ORCID Profile
0000-0003-0441-4596
Current Organisation
University of Queensland
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Research Topics
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Computer Software | Software Engineering | Information Storage, Retrieval And Management | Global Information Systems | Information Systems | Biological Sciences Not Elsewhere Classified | Astronomy And Astrophysics | Programming Techniques | Information Systems Organisation | Computer Hardware | Concurrent Programming | Information Systems Development Methodologies | Astronomical and Space Sciences | Structural Chemistry | Geology | Physical Chemistry (Incl. Structural) | Computer Communications Networks | Other Biological Sciences | Computer Hardware Not Elsewhere Classified | Computer Software Not Elsewhere Classified | Biochemistry And Cell Biology Not Elsewhere Classified | Biochemistry and Cell Biology | Processor Architectures | Artificial Intelligence and Image Processing | Distributed Computing | Computer Hardware not elsewhere classified | Geotectonics | Numerical Computation | Operating Systems | Interorganisational Information Systems | Policy and Administration | Communications Technologies Not Elsewhere Classified | Geology Not Elsewhere Classified | Other Information, Computing And Communication Sciences | Distributed Computing not elsewhere classified | Decision Support And Group Support Systems | Virtual Reality And Related Simulation | Neural Networks, Genetic Alogrithms And Fuzzy Logic | Simulation And Modelling | Public Administration | Web Technologies (excl. Web Search) | Pattern Recognition and Data Mining | Software Engineering | Climatology (Incl. Palaeoclimatology) | Distributed and Grid Systems | Analysis Of Algorithms And Complexity | Mathematical Sciences Not Elsewhere Classified | Social Policy | Diagnostic Applications | Environmental Sciences Not Elsewhere Classified | Mathematical Software | Atomic And Molecular Physics | Numerical Analysis | Interorganisational Information Systems and Web Services |
ANZSRC Socio-Economic Objective (SEO)
Information processing services | Application tools and system utilities | Biological sciences | Physical sciences | Technological and organisational innovation | Communication services not elsewhere classified | Application Tools and System Utilities | Data, image and text equipment | Treatments (e.g. chemicals, antibiotics) | Computer hardware and electronic equipment not elsewhere classified | Library and related information services | Other | Computer software and services not elsewhere classified | Other | Studies in human society | Public Services Policy Advice and Analysis | Earth sciences | Network transmission equipment | Chemical sciences | Climate variability | Information and Communication Services not elsewhere classified | Infectious diseases | Diagnostic methods | Scientific instrumentation | Environmentally Sustainable Information and Communication Services not elsewhere classified | Exploration | Application Software Packages (excl. Computer Games) | Information Processing Services (incl. Data Entry and Capture) | Expanding Knowledge in the Information and Computing Sciences | Structure, Delivery and Financing of Community Services | Other
Related Links
Publications
Fault‐tolerant execution of large parameter sweep applications across multiple VOs with storage constraints
Publisher: Wiley
Date: 25-08-2008
DOI: 10.1002/CPE.1353
Cyberinfrastructure Intership and its Application to e-Science
Publisher: IEEE
Date: 12-2011
An evolutionary programming algorithm for multi-objective optimisation
Publisher: IEEE
Date: 2003
A Taxonomy of Call Ordering Problems
Publisher: IEEE
Date: 2004
Assertion based parallel debugging
Publisher: IEEE
Date: 05-2011
Integrating scientific workflows and large tiled display walls: Bridging the visualization divide
Publisher: IEEE
Date: 09-2011
Message from the Program Committee Chairs
Publisher: IEEE
Date: 10-2017
FPGA based implementation of a Hopfield neural network for solving constraint satisfaction problems
Publisher: IEEE Comput. Soc
Date: 1998
FlashLite: A High Performance Machine for Data Intensive Science
Publisher: IEEE
Date: 12-2015
Flexible IO Services in the Kepler Grid Workflow System
Publisher: IEEE
Date: 2005
Parameter scan of an effective group difference pseudopotential using grid computing
Publisher: Springer Science and Business Media LLC
Date: 06-2004
DOI: 10.1007/BF03040952
An Atmospheric Sciences Workflow and its implementation with Web Services
Publisher: Elsevier BV
Date: 2005
Incorporating Local Ca2 + Dynamics into Single Cell Ventricular Models
Publisher: Springer Berlin Heidelberg
Date: 2008
WorkWays: Interacting with scientific workflows
Publisher: IEEE
Date: 11-2015
DOI: 10.1109/GCE.2014.6
Nimrod/G: an architecture for a resource management and scheduling system in a global computational grid
Publisher: IEEE
Date: 2000
Converting massive TLP to DLP
Publisher: ACM
Date: 07-05-2007
Data centric highly parallel debugging
Publisher: ACM
