Publications
37 results found
Chue Hong NP, Cohen J, Jay C, 2021, Understanding Equity, Diversity and Inclusion Challenges Within the Research Software Community, Cham, International Conference on Computational Science - ICCS 2021, SE4Science Workshop, Publisher: Springer Verlag, ISSN: 0302-9743
Cohen J, Katz DS, Barker M, et al., 2021, The four pillars of research software engineering, IEEE Software, Vol: 38, Pages: 97-105, ISSN: 0740-7459
Building software that can support the huge growth in data and computation required by modern research needs individuals with increasingly specialist skill sets that take time to develop and maintain. The Research Software Engineering movement, which started in the UK and has been built up over recent years, aims to recognise and support these individuals. Why does research software matter to professional software development practitioners outside the research community? Research software can have great impact on the wider world and recent progress means the area can now be considered as a more realistic option for a professional software development career. In this article we present a structure, along with supporting evidence of real-world activities, that defines four elements that we believe are key to providing comprehensive and sustainable support for Research Software Engineering. We also highlight ways that the wider developer community can learn from, and engage with, these activities.
Cohen J, Nowell J, Mortari F, et al., 2019, london-escience/tempss: v0.5
london-escience/tempss: v0.5
Cohen J, Katz DS, Barker M, et al., 2018, Building a Sustainable Structure for Research Software Engineering Activities, 2018 IEEE 14th International Conference on e-Science (e-Science), Publisher: IEEE
Cohen J, Marcon J, Turner M, et al., 2018, Simplifying high-order mesh generation for computational scientists, 10th International Workshop on Science Gateways, Publisher: CEUR Workshop Proceedings, ISSN: 1613-0073
Computational modelling is now tightly integrated into many fields of research in science and industry. Computational fluid dynamics software, for example, gives engineers the ability to model fluid flow around complex geometries defined in Computer-Aided Design (CAD) packages, without the expense of constructing large wind tunnel experiments. However, such modelling requires translation from an initial CAD geometry to a mesh of many small elements that modelling software uses to represent the approximate solution in the numerical method. Generating sufficiently high-quality meshes for simulation is a time-consuming, iterative and error-prone process that is often complicated by the need to interact with multiple command-line tools to generate and visualise the mesh data. In this paper we describe our approach to overcoming this complexity through the addition of a meshing console to Nekkloud, a science gateway for simplifying access to the functionality of the Nektar++ spectral/hp element framework. The meshing console makes use of the NekMesh tool in Nektar++ to help reduce the complexity of the mesh generation process. It offers a web-based interface for specifying parameters, undertaking meshing and visualising results. The meshing console enables Nekkloud to offer support for a full, end-to-end simulation pipeline from initial CAD geometry to simulation results.
Yadav P, Charalampidis I, Cohen J, et al., 2018, A Collaborative Citizen Science Platform for Real-Time Volunteer Computing and Games, IEEE TRANSACTIONS ON COMPUTATIONAL SOCIAL SYSTEMS, Vol: 5, Pages: 9-19, ISSN: 2329-924X
Cohen J, Rayna T, Darlington J, 2017, Understanding Resource Selection Requirements for Computationally Intensive Tasks on Heterogeneous Computing Infrastructure, 13th International Conference on Economics of Grids, Cloud, Systems and Services, Publisher: Springer International Publishing, Pages: 250-262, ISSN: 0302-9743
Cohen J, Moxey D, Cantwell C, et al., 2015, POSITION PAPER: Ensuring an Effective User Experience when Managing and Running Scientific HPC Software, IEEE ACM 1st International Workshop on Software Engineering for High Performance Computing in Science (SE4HPCS), Publisher: IEEE, Pages: 56-59
Cohen J, Cantwell C, Moxey D, et al., 2015, TemPSS: A service providing software parameter templates and profiles for scientific HPC, IEEE International Conference On eScience, Publisher: IEEE, Pages: 78-87, ISSN: 2325-372X
Mead MI, Popoola OAM, Stewart GB, et al., 2013, The use of electrochemical sensors for monitoring urban air quality in low-cost, high-density networks, ATMOSPHERIC ENVIRONMENT, Vol: 70, Pages: 186-203, ISSN: 1352-2310
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- Citations: 461
Cohen J, Moxey D, Cantwell C, et al., 2013, Nekkloud: A Software Environment for High-order Finite Element Analysis on Clusters and Clouds, 2013 IEEE INTERNATIONAL CONFERENCE ON CLUSTER COMPUTING (CLUSTER), ISSN: 1552-5244
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- Citations: 2
Cohen J, Filippis I, Woodbridge M, et al., 2013, RAPPORT: running scientific high-performance computing applications on the cloud, Philos Transact A Math Phys Eng Sci, Vol: 371, ISSN: 1364-503X
Cloud computing infrastructure is now widely used in many domains, but one area where there has been more limited adoption is research computing, in particular for running scientific high-performance computing (HPC) software. The Robust Application Porting for HPC in the Cloud (RAPPORT) project took advantage of existing links between computing researchers and application scientists in the fields of bioinformatics, high-energy physics (HEP) and digital humanities, to investigate running a set of scientific HPC applications from these domains on cloud infrastructure. In this paper, we focus on the bioinformatics and HEP domains, describing the applications and target cloud platforms. We conclude that, while there are many factors that need consideration, there is no fundamental impediment to the use of cloud infrastructure for running many types of HPC applications and, in some cases, there is potential for researchers to benefit significantly from the flexibility offered by cloud platforms.
