CeSC - Scholarly Works in eScience
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Item Open Access The use of electrochemical sensors for monitoring urban air quality in low-cost, high-density networks(Elsevier BV, 2013) Mead, MI; Popoola, OAM; Stewart, GB; Landshoff, P; Calleja, M; Hayes, M; Baldovi, JJ; McLeod, MW; Hodgson, TF; Dicks, J; Lewis, A; Cohen, J; Baron, R; Saffell, JR; Jones, RL; Popoola, Olalekan [0000-0003-2390-8436]; Jones, Roderic [0000-0002-6761-3966]Measurements at appropriate spatial and temporal scales are essential for understanding and monitoring spatially heterogeneous environments with complex and highly variable emission sources, such as in urban areas. However, the costs and complexity of conventional air quality measurement methods means that measurement networks are generally extremely sparse. In this paper we show that miniature, low-cost electrochemical gas sensors, traditionally used for sensing at parts-per-million (ppm) mixing ratios can, when suitably configured and operated, be used for parts-per-billion (ppb) level studies for gases relevant to urban air quality. Sensor nodes, in this case consisting of multiple individual electrochemical sensors, can be low-cost and highly portable, thus allowing the deployment of scalable high-density air quality sensor networks at fine spatial and temporal scales, and in both static and mobile configurations.Item Open Access The National Transport Data Framework(2008-08-18T13:53:32Z) Landshoff, Peter Vincent; Polak, JohnThe NTDF is designed to be a resource for data owners to deposit descriptions into a central catalogue, so that people can search for data and find data and understand their characteristics. The value of this is to individuals, to commercial organizations, and to public bodies. For example, services that provide better information to travellers will help to make their journey less stressful and persuade them to make more use of public transport. Transport operators need very diverse information to help them plan developments to their services: demographic, geographical, economic etc. And policy makers need a similar range of information to help them decide how to divide their budget and afterwards to evaluate how valuable it has been.Item Open Access Multi-Site Videoconferencing for the UK e-Science Programme(National e-Science Centre, 2002) Booth, Stephen; Brooke, John; Caldwell, Kate; Carver, Liz; Daw, Michael; De, Roure David; Flavell, Alan; Galvez, Philippe; Gilmore, Brian; Hughes, Henry; Juby, Ben; Judson, Ivan; Miller, Jim; Newman, Harvey; Osland, Chris; Rogers, SueItem Open Access FutureGRID: A Program for long-term research into GRID systems architecture(2008-06-26) Crowcroft, Jon; Hand, SM; Harris, TL; Herbert, AJ; Parker, Michael A; Pratt, IA; Crowcroft, Jonathon [0000-0002-7013-0121]; Parker, Andy [0000-0001-9798-8411]This is a project to carry out research into long-term GRID architecture, in the University of Cambridge Computer Laboratory and the Cambridge eScience Center, with support from the Microsoft Research Laboratory, Cambridge. It is part of a larger vision for future systems architectures for public computing platforms, including both scientitic GRID and commodity level computing such as games, peer2peer computing and storage services and so forth, based on work in the laboratories in recent years into massively scaleable distributed systems for storage, computation, content distribution and collaboration[26].Item Open Access Reliable ligh-speed Grid data delivery using IP multicast(2008-06-26) Jeacle, Karl; Crowcroft, Jon; Crowcroft, Jonathon [0000-0002-7013-0121]In recent years, much work has been done on attempting to scale multicast data transmissions to hundreds or thousands of receivers. In today's Grid environments, however, a typical application might involve bulk data transfer to just ten or twenty sites. Using multicast for this type of application can provide significant benefits including reduced load on the transmitter, an overall reduction in network traffic, and consequently shorter data transfer times. In this project, we are investigating how multicast can be exploited within such an environment without requiring major changes to applications or underlying networks. The approach taken is to modify TCP to support multicast transfers, and run this modified TCP engine over UDP as a userspace transport protocol. We describe the work to date on the design and implementation, and provide