Date: 21-06-2010
A Metropolitan Area Infrastructure for Data Intensive Science
Publisher: IEEE
Date: 10-2017
A BeeGFS-Based Caching File System for Data-Intensive Parallel Computing
Publisher: Springer International Publishing
Date: 2020
A Scalable and Efficient Prefix-Based Lookup Mechanism for Large-Scale Grids
Publisher: IEEE
Date: 2007
Scheduling parameter sweep applications on global Grids: A deadline and budget constrained cost-time optimization algorithm
Publisher: Wiley
Date: 2005
DOI: 10.1002/SPE.646
Statistical Inference of Protein LEGO Bricks
Publisher: IEEE
Date: 12-2013
DOI: 10.1109/ICDM.2013.73
Statistical assertion: A more powerful method for debugging scientific applications
Publisher: Elsevier BV
Date: 03-2014
Grid Interoperability: An Experiment in Bridging Grid Islands
Publisher: IEEE
Date: 12-2008
Scheduling parameter sweep workflow in the Grid based on resource competition
Publisher: Elsevier BV
Date: 07-2013
Debugging scientific applications in the .NET Framework
Publisher: Elsevier BV
Date: 07-2003
The Nimrod/G Grid Resource Broker for Economics‐Based Scheduling
Publisher: Wiley
Date: 12-10-2009
Communication over a Secured Heterogeneous Grid with the GriddLeS Runtime Environment
Publisher: IEEE
Date: 12-2006
A computational economy for grid computing and its implementation in the Nimrod-G resource broker
Publisher: Elsevier BV
Date: 10-2002
Firewall Traversal in the Grid Architecture
Publisher: IEEE
Date: 09-2010
Debugging scientific applications with statistical assertions
Publisher: Elsevier BV
Date: 2012
Interoperation of world‐wide production e‐Science infrastructures
Publisher: Wiley
Date: 24-03-2009
DOI: 10.1002/CPE.1402
An abstract virtual instrument system for high throughput automatic microscopy
Publisher: Elsevier BV
Date: 05-2010
Relative debugging
Publisher: Association for Computing Machinery (ACM)
Date: 11-1996
Relative debugging in an integrated development environment
Publisher: Wiley
Date: 25-09-2009
DOI: 10.1002/SPE.932
Solving Optimization Problems in Nimrod/OK using a Genetic Algorithm
Publisher: Elsevier BV
Date: 2012
Scalable parallel debugging with statistical assertions
Publisher: Association for Computing Machinery (ACM)
Date: 25-02-2012
Abstract: Traditional debuggers are of limited value for modern scientific codes that manipulate large complex data structures. This paper discusses a novel debug-time assertion, called a "Statistical Assertion", that allows a user to reason about large data structures, and the primitives are parallelised to provide an efficient solution. We present the design and implementation of statistical assertions, and illustrate the debugging technique with a molecular dynamics simulation. We evaluate the performance of the tool on a 12,000 cores Cray XE6.
Nimrod/K: Towards massively parallel dynamic Grid workflows
Publisher: IEEE
Date: 11-2008
Economic models for resource management and scheduling in Grid computing
Publisher: Wiley
Date: 11-2002
DOI: 10.1002/CPE.690
Abstract: The accelerated development in peer‐to‐peer and Grid computing has positioned them as promising next‐generation computing platforms. They enable the creation of virtual enterprises for sharing resources distributed across the world. However, resource management, application development and usage models in these environments is a complex undertaking. This is due to the geographic distribution of resources that are owned by different organizations or peers. The resource owners of each of these resources have different usage or access policies and cost models, and varying loads and availability. In order to address complex resource management issues, we have proposed a computational economy framework for resource allocation and for regulating supply and demand in Grid computing environments. This framework provides mechanisms for optimizing resource provider and consumer objective functions through trading and brokering services. In a real world market, there exist various economic models for setting the price of services based on supply‐and‐demand and their value to the user. They include commodity market, posted price, tender and auction models. In this paper, we discuss the use of these models for interaction between Grid components to decide resource service value, and the necessary infrastructure to realize each model. In addition to usual services offered by Grid computing systems, we need an infrastructure to support interaction protocols, allocation mechanisms, currency, secure banking and enforcement services. We briefly discuss existing technologies that provide some of these services and show their usage in developing the Nimrod‐G grid resource broker. Furthermore, we demonstrate the effectiveness of some of the economic models in resource trading and scheduling using the Nimrod/G resource broker, with deadline and cost constrained scheduling for two different optimization strategies, on the World‐Wide Grid testbed that has resources distributed across five continents. Copyright © 2002 John Wiley & Sons, Ltd.