North R, Cohen J, Wilkins S, et al., 2009, Field deployments of the environmental monitoring, Traffic Engineering and Control, Vol: 50, Pages: 484-488, ISSN: 0041-0683
This paper describes how the technologies developed in the MESSAGE project have been deployed in a series of real-world experiments to examine the relationship between transport and air pollution. Three different sensor systems have been developed to allow deployment on infrastructure, people and vehicles for both short and long term studies. This paper describes the field trials conducted using each of these systems in turn. The initial conclusions regarding the coordinated use of these sensors in the management of transport and air pollution are presented.
Cohen J, North R, Wilkins S, et al., 2009, Creating the message infrastructure, Traffic Engineering and Control, Vol: 50, Pages: 480-483, ISSN: 0041-0683
MESSAGE set out to make use of the ever-increasing power of computer infrastructure in order to support the capture, processing, archiving, analysis and visualisation of pollution data. This paper describes how the MESSAGE e-Science architecture was developed facilitating the whole process from the capture of data through to its use. This covers the difficult process of taking data from sensor nodes, pre-processing it where necessary and then storing it in an infrastructure capable of making it available for use in a wide range of different applications and processes.
Cohen J, Fuchs B, North R, et al., 2009, Computational grid-based data management and analysis for a mobile sensor network deployment
Sensor network data can provide manifold opportunities to extract information from a target environment and understand it more accurately. In the case of environmental pollution, complex air movement and dispersion patterns mean that a large amount of data is needed to analyse and model pollution episodes effectively. To enable improved pollution management, captured data must undergo processing that is often computationally intensive and must be carried out in near real-time. This paper describes work in the MESSAGE project to design, build and trial a mobile sensor network deployment using a Grid-based infrastructure for data management and analysis.
North R, Van Baalen J, Cohen J, et al., 2009, On-demand evaluation of alternative strategies for environmental traffic management
Across the world, air quality regulations are breached due to localized high pollution episodes, or "hotspots". Advances in air pollution monitoring techniques enable hotspots to be identified more effectively; however challenges remain as to how best to reduce the incidence and impact of these episodes. Where road traffic is the dominant source of pollutants, ITS measures, including alternative traffic management strategies, may be deployed to mitigate the hotspot and contribute towards regulatory compliance. However, the effective evaluation of such ITS measures requires the use of computationally expensive microscopic traffic and emissions models in order to appropriately represent changes in vehicle emission profiles. This paper demonstrates how advances in distributed computing can be combined with the latest generation of traffic and emissions models to provide robust and rapid evaluation of alternative traffic management scenarios.
Cohen J, Darlington J, 2009, HIGH PERFORMANCE UTILITY RESOURCE DEPLOYMENT AND BROKERING FOR SCIENTIFIC APPLICATIONS, ASME International Design Engineering Technical Conferences/Computers and Information in Engineering Conference, Publisher: AMER SOC MECHANICAL ENGINEERS, Pages: 1115-1124
Cohen J, Richardson C, Harder U, et al., 2009, Node-level Architecture Design and Simulation of the MAGOG Grid Middleware, Seventh Australasian Symposium on\r\nGrid Computing and e-Research (AusGrid 2009), Publisher: Australian Computer Society, Pages: 57-66, ISSN: 1445-1336
The Middleware for Activating the Global Open Grid (MAGOG) provides a novel solution to the problem of discovering remote resources in a globally interconnected environment such as the Internet, in situations where users want to gain access to such resources to carry out remote computation. While existing Grid middleware enables the building of Grid infrastructures within closed environments where all users are known to each other, or where there is some preexisting relationship between resource providers and users, the true Grid model should enable any users at any location to access remote resources without any prior relationship with the provider. MAGOG is a peer-to-peer based architecture that provides the means to enable discovery of resources in such an environment and to enable the agreement of pricing and Service Level Agreements (SLAs) for the use of these resources. This paper provides a high-level overview of the design of MAGOG and early simulation work that has been carried out to verify this design. It then focuses on the initial design for the middleware client that players in the market will need to deploy in order to become a node in the environment.
