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Evaluation of Google App Engine for hosting GIS services (2010)
We have performed a short study in which an OGC-compliant Web Map Service was implemented in the Google App Engine environment, in order to test GAE's suitability for hosting GIS services. More details can be found at the project's website.
Contact: Dr Jon Blower
MashMyData (Feb 2010 - Jan 2011)
This project will develop a proof-of-concept web portal to demonstrate the intercomparison of environmental datasets on the web. We will use the latest Web GIS technologies to allow scientists to visualize and intercompare datasets without the need to understand the low-level technical details of the data's format or physical location. Test case scientists will be able to simultaneously visualize data from many sources, including their own uploaded data, data shared by their colleagues and third-party datasets (both public and restricted-access), as well as being able to perform simple quantitative comparison calculations, such as calculating the misfit between a numerical model and a set of observations over a user-selected region of space and time.
This project is a collaboration between the ReSC and the Centre for Environmental Data Archival (CEDA). It is funded by NERC under the Technologies Proof of Concept programme
Contact: Dr Alastair Gemmell
BlogMyData (Feb-Oct 2010)
This project will combine two existing systems to create a new Virtual Research Environment for environmental scientists. By combining the capabilities of an online environmental data visualization system with a sophisticated blogging and collaboration engine, we will create a new facility for scientists to collaborate on important tasks of data interpretation, focusing on the diagnosis of the latest cutting-edge numerical simulations of the climate and oceans.
This project is a collaboration between the ReSC and the Chemistry Department of the University of Southampton. It is funded by JISC under the Virtual Research Environment Rapid Innovation theme, and was enabled by the e-Research South platform grant.
Project website and blog
Contact: Dr Jon Blower
MyOcean (2009 - 2012)
MyOcean is the implementation project of the GMES Marine Core Service, aiming at deploying the first concerted and integrated pan-European capacity for Ocean Monitoring and Forecasting. MyOcean builds upon past projects including MERSEA and ECOOP.
The ReSC's role in MyOcean is to provide an INSPIRE-compliant visualization system for ocean data based upon the OGC Web Map Service.
Contact: Dr Jon Blower
e-Research South (2008 - present)
e-Research South is an e-Research consortium consisting of the Universities of Oxford, Reading and Southampton and the STFC e-Science Centre. e-Research South aims to create a sustainable research platform across participating organisations and their collaborators by applying innovative computing technology to interdisciplinary problems of increasing scale and complexity.
Contact: Dan Bretherton
Dynamic online visualization of large-volume environmental data (2007 - present)
The ReSC has produced a website that demonstrates how Web-GIS and Google Earth technology can be used to interactively visualize terabytes of environmental data online, without the need to download large data files. Data from different sources can be displayed and explored using a web interface and Google Earth. Although the demonstrator only currently contains output from numerical models and satellite analyses, exactly the same techniques can be used to explore many types of geospatial data. This technology is being applied in the European projects MERSEA and ECOOP.
Contact: Dr Jon Blower
Demonstrator website, Paper (PDF, preprint), Poster (PDF), Software User stories
ECOOP (2007 - 2010)
The goal of ECOOP is to build up a sustainable pan-European capacity in providing timely, quality assured marine service (including data, information products, knowledge and scientific advices) in European coastal-shelf seas.
The ReSC is involved in ECOOP in two ways. Firstly, the ncWMS/godiva2 software is being used to form a 'Dynamic Quick View' (DQV) facility for the visualisation of coastal oceanography models run at the other ECOOP partners. This tailored version of the software enables users to obtain a quick look at the model output to view the main trends in the data, and to rapidly check for any errors or problems.
Secondly, the ReSC is involved in the production of two 'DEcision Support Systems' (DESS). These systems form demonstrations to illustrate the ways in which European coastal operational oceanography datasets can be presented to aid users and decision makers in specific marine sectors. The ReSC has developed a North Sea Fisheries DESS and a North Sea Ecosystem DESS.
Contacts: Dr Jon Blower, Dr Alastair Gemmell.
GENESI-DR (2007 - 2010)
ReSC, in collaboration with the University's Meteorology Department, is participating in the ESA-led, European Commission-funded GENESI-DR project (Ground European Network for Earth Science Interoperations - Digital Repositories). GENESI-DR aims to provide reliable, easy, long-term access to Earth Science data via the Internet. ReSC is developing a Visualization and Validation Service (VVS) for analysing and visualising data from the GlobModel validation application.