A scalable parallel debugging library with pluggable communication protocols
Publisher: IEEE
Date: 05-2012
Supporting relative debugging for large-scale UPC programs
Publisher: Elsevier BV
Date: 2014
Statistical Compression of Protein Folding Patterns for Inference of Recurrent Substructural Themes
Publisher: IEEE
Date: 04-2017
DOI: 10.1109/DCC.2017.46
The Grid Economy
Publisher: Institute of Electrical and Electronics Engineers (IEEE)
Date: 03-2005
Run-time thread sorting to expose data-level parallelism
Publisher: IEEE
Date: 07-2008
Deploying Scientific Applications to the PRAGMA Grid Testbed: Strategies and Lessons
Publisher: IEEE
Date: 2006
NG-TEPHRA: A Massively Parallel, Nimrod/G-enabled Volcanic Simulation in the Grid and the Cloud
Publisher: IEEE
Date: 12-2010
Uniting extrinsic vectorization and shell structure for efficient SIMD evaluation of electron repulsion integrals
Publisher: Elsevier BV
Date: 06-2008
Lessons learned through driving science applications in the PRAGMA grid
Publisher: Inderscience Publishers
Date: 2007
Structural optimisation with damage tolerance constraints
Publisher: Elsevier BV
Date: 03-2005
An Integrated Grid Development Environment in Eclipse
Publisher: IEEE
Date: 2007
Topic 11: Multicore and Manycore Programming
Publisher: Springer Berlin Heidelberg
Date: 2013
Spaces: Support for Decoupled Communication in Wide-Area Parallel Applications
Publisher: IEEE
Date: 08-2007
DOI: 10.1109/GCC.2007.117
New insights into the analysis of the electrode kinetics of flavin adenine dinucleotide redox center of glucose oxidase immobilized on carbon electrodes
Publisher: American Chemical Society (ACS)
Date: 13-03-2014
DOI: 10.1021/LA404872P
Abstract: New insights into electrochemical kinetics of the flavin adenine dinucleotide (FAD) redox center of glucose-oxidase (GlcOx) immobilized on reduced graphene oxide (rGO), single- and multiwalled carbon nanotubes (SW and MWCNT), and combinations of rGO and CNTs have been gained by application of Fourier transformed AC voltammetry (FTACV) and simulations based on a range of models. A satisfactory level of agreement between experiment and theory, and hence establishment of the best model to describe the redox chemistry of FAD, was achieved with the aid of automated e-science tools. Although still not perfect, use of Marcus theory with a very low reorganization energy (≤0.3 eV) best mimics the experimental FTACV data, which suggests that the process is gated as also deduced from analysis of FTACV data obtained at different frequencies. Failure of the simplest models to fully describe the electrode kinetics of the redox center of GlcOx, including those based on the widely employed Laviron theory is demonstrated, as is substantial kinetic heterogeneity of FAD species. Use of a SWCNT support lifies the kinetic heterogeneity, while a combination of rGO and MWCNT provides a more favorable environment for fast communication between FAD and the electrode.
Finding my own voice through the breast cancer journey: Humour, sadness and smurfs
Publisher: Wiley
Date: 14-01-2015
DOI: 10.1002/JMRS.92
Runtime Verification of Scientific Codes Using Statistics
Publisher: Elsevier BV
Date: 2016
A comparison of two methods for solving 0–1 integer programs using a general purpose simulated annealing algorithm
Publisher: Springer Science and Business Media LLC
Date: 02-1996
DOI: 10.1007/BF02601642
Targeting EphA3 Inhibits Cancer Growth by Disrupting the Tumor Stromal Microenvironment
Publisher: American Association for Cancer Research (AACR)
Date: 13-08-2014
DOI: 10.1158/0008-5472.CAN-14-0218
Abstract: Eph receptor tyrosine kinases are critical for cell–cell communication during normal and oncogenic tissue patterning and tumor growth. Somatic mutation profiles of several cancer genomes suggest EphA3 as a tumor suppressor, but its oncogenic expression pattern and role in tumorigenesis remain largely undefined. Here, we report unexpected EphA3 overexpression within the microenvironment of a range of human cancers and mouse tumor xenografts where its activation inhibits tumor growth. EphA3 is found on mouse bone marrow–derived cells with mesenchymal and myeloid phenotypes, and activation of EphA3+/CD90+/Sca1+ mesenchymal/stromal cells with an EphA3 agonist leads to cell contraction, cell–cell segregation, and apoptosis. Treatment of mice with an agonistic α-EphA3 antibody inhibits tumor growth by severely disrupting the integrity and function of newly formed tumor stroma and microvasculature. Our data define EphA3 as a novel target for selective ablation of the tumor microenvironment and demonstrate the potential of EphA3 agonists for anticancer therapy. Cancer Res 74(16) 4470–81. ©2014 AACR.