Cohen J, Darlington J, 2008, High performance utility resource deployment and brokering for scientific applications, Proceedings of the ASME Design Engineering Technical Conference, Vol: 3, Pages: 1115-1124
As computing power continues to grow and high performance computing use increases, ever bigger scientific experiments and tasks can be carried out. However, the management of the computing power necessary to support these ever growing tasks is getting more and more difficult. Increased power consumption, heat generation and space costs for the larger numbers of resources that are required can make local hosting of resources too expensive. Emergence of utility computing platforms offers a solution. We present our recent work to develop an update to our computational markets environment for support of application deployment and brokering across multiple utility computing environments. We develop a prototype to demonstrate the potential benefits of such an environment and look at the longer term changes in the use of computing that might be enabled by such developments. Copyright © 2008 by ASME.
North R, Richards M, Cohen J, et al., 2008, A mobile environmental sensing system to manage transportation and urban air quality, IEEE International Symposium on Circuits and Systems, Publisher: IEEE, Pages: 1994-+, ISSN: 0271-4302
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- Citations: 4
McGough S, Lee W, Cohen J, et al., 2007, ICENI, Workflows for e-Science: Scientific Workflows for Grids, Publisher: Springer, ISBN: 978-1-84628-519-6
Performing large-scale science is becoming increasingly complex.\r\nScientists have resorted to the use of computing tools to enable\r\nand automate their experimental process. As acceptance of the\r\ntechnology grows, it will become commonplace that computational\r\nexperiments will involve larger data sets, more computational\r\nresources, and scientists (often referred to as e-Scientists)\r\ndistributed across geographical and organizational boundaries. We\r\nsee the {\\em Grid} paradigm as an abstraction to a large\r\ncollection of distributed heterogeneous resources, including\r\ncomputational, storage, and instrument elements, controlled and\r\nshared by different organizations. Grid computing should\r\nfacilitate the e-Scientist's ability to run applications in a\r\ntransparent manner.\r\n
Altmann J, Courcoubetis C, Darlington J, et al., 2007, GridEcon - The economic-enhanced next-generation internet, 4th International Workshop on Grid Economics and Business Models (GECON 2007), Publisher: SPRINGER-VERLAG BERLIN, Pages: 188-+, ISSN: 0302-9743
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- Citations: 8
Steele I, Clay N, Lee W, et al., 2006, A free market in telescope time II: a test implementation, Publisher: SPIE
Darlington J, Cohen J, Lee WH, 2006, An architecture for a next-generation Internet based on web services and utility computing, Enabling Technologies: Infrastructure for Collaborative Enterprises, 2006. WETICE '06. 15th IEEE International Workshops on, Pages: 169-174, ISSN: 1524-4547
Cohen J, Lee W, Darlington J, et al., 2006, A service-oriented utility grid architecture utilising pay-per-use resources, 1st International Conference on Communication Systems Software and Middleware, Publisher: IEEE, Pages: 612-+
Panagiotidi S, Cohen J, Darlington J, et al., 2006, Service-enabling legacy applications for the GENIE project, 5th UK e-Science All Hands Meeting (AHM 2006), Publisher: NATL E-SCIENCE CENTRE, Pages: 305-+
Cohen J, Lee W, Darlington J, 2005, Payment and Negotiation for the Next Generation Grid, Concurrency and Computation: Practice and Experience, ISSN: 1532-0626
McGough S, Cohen J, Darlington J, et al., 2005, An End-to-end Workflow Pipeline for Large-scale Grid Computing, Vol: 3, Pages: 259-281
In this paper we describe a service-based, software architecture that enables end-to-end, high-level workflow processing in a Grid environment consisting of many heterogeneous resources. Our architecture is essentially a pipeline that extends from the abstract application specification phase to the deployment and execution stages through to returning the results to the user. We envision a large-scale Grid environment that contains heterogeneous resources. Our architecture caters for flexible deployment, performance, reliability and charging for resource usage. These are addressed at the specification level as well as at the realisation (brokering) and execution levels. The proposed architecture is derived from previous work in LeSC that has produced the ICENI pipeline, and our experience with e-Science projects, such as GENIE, e-Protein and RealityGrid from which we derive a set of key requirements.\r\n
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