers of cores per chip and widening shared-memory nodes, we present an extended version of the algorithm that in addition to message-passing event semantics also preserves and restores shared-memory event semantics.

关键词： Clocks Message systems Semantics Synchronization Algorithm design and analysis Interpolation

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Process algebra modelling styles for biomolecular processes

Process algebra modelling styles for biomolecular processes

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作者： Calder, Muffy Hillston, Jane Department of Computing Science University of Glasgow Glasgow G12 8QQ United Kingdom Laboratory for Foundations of Computer Science Centre for Systems Biology Edinburgh University of Edinburgh Edinburgh EHA 9AB United Kingdom

ISBN: (纸本)364204185X

We investigate how biomolecular processes are modelled in process algebras, focussing on chemical reactions. We consider various modelling styles and how design decisions made in the definition of the process algebra have an impact on how a modelling style can be applied. Our goal is to highlight the often implicit choices that modellers make in choosing a formalism, and illustrate, through the use of examples, how this can affect expressability as well as the type and complexity of the analysis that can be performed. © 2009 Springer Berlin Heidelberg.

关键词： Algebra

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On the Design of RNA Sequences for Realizing Extended Shapes

On the Design of RNA Sequences for Realizing Extended Shapes

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International Joint Conference on Bioinformatics, Systems Biology and Intelligent computing, IJCBS

作者： Marc Hellmuth Daniel Merkle Martin Middendorf Interdisciplinary Centre of Bioinformatics Department of Computer Science University of Leipzig Leipzig Germany Department of Mathematics and Computer Science University of Southern Denmark Odense Denmark Parallel Computing and Complex Systems Group Department of Computer Science University of Leipzig Leipzig Germany

It is known that for two given secondary structures (defined by position of base pairings) an RNA string can easily be found that can fold into both structures. But for more than two secondary structures this is not necessarily possible. Moreover, when four or more secondary structures are given the problem to determine the least number of positions, such that after the removal of all incident base pairs, a compatible RNA sequence can be found, is known to be NP-complete (\cite{real_shapes}). In this paper we introduce pseudo edges that are used to forbid that certain base pairs can bind and therefore can be used to define the properties of possible RNA secondary structures. We study the complexity of the problem to design an RNA sequence that can fold into different secondary structures each of them is described by a set of required and forbidden base pairs. We refine the NP-completeness results of \cite{real_shapes} and show an analoguous NP-completeness result for the realization problem concerning the removal of (pseudo) edges. We also present a polynomial time method for checking the realizability of extended shape graphs. Furthermore, we empirically analyze the influence of pseudo edges on the realizability for sets of random RNA sequences and for sets of aptamers.

关键词： RNA Shape Switches computer science Bioinformatics Sequences Systems biology Intelligent systems Biology computing Concurrent computing

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Large-scale lattice-Boltzmann simulations over lambda networks

Large-scale lattice-Boltzmann simulations over lambda networ...

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2007 Lighting the Blue Touchpaper for UK e-science - Closing Conference of ESLEA Project, ESLEA 2007

作者： Saksena, Radhika S. Coveney, Peter V. Pinning, Robin L. Booth, Stephen P. Centre for Computational Science Department of Chemistry University College London 20 Gordon Street LondonWC1H 0AJ United Kingdom Manchester Computing University of Manchester Oxford Road ManchesterM13 9PL United Kingdom Edinburgh Parallel Computing Centre University of Edinburgh EdinburghEH9 3JZ United Kingdom

Amphiphilic molecules are of immense industrial importance, mainly due to their tendency to align at interfaces in a solution of immiscible species, e.g., oil and water, thereby reducing surface tension. Depending on the concentration of amphiphiles in the solution, they may assemble into a variety of morphologies, such as lamellae, micelles, sponge and cubic bicontinuous structures exhibiting non-trivial rheological properties. The main objective of this work is to study the rheological properties of very large, defect-containing gyroidal systems (of up to 10243 lattice sites) using the lattice-Boltzmann method. Memory requirements for the simulation of such large lattices exceed that available to us on most supercomputers and so we use MPICH-G2/MPIg to investigate geographically distributed domain decomposition simulations across HPCx in the UK and TeraGrid in the US. Use of MPICH-G2/MPIg requires the port-forwarder to work with the grid middleware on HPCx. Data from the simulations is streamed to a high performance visualisation resource at UCL (London) for rendering and visualisation. © Copyright owned by the author(s) under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike Licence.

关键词： Supercomputers

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Cluster computing and Grid 2005 works in progress

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IEEE Distributed Systems Online 2005年第9期6卷 2页

作者： Wang, Frank Helian, Na Wu, Sining Deng, Yuhui Zhou, Ke Guo, Yike Thompson, Steve Johnson, Ian Milward, Dave Maddock, Robert Khoo, Benjamin Bharadwaj, Veeravalli Cambridge-Cranfield High Performance Computing Facility London Metropolitan University Cranfield University Imperial College Xyratex Department of Grid Computing and E-science Centre for Grid Computing Data Mining at the London Metropolitan University Centre for Grid Computing Cranfield University London E-science Centre Parallel Computing Centre Imperial College National University of Singapore Department of Electrical and Computer Engineering National University of Singapore

A grid-oriented storage (GOS) project, which aims to support advanced data bank services and data reservoirs for sharing data on the gird, is discussed. The GOS appliance is a disk array that connects directly to the grid using a Globus XIO interface and fits in the thin server categorization. The security model of the GOS is based on the Grid security Infrastructure (GSI). A dynamic estimation scheme for fault-free scheduling in grid systems is also discussed. Most of the grid falls into one of the two categories, planned and negotiated, and dynamic and voluntary. This discrepancy is the main reason behind the complexity in designing robust and fault tolerant scheduling algorithms for both resource categories.