Applications Development for the Computational Grid
Publisher: Springer Berlin Heidelberg
Date: 2006
DOI: 10.1007/11610113_1
Persistence and Communication State Transfer in an Asynchronous Pipe Mechanism
Publisher: IGI Global
Date: 07-2009
Abstract: Wide-area distributed systems offer new opportunities for executing large-scale scientific applications. On these systems, communication mechanisms have to deal with dynamic resource availability and the potential for resource and network failures. Connectivity losses can affect the execution of workflow applications, which require reliable data transport between components. We present the design and implementation of p-channels, an asynchronous and fault-tolerant pipe mechanism suitable for coupling workflow components. Fault-tolerant communication is made possible by persistence, through adaptive caching of pipe segments while providing direct data streaming. We present the distributed algorithm for implementing: (a) caching of pipe data segments (b) asynchronous read operation and (c) communication state transfer to handle dynamic process joins and leaves.
A WSRF-Compliant Debugger for Grid Applications
Publisher: IEEE
Date: 2007
Relative debugging for data-parallel programs: a ZPL case study
Publisher: Institute of Electrical and Electronics Engineers (IEEE)
Date: 10-2000
DOI: 10.1109/4434.895105
A computational pipeline for the IUCN risk assessment for meso-American reef ecosystem
Publisher: IEEE
Date: 10-2017
A Scheduler based on Resource Competition for Parameter Sweep Workflow
Publisher: Elsevier BV
Date: 2011
Perspectives of the International Conference of Computational Science 2014
Publisher: Elsevier BV
Date: 09-2015
Towards a special-purpose computer for Hartree–Fock computations
Publisher: Springer Science and Business Media LLC
Date: 28-04-2007
REMUS: A Rerouting and Multiplexing System for Grid Connectivity Across Firewalls
Publisher: Springer Science and Business Media LLC
Date: 28-06-2008
WorkWays: interacting with scientific workflows
Publisher: Wiley
Date: 21-05-2015
DOI: 10.1002/CPE.3525
Active Data: Supporting the Grid Data Life Cycle
Publisher: IEEE
Date: 05-2007
Application of grid computing to parameter sweeps and optimizations in molecular modeling
Publisher: Elsevier BV
Date: 2005
Evaluating the performance of a SISAL implementation of the abingdon cross image processing benchmark
Publisher: Springer Science and Business Media LLC
Date: 04-1995
DOI: 10.1007/BF02577786
Parallel line search
Publisher: Springer New York
Date: 2009
On ERI sorting for SIMD execution of large-scale Hartree–Fock SCF
Publisher: Elsevier BV
Date: 06-2008
Embedding optimization in computational science workflows
Publisher: Elsevier BV
Date: 05-2010
A parallel interior point method and its application to facility location problems
Publisher: Springer Science and Business Media LLC
Date: 1998
High-throughput cardiac science on the Grid
Publisher: The Royal Society
Date: 28-08-2010
Abstract: Cardiac electrophysiology is a mature discipline, with the first model of a cardiac cell action potential having been developed in 1962. Current models range from single ion channels, through very complex models of in idual cardiac cells, to geometrically and anatomically detailed models of the electrical activity in whole ventricles. A critical issue for model developers is how to choose parameters that allow the model to faithfully reproduce observed physiological effects without over-fitting. In this paper, we discuss the use of a parametric modelling toolkit, called N imrod , that makes it possible both to explore model behaviour as parameters are changed and also to tune parameters by optimizing model output. Importantly, N imrod leverages computers on the Grid, accelerating experiments by using available high-performance platforms. We illustrate the use of N imrod with two case studies, one at the cardiac tissue level and one at the cellular level.