some early experimental results.Item Open Access A semantic Grid for molecular science(2008-06-26) Murray-Rust, Peter; Glen, Robert C; Rzepa, Henry S; Stewart, James JP; Townsend, Joseph A; Willighagen, Egon L; Yong, ZhangThe properties of molecules have very well defined semantics and allow the creation of a semantic GRID. Markup languages (CML - Chemical Markup Language) and dictionary-based ontologies have been designed to support a wide range of applications, including chemical supply, publication and the safety of compounds. Many properties can be computed by Quantum Mechanical (QM) programs and we have developed a "black-box" system based on XML wrappers for all components. This is installed on a Condor system on which we have computed properties for 250, 000 compounds. The results of this will be available in an OpenData/OpenSource peer-to-peer (P2P) system (WorldWide Molecular Matrix - WWMM).Item Open Access Visualisation and Grid applications of electromagnetic scattering from aircraft(2008-06-26) Spivack, Mark; Usher, Andrew; Yang, Xiaobo; Hayes, Mark; Spivack, Mark [0000-0002-1876-950X]Electromagnetic scattering behaviour plays a central role in the design of aircraft and other complex structures. This paper describes progress on visualisation tools in this area and on initial development of a web portal to enable scientists at remote locations to collaborate.Item Open Access Distributed computational fluid dynamics(2003) Jenkins, KW; Yang, X; Hayes, M; Cant, RS; Cant, Stewart [0000-0003-1851-6665]Computational fluid dynamics simulations of relevance to jet-engine design, for instance, are extremely computationally demanding and the use of large-scale distributed computing will allow the solution of problems that cannot be tackled using current resources. It is often appropriate to leave the large datasets generated by CFD codes local to the compute resource in use at the time. This naturally leads to a distributed database of results that will need to be federated as a coherent resource for the engineering community. We describe the use of Globus and Condor within Cambridge for sharing computer resources, progress on defining XML standards for the annotation of CFD datasets and a distributed database framework for them.Item Open Access Applications of Grid techniques in the CFD field(2008-06-26) Yang, Xiaobo; Hayes, MarkBesides the widely used Reynolds-averaged Navier-Stokes (RANS) solver, Large Eddy Simulation (LES) and Direct Numerical Simulation (DNS) are becoming more and more practical in today's Computational Fluid Dynamics (CFD) studies. All these techniques are in constant pursuit of ever larger computing resources in order to produce acceptable and reasonable results. A new technique, the Grid technique, offers the possibility of aggregating the capabilities of geographically distributed computing resources. In this paper, a brief description of the Grid technique is presented followed by the current progress in the study of its application to CFD between the Cambridge eScience Centre and the CFD group at the Cambridge University Engineering Department.Item Open Access The Cambridge CFD grid for large-scale distributed CFD applications(Elsevier BV, 2005-01-01) Yang, X; Hayes, M; Jenkins, K; Cant, S; Cant, Stewart [0000-0003-1851-6665]The Cambridge CFD (computational fluid dynamics) Grid is a distributed problem solving environment for large-scale CFD applications set up between the Cambridge eScience Centre and the CFD Lab in the Engineering Department at the University of Cambridge. A Web portal, the Cambridge CFD Web Portal (CamCFDWP) has been developed to provide transparent integration of the CFD applications to non-computer scientist end users. In addition to the basic services provided of authentication, job submission and file transfer, the CamCFDWP makes use of CML (extensive markup language) techniques which make it possible to easily share datasets between different groups of users. A Web service interface has recently been implemented for a CFD database which could be integrated in the Cam CFDWP in the near future. We also review how this Web service can be made secure using SSL, XML signatures and XML encryption.Item Open Access The use of CML and CML in Computational Chemistry and Physics Programs(2008-06-26) Wakelin, Jon; Garcia, A; Murray-Rust, PeterThis work addresses problems associated with data exchange and data representation in the computational chemistry and physics