Contacts: Dr Jon Blower, Dr Stefano Migliorini
Article in ESA news
G-Rex: Grid Remote EXecution (2007 - present)
G-Rex is a means of wrapping command-line programs and allowing them to be used remotely over the Internet. When deployed as a G-Rex service, a program can be run from anywhere on the Internet exactly as if it were a local program. G-Rex services can be composed into work-flows using simple shell scripts, where the G-Rex client program, grexrun, is used instead of the remote program. Output from the remote program is automatically transferred back to the user while the program is running, and each output file is deleted from the remote system when it is no longer needed. In other words, output from the remote program effectively becomes output from grexrun. G-Rex can run programs on remote clusters, high performance computing systems designed for parallel processing. G-Rex is being used as the core grid middleware for the NERC Cluster Grid (see below).
Contact: Dan Bretherton
NERC Cluster Grid (2007 - present)
The NERC Cluster Grid is a network of high performance clusters belonging to Natural Environment Research Council (NERC) research institutes in different parts of the country. The Grid is being used by NERC scientists to run large ocean, atmosphere and climate models that require between 4 and 100 processors to run. Scientists use the G-Rex middleware (see above) to run their models on clusters situated at other institutes. The models can output up to a Terabyte of data during runs lasting several days. G-Rex ensures that this output is brought back to the scientist while a model is running. This allows the scientific progress of the run to be monitored, and prevents large amounts of data accumulating at the remote institute where there may not be enough space to store it. The Ganglia distributed monitoring system collects load and performance data from all the clusters in the Grid. The NERC Cluster Grid Portal includes the Ganglia Web Frontend and cluster activity reports. More information about the NERC Cluster Grid and G-Rex can be found in the following poster and presentation material.
- ClusterGridPoster-AHM2007_v1.5.pdf: Poster for UK e-Science All Hands Meeting, September 2007
- G-Rex_Presentation-CCF_Nov07.pdf: Presentation for NERC Cluster Compute Forum, November 2007
Contact: Dan Bretherton
OceanDIVA: Ocean Data Inter-comparison and Visualization Application (2007 - present)
OceanDIVA was developed as a model-data comparison and validation tool for oceanography that can be used with standards-compliant datasets across the internet.
OceanDIVA is a Java web application developed by, and hosted at the Reading e-Science Centre, within the Environmental Systems Science Centre at the University of Reading. It produces data on the misfit between in-situ ocean observation profiles and gridded model output. The in-situ data and the model data must be in NetCDF format, and can be located either locally at Reading, or read in remotely via the OPeNDAP protocol. Output can take two forms - either KMZ (zipped KML) for viewing in Google Earth, or a series of png images of Probability Density Functions (PDFs) of model-observations misfits in selected ocean regions.
KMZ output allows the user to view the geospatial distribution of the data and misfits [screenshot], whereas the PDF output allows the user to get more statistical information about the distribution of misfits within a given region(s) [screenshot].
![[screenshot]](OceanDIVA/KMZ_screenshot_TLev.jpg){kind=link}
![[screenshot]](OceanDIVA/PDF_screenshot_ZLev.png){kind=link}
Contact: Alastair Gemmell
Climate-G (2008-present)
The Climate-G testbed provides an experimental large scale data environment for climate change addressing challenging data and metadata management issues. The main scope of Climate-G is to allow scientists to carry out geographical and cross-institutional climate data discovery, access, visualization and sharing. Climate-G is a multidisciplinary collaboration involving both climate and computer scientists and it currently involves several partners including: Centro Euro-Mediterraneo per i Cambiamenti Climatici (CMCC), Institut Pierre-Simon Laplace (IPSL), Fraunhofer Institut für Algorithmen und Wissenschaftliches Rechnen (SCAI), National Center for Atmospheric Research (NCAR), University of Reading, University of Catania and University of Salento.
Contact: Jon Blower
Sharing and visualizing large-volume environmental data (SHAVER) (2007 - 2009)
SHAVER is a one-year NERC Knowledge Transfer project (January-December 2008). The ReSC will work with colleagues at Unidata, the University of Tasmania and the Open Planning Project to transfer key innovations from the DEWS project into two widely-used software systems for geospatial data access and visualization: THREDDS and GeoServer. This project will enable the efficient sharing and visualization of four-dimensional environmental data using OGC Web Services.
Contact: Dr Jon Blower
NERC Data Portals Prototype Project (2007 - 2008)
The ReSC participated in the development of a prototype web portal for discovering and visualizing environmental data. Using technologies from the NERC Data Grid, the portal allows users to search for, visualize and overlay many different datasets, including geological maps, land usage maps, oceanographic data and weather station data. Data are displayed using Google Earth or a web-based geographic information system.