<title>Economic models for management of resources in peer-to-peer and grid computing</title>
Publisher: SPIE
Date: 27-07-2001
DOI: 10.1117/12.434872
Parameter Space Exploration Using Scientific Workflows
Publisher: Springer Berlin Heidelberg
Date: 2009
Leveraging e-Science infrastructure for electrochemical research
Publisher: The Royal Society
Date: 28-08-2011
Abstract: As in many scientific disciplines, modern chemistry involves a mix of experimentation and computer-supported theory. Historically, these skills have been provided by different groups, and range from traditional ‘wet’ laboratory science to advanced numerical simulation. Increasingly, progress is made by global collaborations, in which new theory may be developed in one part of the world and applied and tested in the laboratory elsewhere. e-Science, or cyber-infrastructure, underpins such collaborations by providing a unified platform for accessing scientific instruments, computers and data archives, and collaboration tools. In this paper we discuss the application of advanced e-Science software tools to electrochemistry research performed in three different laboratories – two at Monash University in Australia and one at the University of Oxford in the UK. We show that software tools that were originally developed for a range of application domains can be applied to electrochemical problems, in particular Fourier voltammetry. Moreover, we show that, by replacing ad-hoc manual processes with e-Science tools, we obtain more accurate solutions automatically.
Mrgrid: A portable grid based molecular replacement pipeline
Publisher: Public Library of Science (PLoS)
Date: 06-04-2010
Parallel non-linear optimization
Publisher: ACM Press
Date: 1997
Moving small files in a networked environment
Publisher: Elsevier BV
Date: 02-2023
Automatic design optimization using parallel workflows
Publisher: Elsevier BV
Date: 05-2010
A global sensitivity tool for cardiac cell modeling: Application to ionic current balance and hypertrophic signaling
Publisher: IEEE
Date: 08-2010
A Unified Data Grid Replication Framework
Publisher: IEEE
Date: 12-2006
Distributed Ant: A system to support application deployment in the grid
Publisher: IEEE
Date: 2004
DOI: 10.1109/GRID.2004.23
Design and implementation of assertions for the common language infrastructure
Publisher: Institution of Engineering and Technology (IET)
Date: 2003
Accidental Translationists: A Perspective From the Trenches
Publisher: Institute of Electrical and Electronics Engineers (IEEE)
Date: 07-2022
Runtime Verification of Scientific Computing: Towards an Extreme Scale
Publisher: IEEE
Date: 11-2017
Otitis Media Associated with Cryptosporidium baileyi in a Saker Falcon (Falco cherrug)
Publisher: Elsevier BV
Date: 05-2013
DOI: 10.1016/J.JCPA.2012.09.005
Abstract: A 7-week-old male Saker falcon died with a history of severe refractory dyspnoea and respiratory signs. Microscopical lesions included moderate to severe lymphoplasmacytic inflammation of the middle ears, conjunctivae, third eyelids, choanae, salivary glands of the tongue, turbinates, larynx, trachea, syrinx and bronchi. The lesions were associated with variable numbers of Cryptosporidium spp., further confirmed by transmission electron microscopy and in-situ hybridization. Cryptosporidium baileyi was identified by DNA sequence analysis. C. baileyi may therefore be a cause of otitis media in raptors as it is in man. It is most likely that the middle ears of the Saker falcon acquired the infection through the eustachian tubes that originate near the pharynx in the oral cavity. This is the first description of otitis media associated with C. baileyi in a bird or a mammal except man.
Scheduling Multiple Parameter Sweep Workflow Instances on the Grid
Publisher: IEEE
Date: 12-2009
A Flexible Grid Framework for Automatic Protein-Ligand Docking
Publisher: IEEE
Date: 12-2006
Technical considerations when implementing digital infrastructure for social policy
Publisher: Wiley
Date: 08-10-2020
DOI: 10.1002/AJS4.135
Abstract: Big data and advanced computational methods are increasingly being used to inform decision making in social policy globally. As a result, there is a pressing need to identify best practice digital infrastructure design that allows policymakers and social sciences researchers to access, manipulate and use big data soundly and ethically, while identifying and resolving issues that can lead to unintended consequences and adverse social policy outcomes. However, building such digital infrastructure continues to be a technical challenge for users of big social and administrative data. This paper presents a model to evaluate and design best practice infrastructure for the use of big data in social policy. Our model identifies key technical infrastructure considerations for six stages of a data analysis pipeline, namely (1) data storage, (2) data integration, (3) data access, (4) data analysis, (5) data interpretation and (6) data operationalisation. We demonstrate the model via two applications: the E‐Verify online employment rights system and the Australian COVIDSafe app. The model provides a high‐level guide for social policymakers and researchers to consider systematically the relevant technical considerations when designing or upgrading digital infrastructure that uses analytical tools and big datasets from multiple sources.