关键词： Data storage equipment

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Grid-based metadata services

Grid-based metadata services

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Proceedings - 16th International Conference on Scientific and Statistical Databse Management, SSDBM 2004

作者： Deelman, Ewa Singh, Gurmeet Atkinson, Malcolm P. Chervenak, Ann Hong, Neil P. Chue Kesselman, Carl Patil, Sonal Pearlman, Laura Su, Mei-Hui Information Sciences Institute University of Southern California Department of Computing Science University of Glasgow Division of Informatics University of Edinburgh Edinburgh Parallel Computing Centre United Kingdom

Data sets being managed in Grid environments today are growing at a rapid rate, expected to reach 100s of Petabytes in the near future. Managing such large data sets poses challenges for efficient data access, data publication and data discovery. In this paper we focus on the data publication and discovery process through the use of descriptive metadata. This metadata describe the properties of individual data items and collections. We discuss issues of metadata services in service rich environments, such as the Grid. We describe the requirements and the architecture for such services in the context of Grid and the available Grid services. We present a data model that can capture the complexity of the data publication and discovery process. Based on that model we identify a set of interfaces and operations that need to be provided to support metadata management. We present a particular implementation of a Grid metadata service, basing it on existing Grid services technologies. Finally we examine alternative implementations of that service.

关键词： Metadata

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Grid-based metadata services

Grid-based metadata services

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International Working Conference on Scientific and Statistical Database Management

作者： E. Deelman G. Singh M.P. Atkinson A. Chervenak N.P. Chue Hong C. Kesselman S. Patil L. Pearlman Mei-Hui Su Information Sciences Institute University of Southern California USA Department of Computing Science Division of Informatics University of Glasgow University of Edinburgh UK Edinburgh Parallel Computing Centre UK

Data sets being managed in grid environments today are growing at a rapid rate, expected to reach 100s of petabytes in the near future. Managing such large data sets poses challenges for efficient data access, data publication and data discovery. In this paper we focus on the data publication and discovery process through the use of descriptive metadata. This metadata describe the properties of individual data items and collections. We discuss issues of metadata services in service rich environments, such as the grid. We describe the requirements and the architecture for such services in the context of grid and the available grid services. We present a data model that can capture the complexity of the data publication and discovery process. Based on that model we identify a set of interfaces and operations that need to be provided to support metadata management. We present a particular implementation of a grid metadata service, basing it on existing grid services technologies. Finally we examine alternative implementations of that service.

关键词： Collaboration Environmental management Physics Astronomy Instruments Data analysis Image databases Context-aware services Data models Space technology

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Performance analysis tools for parallel Java applications on shared-memory systems

Performance analysis tools for parallel Java applications on...

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International Conference on parallel Processing (ICPP)

作者： J. Guitart J. Torres E. Ayguade J.M. Bull European Center for Parallelism of Barcelona CEPBA Computer Architecture Department Technical University of Catalonia Barcelona Spain Edinburgh Parallel Computing Centre EPCC University of Edinburgh Edinburgh UK

In this paper we describe an instrumentation environment for the performance analysis and visualization of parallel applications written in JOMP, an OpenMP-like interface for Java. The environment includes two complementary approaches. The first one has been designed to provide a detailed analysis of the parallel behavior at the JOMP programming model level. At this level, the user is faced with parallel, work-sharing and synchronization constructs, which are the core of JOMP. The second mechanism has been designed to support an in-depth analysis of the threaded execution inside the Java virtual machine (JVM). At this level of analysis, the user is faced with the supporting threads layer monitors and conditional variables. The paper discusses the implementation of both mechanisms and evaluates the overhead incurred by them.

关键词： Performance analysis Java Yarn parallel processing Instruments Proposals parallel programming Application software Visualization Runtime

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Preface

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Lecture Notes in computer science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 2001年 2037卷 V-VI页

作者： Boers, Egbert J. W. Cagnoni, Stefano Gottlieb, Jens Hart, Emma Lanzi, Pier Luca Raidl, Günther R. Smith, Robert E. Tijink, Harald Leiden Institute of Advanced Computer Science Leiden University Niels Bohrweg 1 Leiden Netherlands Dept. of Computer Engineering University of Parma Parco Area delle Scienze 181/a Parma Italy SAP AG Neurottstrasse 16 Walldorf Germany Napier University School of Computing 219 Colinton Road Edinburgh United Kingdom Polytechnic of Milan Piazza Leonardo da Vinci 32 Milan Italy Algorithms and Data Structur es Group Institute of Computer Graphics Vienna University of Technology Favoritenstrasse 9-11/186 Vienna Austria The Intelligent Computer Systems Centre The University of The West of England Coldharbour Lane Frenchay Bristol United Kingdom Data and Knowledge Systems Department National Aerospace Laboratory NLR P.O. Box 153 Emmeloord Netherlands

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