Grid for Coupled Ensemble Prediction (GCEP) (2006-2009)
GCEP is a NERC e-Science project involving the ReSC, CGAM, the British Antarctic Survey (BAS) and CCLRC. The purpose of GCEP is to test the sensitivity of the climate on decadal timescales to initial conditions of the ocean, and the distributions of ice, soil moisture and snow cover. If any aspect of climate can be predicted on these timescales, it is these slowly-varying properties that will contain the necessary information. We shall run ensembles of the Hadley Centre's full HadCM3 model on a Grid of PC clusters in Reading, BAS and RAL, and also on the National Grid Service.
This project is in its early stages: please see this poster for more information.
Contact: Prof. Keith Haines
A Virtual Research Environment for Archaeology
The Virtual Environments for Research in Archaeology (VERA) project aims to produce a fully-fledged virtual research environment for the archaeological community. It will address user needs, enhancing the means of efficiently documenting archaeological excavation and its associated finds, and create a suitable Web portal that provides enhanced tools for the user community. VERA aims to develop utilities that help encapsulate the working practices of current research archaeologists unfamiliar with virtual research environments.
Contact: Prof. Mark Baker
MERSEA (2002-2008)
MERSEA (Marine Environment and Security for the European Area) is an EU Framework VI project linked to the international ocean forecasting experiment GODAE. The overall objectives of MERSEA are:
- to integrate data from existing spaceborne observations and in-situ monitoring networks through ocean modelling and data assimilation systems (Topaz, Mercator, Foam, MFS), for a better understanding of the ocean.
- to deliver information products related to maritime transports, tourism, exploitation and management of ocean resources (offshore oil industry, fisheries, aquaculture farms), and environmental issues, from local (pollution crisis, diffusive pollution, impact studies) to global (ocean climate variability and change, contribution to seasonal climate prediction).
- to demonstrate the opportunity and importance of such integrated systems (in-situ data, EO data and models) for hindcast, nowcast and forecast purposes in the context of specific GMES requirements and demands, and to stimulate the market by demonstrating and convincing this community that are cost-effective and highly needed. The MERSEA project is directly related to the GMES Action Plan, and will be the European portal for GODAE.
ReSC are contributing to this project by providing access to real-time Met Office data via the Live Access Server (LAS) and the GODIVA portal page.
As an experimental service, ReSC have created a version of the Godiva2 web visualization system for MERSEA data, known as the Dynamic Quick View (DQV) system. DQV website, Poster (PDF)
Delivering Environmental Web Services (DEWS) (2005 - 2007)
This is a £2.2M DTI Inter-Enterprise Computing (IEC) project, led by the Met Office and involving the ReSC, BADC, Lost Wax, IBM and BMT. The project will apply recent research in inter enterprise computing technologies to the provision of time-critical high volume environmental information in the Health and Marine sectors. It will provide a functional demonstrator in each area using the same underlying Web Services architecture, evaluating standards for interoperability, scalability, data exchange, security and reliability. The demonstrators will be used to promote early adoption routes and the technology outputs will add to the national resources in these areas. The project's Dissemination Plan will ensure that the outputs are exploited as widely as possible and that others involved in working with UK environmental data and information (both nationally and internationally) can make use of these research applications.
Posters: non-technical overview (zipped PDF), technical overview (PPT)
Search and Rescue (2004 - 2005)
This project arose from the EDAS project (see below) as a collaboration between the ReSC, British Maritime Technology (BMT) and the Met Office. British Maritime Technology produce a piece of software called SARIS, which makes predictions of the drift paths of objects that have fallen overboard. These objects might be people, cargo, lifeboats etc. The Coastguard uses SARIS to work out where to search for these objects, given that they will have drifted from their original location due to ocean currents and winds. The operational version of SARIS uses pre-stored datasets of tides and so forth to make its predictions. As part of a project with BMT and the Met Office, SARIS was modified to make its predictions using Met Office forecasts, which are downloaded on demand via the GADS Web Service hosted here in Reading. This modified prototype is not operational yet, but demonstrates the potential for using live, online systems to improve this kind of operational facility.
Storing and manipulating gridded data in spatially-enabled databases (2004 - 2006)
Modern computer simulations of the oceans and atmosphere produce large amounts of data on the terabyte scale. Data providers need a manageable system for storing these datasets, whilst enabling the many consumers of the data to access them in a convenient and secure manner. The matter is complicated by the plethora of file formats (e.g. NetCDF, HDF, GRIB) that are used for holding environmental data. There is increasing justification for using database management systems for storing and manipulating gridded data. The ReSC is evaluating Barrodale Computing Service's Grid DataBlade with IBM's Informix database on behalf of the environmental science community. Please see this poster for more details.