Worqbench: An Integrated Framework for e-Science Application Development
Publisher: IEEE
Date: 12-2006
Big Data Meets Computational Science, Preface for ICCS 2014
Publisher: Elsevier BV
Date: 2014
A local sensitivity analysis method for developing biological models with identifiable parameters: Application to cardiac ionic channel modelling
Publisher: Elsevier BV
Date: 02-2013
Interoperable grid agent middleware for scientific instruments and sensors
Publisher: ACM
Date: 27-11-2006
A Virtual Connectivity Layer for Grids
Publisher: IEEE
Date: 12-2009
Multi-objective engineering shape optimization using differential evolution interfaced to the Nimrod/O tool
Publisher: IOP Publishing
Date: 06-2010
eResearch solutions for high throughput structural biology
Publisher: IEEE
Date: 2007
High-throughput protein structure determination using grid computing
Publisher: IEEE
Date: 05-2009
Special Theme: Project Management in E-Science: Challenges and Opportunities
Publisher: Springer Science and Business Media LLC
Date: 06-2011
Displacement problem and dynamically scheduling aircraft landings
Publisher: Informa UK Limited
Date: 2004
Neuroscience instrumentation and distributed analysis of brain activity data: a case for eScience on global Grids
Publisher: Wiley
Date: 2005
DOI: 10.1002/CPE.888
Uncertainty and technical efficiency in Finnish agriculture: A state-contingent approach
Publisher: Oxford University Press (OUP)
Date: 08-2011
DOI: 10.1093/ERAE/JBR014
Estimation of electrode kinetic and uncompensated resistance parameters and insights into their significance using Fourier transformed ac voltammetry and e-science software tools
Publisher: Elsevier BV
Date: 02-2013
Overview to the PRAGMA Workshop on eScience Highlights
Publisher: IEEE
Date: 2008
QacR-cation recognition is mediated by a redundancy of residues capable of charge neutralization
Publisher: American Chemical Society (ACS)
Date: 11-07-2008
DOI: 10.1021/BI8008246
Electrochemical Parameter Optimization Using Scientific Workflows
Publisher: IEEE
Date: 12-2010
The GriddLeS Data Replication Service
Publisher: IEEE
Date: 2005
A survey on software methods to improve the energy efficiency of parallel computing
Publisher: SAGE Publications
Date: 09-09-2016
Abstract: Energy consumption is one of the top challenges for achieving the next generation of supercomputing. Codesign of hardware and software is critical for improving energy efficiency (EE) for future large-scale systems. Many architectural power-saving techniques have been developed, and most hardware components are approaching physical limits. Accordingly, parallel computing software, including both applications and systems, should exploit power-saving hardware innovations and manage efficient energy use. In addition, new power-aware parallel computing methods are essential to decrease energy usage further. This article surveys software-based methods that aim to improve EE for parallel computing. It reviews the methods that exploit the characteristics of parallel scientific applications, including load imbalance and mixed precision of floating-point (FP) calculations, to improve EE. In addition, this article summarizes widely used methods to improve power usage at different granularities, such as the whole system and per application. In particular, it describes the most important techniques to measure and to achieve energy-efficient usage of various parallel computing facilities, including processors, memories, and networks. Overall, this article reviews the state-of-the-art of energy-efficient methods for parallel computing to motivate researchers to achieve optimal parallel computing under a power budget constraint.
Parallel programming on a high-performance application-runtime
Publisher: Wiley
Date: 25-12-2008
DOI: 10.1002/CPE.1325
Sensitivity of Rabbit Ventricular Action Potential and Ca2+Dynamics to Small Variations in Membrane Currents and Ion Diffusion Coefficients
Publisher: Hindawi Limited
Date: 2013
DOI: 10.1155/2013/565431
Abstract: Little is known about how small variations in ionic currents and Ca 2 + and Na + diffusion coefficients impact action potential and Ca 2 + dynamics in rabbit ventricular myocytes. We applied sensitivity analysis to quantify the sensitivity of Shannon et al. model (Biophys. J., 2004) to 5%–10% changes in currents conductance, channels distribution, and ion diffusion in rabbit ventricular cells. We found that action potential duration and Ca 2 + peaks are highly sensitive to 10% increase in L-type Ca 2 + current moderately influenced by 10% increase in Na + - Ca 2 + exchanger, Na + - K + pump, rapid delayed and slow transient outward K + currents, and Cl − background current insensitive to 10% increases in all other ionic currents and sarcoplasmic reticulum Ca 2 + fluxes. Cell electrical activity is strongly affected by 5% shift of L-type Ca 2 + channels and Na + - Ca 2 + exchanger in between junctional and submembrane spaces while Ca 2 + -activated Cl − -channel redistribution has the modest effect. Small changes in submembrane and cytosolic diffusion coefficients for Ca 2 + , but not in Na + transfer, may alter notably myocyte contraction. Our studies highlight the need for more precise measurements and further extending and testing of the Shannon et al. model. Our results demonstrate usefulness of sensitivity analysis to identify specific knowledge gaps and controversies related to ventricular cell electrophysiology and Ca 2 + signaling.