communities. Recent computational developments, such as Condor and the Grid, have paved the way for new kinds of simulations that demand more rigorous data handling. To this end, the paper discusses the use of XML and the Chemical Markup Language (CML) in theoretical chemistry and physics. Extensions to the core CML language, known as CMLComp, are also discussed. However, the majority of atomic scale simulation software is written in Fortran. Fortran's lack of XML support represents a potential barrier to the adoption of CML in these fields. This has prompted the authors to develop XML and CML processing tools for Fortran, including native SAX and DOM implementations, as well as libraries for generating well formed XML and CML. These libraries have been used to extend existing simulation packages to work with the CML and CMLComp languages. Finally, we give a practical example that highlights how these XML aware applications can be effectively used as workflow components in complex chemical and physical simulations.Item Open Access JUMBO - An XML infrastructure for eScience(2008-06-26) Yong, Zhang; Murray-Rust, Peter; Dove, Martin T; Glen, Robert C; Rzepa, Henry S; Townsend, Joseph A; Tyrrell, Simon M; Wakelin, Jon; Willighagen, Egon LJUMBO is an OpenSource toolkit addressing the semantic and ontological impedances that are major barriers to interoperability in computational chemistry and physics. Users build XMLSchemas from generic XML components to support particular computational tasks, such as high-throughput chemistry. JUMBO components provide a complete semantic description of information to or from a code such as MOPAC or GAMESS. Codes are edited to use JUMBO libraries as adapters to program-independent XML objects, or output is transduced using a generic parser, JUMBOMarker. The JUMBO system is designed for flexible collaborative contributions.Item Open Access Extending Globus to support Multicast Transmission(2008-06-26) Jeacle, Karl; Crowcroft, Jon; Crowcroft, Jonathon [0000-0002-7013-0121]The Globus Toolkit is an open source software toolkit that has become the de-facto standard for middleware used to build Grid services. Globus XIO is an eXtensible Input/Output library for Globus. It provides a POSIX-like API to swappable I/O implementations - essentially "I/O plugins" for Globus. TCP-XM is a modified TCP engine that supports multicast transmission. We have taken this protocol and wrapped it using XIO to extend the Globus Toolkit to support multicast transmission. This paper describes the implementation and operation of our Globus XIO multicast transport driver. It provides an overview of the TCP-XM protocol design, and describes some initial experimental results.Item Open Access CamGrid: Experiences in constructing a university-wide, Condor-based grid at the University of Cambridge(2008-06-26) Calleja, Mark; Beckles, B; Keegan, M; Hayes, Mark; Parker, A; Dove, Martin TIn this article we describe recent work done in building a university-wide grid at the University of Cambridge based on the Condor middleware [1]. Once the issues of stakeholder concerns (e.g. security policies) and technical problems (e.g. firewalls and private IP addresses) have been taken into account, a solution based on two separate Condor environments was decided on. The first of these is a single large pool administered centrally by the University Computing Service (UCS) and the second a federated service of flocked Condor pools belonging to various departments and run over a Virtual Private Network (VPN). We report on the current status of this ongoing work.Item Open Access Developing web services in a computational grid environment(2004) Yang, X; Hayes, M; Usher, A; Spivack, M; Spivack, Mark [0000-0002-1876-950X]Grid and Web services are both hot topics today. In this paper, we will present some ongoing work and planned future work at the Cambridge eScience Centre. After an introduction to these technologies in the context of Grid applications development, we describe two use-cases: a database of results in computational fluid dynamics (CFD) and a small computational Grid for aircraft engineering design. As Grid services are moving towards Web services, we continue to make use of the Globus Toolkit v2.4 (GT2.4), without adopting the Open Grid Services Architecture (OGSA) wholesale. In our scenario, GT2.4 integrates distributed computing resources including HPC and clusters while Web services wrap the scientific code as a service.