Contact: Adit Santokhee
AMS Demonstration Project (2004 - 2005)
The ReSC is helping (with the Department of Animal and Microbial Sciences and the Centre for Advanced Computing and Emerging Technologies) to co-ordinate a demonstration project to showcase the potential of e-Science to be a powerful way of bringing together existing computing resources to solve scientific problems at the University of Reading. This project will help to raise awareness of e-Science within the University and encourage others to start projects of their own.
The biological problem consists of investigating the evolution of a class of parasitic genetic elements known as LINE-1 retrotransposons that inhabit the human genome. Intra-genomic parasites such as LINE-1s can and do adversely affect the organism whose genome they inhabit. It is therefore of interest to understand the long-term evolution and behaviour of these elements. One way to do this is to construct family trees or 'phylogenies' of LINE-1s that identify their ancestral and descendant relationships; much like a genealogy or family tree of individuals.
Constructing these family trees is an extremely computationally-intensive task. However, the running time can be vastly reduced by using distributed computing. In this project, we are using a combination of dedicated computing clusters and Condor pools of desktop machines. We estimate that these resources will complete the job in a matter of a couple of weeks; if only a single machine were used the time required would be almost two years.
Contact: Dr Jon Blower (ReSC), Prof. Mark Pagel (AMS), Prof. Vassil Alexandrov (ACET)
GODIVA (2003-2006)
(Grid for Ocean Diagnostics Interactive Visualisation and Analysis, homepage, flyer from SC2004)
The aims of this NERC e-Science pilot project are to permit scientists to visualise and carry out computational analyses easily on large amounts of output from climate, atmospheric and oceanic models using remote data stores and computational facilities. The project is coordinated from Reading with other PIs in Southampton, Imperial College, Rutherford Laboratory and Manchester Computer Science. Reading's e-Science focus is on Web Services and Workflows and their use to provide access to large data sets, including real-time Met Office data, with Web portals being used to provide interactivity (http://www.nerc-essc.ac.uk/las and http://www.nerc-essc.ac.uk/godiva).
The project's scientific focus is on the oceans thermohaline circulation and analysis of signals associated with in model data and data assimilation products.
Contact: Dr Chunlei Liu
GADS (2003 - 2005)
Grid Access Data Service. This is a Web Service that provides access to gridded climatological data in an intuitive and flexible manner. Users do not need to know any details about how, where or in what format the data are stored. Data can be downloaded in a variety of formats (e.g. netCDF, GRIB) and the service is readily extensible to accommodate new formats. Please see the users' guide for information on how to use the service, or the installation guide if you would like to install the service for yourself.
Contact: Dr Jon Blower
Distributed System Diagnostics for Weather and Climate (2003 - 2006)
With the production of ever larger climate data sets archived at a variety of data centres it is becoming increasingly difficult to perform diagnostic studies at a single site in terms of the available local computing resources. The aim of this e-Science PhD studentship project is to develop the means to perform distributed diagnostics from large distributed data sets and return the results to the user. The project will use the TRACK feature tracking and diagnostics code (used for following atmospheric storms and ocean eddies) as a testbed, and will involve the development of web service interfaces linked to grid computing infra-structures.
Contact: Lizzie Froude (PhD student, began in October 2003)
Flexible On-line Environmental Data Systems (EDAS) (2003 - 2004)
This is a South East England Development Agency (SEEDA) funded project and run from the Reading Enterprise Hub. The EDAS Cluster will join providers and end-users of Environmental data with organisations that can help bridge the gap. Delivery of data can span a wide range of business areas but the initial focus will be maritime applications, in particular Marine Coastguard agency needs. Companies within the SEEDA area are expected to benefit from this initial Cluster focus. Opportunities in other areas such as land based applications, and companies outside the SEEDA area, including abroad, will be addressed. The Cluster will demonstrate the principal, technological capability and end-user benefits of systems to new Cluster members. This demonstration will generate mutual understanding of end-users' needs and suppliers' capabilities in Environmental data provision The Cluster will facilitate collaborative bidding for R&D funds to develop Internet Data Broker systems.
Contacts: Ian Dwyer; Jerry Stanley; Project website.
- Ganglia Web Frontend: Load and performance statistics
- Portal: Cluster activity reports