Virtual microscopy and analysis using scientific workflows
Publisher: IEEE
Date: 12-2009
Constructing School Timetables Using Simulated Annealing: Sequential and Parallel Algorithms
Publisher: Institute for Operations Research and the Management Sciences (INFORMS)
Date: 1991
DOI: 10.1287/MNSC.37.1.98
Abstract: This paper considers a solution to the school timetabling problem. The timetabling problem involves scheduling a number of tuples, each consisting of class of students, a teacher, a subject and a room, to a fixed number of time slots. A Monte Carlo scheme called simulated annealing is used as an optimisation technique. The paper introduces the timetabling problem, and then describes the simulated annealing method. Annealing is then applied to the timetabling problem. A prototype timetabling environment is described followed by some experimental results. A parallel algorithm which can be implemented on a multiprocessor is presented. This algorithm can provide a faster solution than the equivalent sequential algorithm. Some further experimental results are given.
Bridging organizational network boundaries on the grid
Publisher: IEEE
Date: 2005
Translational Research in Computer Science
Publisher: Institute of Electrical and Electronics Engineers (IEEE)
Date: 09-2019
Special Issue: Middleware for Grid Computing
Publisher: Wiley
Date: 15-11-2007
DOI: 10.1002/CPE.1281
Scalable relative debugging
Publisher: Institute of Electrical and Electronics Engineers (IEEE)
Date: 03-2014
DOI: 10.1109/TPDS.2013.86
A Programming Framework for Incremental Data Distribution in Iterative Applications
Publisher: IEEE
Date: 12-2008
Hopfield neural networks for timetabling: formulations, methods, and comparative results
Publisher: Elsevier BV
Date: 02-2003
The WorkWays Problem Solving Environment
Publisher: Elsevier BV
Date: 2014
A case for economy grid architecture for service oriented grid computing
Publisher: IEEE Comput. Soc
Date: 2001
Recent advances in e-Science
Publisher: Elsevier BV
Date: 02-2013
A data-centric framework for debugging highly parallel applications
Publisher: Wiley
Date: 21-11-2015
DOI: 10.1002/SPE.2239
Persistence and communication state transfer in an asynchronous pipe mechanism
Publisher: IEEE
Date: 12-2007
WorkWays: Interactive workflow-based science gateways
Publisher: IEEE
Date: 10-2012
The Virtual Laboratory: A Toolset for Utilising the World-Wide Grid to Design Drugs
Publisher: IEEE
Date: 2002
Simplified grid computing through spreadsheets and netsolve
Publisher: IEEE
Date: 2004
Efficiency analysis in the presence of uncertainty
Publisher: Springer Science and Business Media LLC
Date: 22-08-2010
A general meta-heuristic based solver for combinatorial optimisation problems
Publisher: Springer Science and Business Media LLC
Date: 2001
Executing Large Parameter Sweep Applications on a Multi-VO Testbed
Publisher: IEEE
Date: 05-2007
Pulse propagation in polarization-sensitive semiconductor optical amplifiers
Publisher: IEEE
Date: 07-2006
How precise are reported protein coordinate data?
Publisher: International Union of Crystallography (IUCr)
Date: 27-02-2014
DOI: 10.1107/S1399004713031787
Abstract: Atomic coordinates in the Worldwide Protein Data Bank (wwPDB) are generally reported to greater precision than the experimental structure determinations have actually achieved. By using information theory and data compression to study the compressibility of protein atomic coordinates, it is possible to quantify the amount of randomness in the coordinate data and thereby to determine the realistic precision of the reported coordinates. On average, the value of each C α coordinate in a set of selected protein structures solved at a variety of resolutions is good to about 0.1 Å.
The virtual tea room - experiences with a new type of social space
Publisher: IEEE Comput. Soc
Date: 2001
Model Optimization and Parameter Estimation with Nimrod/O
Publisher: Springer Berlin Heidelberg
Date: 2006
DOI: 10.1007/11758501_96
Extending the Eclipse Parallel Tools Platform Debugger with Scalable Parallel Debugging Library
Publisher: Elsevier BV
Date: 2013
Underworld-GT applied to Guangdong, a tool to explore the geothermal potential of the crust
Publisher: Springer Science and Business Media LLC
Date: 30-01-2015
Robust workflows for science and engineering
Publisher: ACM
Date: 16-11-2009
Relative debugging for a highly parallel hybrid computer system
Publisher: ACM
Date: 15-11-2015
Application deployment over heterogeneous grids using distributed ant
Publisher: IEEE
Date: 2005
RSCS: A Parallel Simplex Algorithm for the Nimrod/O Optimization Toolset
Publisher: Hindawi Limited
Date: 2006
DOI: 10.1155/2006/906394
Abstract: This paper describes a method of parallelisation of the popular Nelder-Mead simplex optimization algorithms that can lead to enhanced performance on parallel and distributed computing resources. A reducing set of simplex vertices are used to derive search directions generally closely aligned with the local gradient. When tested on a range of problems drawn from real-world applications in science and engineering, this reducing set concurrent simplex (RSCS) variant of the Nelder-Mead algorithm compared favourably with the original algorithm, and also with the inherently parallel multidirectional search algorithm (MDS). All algorithms were implemented and tested in a general-purpose, grid-enabled optimization toolset.
An IDE framework for grid application development
Publisher: IEEE
Date: 09-2008
Cluster and Grid Infrastructure for Computational Chemistry and Biochemistry
Publisher: Wiley
Date: 09-06-2005
ISENGARD: an infrastructure for supporting e‐science and grid application development
Publisher: Wiley
Date: 10-10-2010
DOI: 10.1002/CPE.1662
Influence of savanna fire on Australian monsoon season precipitation and circulation as simulated using a distributed computing environment
Publisher: American Geophysical Union (AGU)
Date: 10-2007
DOI: 10.1029/2007GL030879
Parameter Estimation Using Scientific Workflows
Publisher: IEEE
Date: 12-2008
The Virtual Laboratory: a toolset to enable distributed molecular modelling for drug design on the World-Wide Grid
Publisher: Wiley
Date: 2003
DOI: 10.1002/CPE.704
RSCS: A Parallel Simplex Algorithm for the Nimrod/O Optimization Toolset
Publisher: IEEE
Date: 2004
Addressing Mechanisms for Large Virtual Memories
Publisher: Oxford University Press (OUP)
Date: 08-1992
A debugging and testing tool for supporting software evolution
Publisher: Springer Science and Business Media LLC
Date: 08-1996
DOI: 10.1007/BF00132573
A Local Sensitivity Analysis Method for Developing Biological Models with Identifiable Parameters: Application to L-type Calcium Channel Modelling
Publisher: IEEE
Date: 12-2010
Scheduling Aircraft Landings—The Static Case
Publisher: Institute for Operations Research and the Management Sciences (INFORMS)
Date: 05-2000
DOI: 10.1287/TRSC.34.2.180.12302
Abstract: In this paper, we consider the problem of scheduling aircraft (plane) landings at an airport. This problem is one of deciding a landing time for each plane such that each plane lands within a predetermined time window and that separation criteria between the landing of a plane and the landing of all successive planes are respected. We present a mixed-integer zero–one formulation of the problem for the single runway case and extend it to the multiple runway case. We strengthen the linear programming relaxations of these formulations by introducing additional constraints. Throughout, we discuss how our formulations can be used to model a number of issues (choice of objective function, precedence restrictions, restricting the number of landings in a given time period, runway workload balancing) commonly encountered in practice. The problem is solved optimally using linear programming-based tree search. We also present an effective heuristic algorithm for the problem. Computational results for both the heuristic and the optimal algorithm are presented for a number of test problems involving up to 50 planes and four runways.
Scalable parallel debugging with statistical assertions
Publisher: ACM
Date: 25-02-2012
The RMIT Data Flow Computer: A Hybrid Architecture
Publisher: Oxford University Press (OUP)
Date: 03-1990
A very high speed architecture for simulated annealing
Publisher: Institute of Electrical and Electronics Engineers (IEEE)
Date: 05-1992
DOI: 10.1109/2.144393
Multi-objective optimisation in scientific workflow
Publisher: Elsevier BV
Date: 2017
Are you interested in computers and electronics?
Publisher: ACM
Date: 12-2000
Integration of modern data management practice with scientific workflows
Publisher: IEEE
Date: 10-2012
Revising the diagnosis of personality disorder: Can it be single, clinical and factorial?
Publisher: SAGE Publications
Date: 16-11-2017
Parameter Exploration in Science and Engineering Using Many-Task Computing
Publisher: Institute of Electrical and Electronics Engineers (IEEE)
Date: 06-2011
ERI sorting for emerging processor architectures
Publisher: Elsevier BV
Date: 08-2009
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