Grid Remote Execution (G-Rex) of Climate Models

G-Rex is light-weight Java middleware that allows scientific applications deployed on remote computer systems to be launched and controlled as if they are running on the user's own computer. G-Rex is particularly suited to ocean and climate modelling applications because output from the model is transferred back to the user while the run is in progress, which prevents the accumulation of large amounts of data on the remote cluster. The G-Rex server is a RESTful Web application that runs inside a servlet container on the remote system, and the client component is a Java command line program that can easily be incorporated into existing scientific work-flow scripts. The NEMO and POLCOMS ocean models have been deployed as G-Rex services in the NERC Cluster Grid, and G-Rex is the core grid middleware in the GCEP and GCOMS e-science projects.

Running Climate Models On The NERC Cluster Grid Using G-Rex

Compute grids are used widely in many areas of environmental science, but there has been limited uptake of grid computing by the climate modelling community, partly because the characteristics of many climate models make them difficult to use with popular grid middleware systems. In particular, climate models usually produce large volumes of output data, and running them usually involves complicated workflows implemented as shell scripts. For example, NEMO (Smith et al. 2008) is a state-of-the-art ocean model that is used currently for operational ocean forecasting in France, and will soon be used in the UK for both ocean forecasting and climate modelling. On a typical modern cluster, a particular one year global ocean simulation at 1-degree resolution takes about three hours when running on 40 processors, and produces roughly 20 GB of output as 50000 separate files. 50-year simulations are common, during which the model is resubmitted as a new job after each year. Running NEMO relies on a set of complicated shell scripts and command utilities for data pre-processing and post-processing prior to job resubmission. Grid Remote Execution (G-Rex) is a pure Java grid middleware system that allows scientific applications to be deployed as Web services on remote computer systems, and then launched and controlled as if they are running on the user's own computer. Although G-Rex is general purpose middleware it has two key features that make it particularly suitable for remote execution of climate models: (1) Output from the model is transferred back to the user while the run is in progress to prevent it from accumulating on the remote system and to allow the user to monitor the model; (2) The client component is a command-line program that can easily be incorporated into existing model work-flow scripts. G-Rex has a REST (Fielding, 2000) architectural style, which allows client programs to be very simple and lightweight and allows users to interact with model runs using only a basic HTTP client (such as a Web browser or the curl utility) if they wish. This design also allows for new client interfaces to be developed in other programming languages with relatively little effort. The G-Rex server is a standard Web application that runs inside a servlet container such as Apache Tomcat and is therefore easy to install and maintain by system administrators. G-Rex is employed as the middleware for the NERC1 Cluster Grid, a small grid of HPC2 clusters belonging to collaborating NERC research institutes. Currently the NEMO (Smith et al. 2008) and POLCOMS (Holt et al, 2008) ocean models are installed, and there are plans to install the Hadley Centre’s HadCM3 model for use in the decadal climate prediction project GCEP (Haines et al., 2008). The science projects involving NEMO on the Grid have a particular focus on data assimilation (Smith et al. 2008), a technique that involves constraining model simulations with observations. The POLCOMS model will play an important part in the GCOMS project (Holt et al, 2008), which aims to simulate the world’s coastal oceans. A typical use of G-Rex by a scientist to run a climate model on the NERC Cluster Grid proceeds as follows :(1) The scientist prepares input files on his or her local machine. (2) Using information provided by the Grid’s Ganglia3 monitoring system, the scientist selects an appropriate compute resource. (3) The scientist runs the relevant workflow script on his or her local machine. This is unmodified except that calls to run the model (e.g. with “mpirun”) are simply replaced with calls to "GRexRun" (4) The G-Rex middleware automatically handles the uploading of input files to the remote resource, and the downloading of output files back to the user, including their deletion from the remote system, during the run. (5) The scientist monitors the output files, using familiar analysis and visualization tools on his or her own local machine. G-Rex is well suited to climate modelling because it addresses many of the middleware usability issues that have led to limited uptake of grid computing by climate scientists. It is a lightweight, low-impact and easy-to-install solution that is currently designed for use in relatively small grids such as the NERC Cluster Grid. A current topic of research is the use of G-Rex as an easy-to-use front-end to larger-scale Grid resources such as the UK National Grid service.

A Conceptual Model for Group Support Systems in Local Councils

This paper proposes a conceptual model of a context-aware group support system (GSS) to assist local council employees to perform collaborative tasks in conjunction with inter- and intra-organisational stakeholders. Most discussions about e-government focus on the use of ICT to improve the relationship between government and citizen, not on the relationship between government and employees. This paper seeks to expose the unique culture of UK local councils and to show how a GSS could support local government employer and employee needs.

Storm prediction research and its application to the oil/gas industry

The accurate prediction of storms is vital to the oil and gas sector for the management of their operations. An overview of research exploring the prediction of storms by ensemble prediction systems is presented and its application to the oil and gas sector is discussed. The analysis method used requires larger amounts of data storage and computer processing time than other more conventional analysis methods. To overcome these difficulties eScience techniques have been utilised. These techniques potentially have applications to the oil and gas sector to help incorporate environmental data into their information systems

The Geostationary Earth Radiation Budget Project

This paper reports on a new satellite sensor, the Geostationary Earth Radiation Budget (GERB) experiment. GERB is designed to make the first measurements of the Earth's radiation budget from geostationary orbit. Measurements at high absolute accuracy of the reflected sunlight from the Earth, and the thermal radiation emitted by the Earth are made every 15 min, with a spatial resolution at the subsatellite point of 44.6 km (north–south) by 39.3 km (east–west). With knowledge of the incoming solar constant, this gives the primary forcing and response components of the top-of-atmosphere radiation. The first GERB instrument is an instrument of opportunity on Meteosat-8, a new spin-stabilized spacecraft platform also carrying the Spinning Enhanced Visible and Infrared (SEVIRI) sensor, which is currently positioned over the equator at 3.5°W. This overview of the project includes a description of the instrument design and its preflight and in-flight calibration. An evaluation of the instrument performance after its first year in orbit, including comparisons with data from the Clouds and the Earth's Radiant Energy System (CERES) satellite sensors and with output from numerical models, are also presented. After a brief summary of the data processing system and data products, some of the scientific studies that are being undertaken using these early data are described. This marks the beginning of a decade or more of observations from GERB, as subsequent models will fly on each of the four Meteosat Second Generation satellites.

Exploiting CAFS-ISP

In the summer of 1982, the ICLCUA CAFS Special Interest Group defined three subject areas for working party activity. These were: 1) interfaces with compilers and databases, 2) end-user language facilities and display methods, and 3) text-handling and office automation. The CAFS SIG convened one working party to address the first subject with the following terms of reference: 1) review facilities and map requirements onto them, 2) "Database or CAFS" or "Database on CAFS", 3) training needs for users to bridge to new techniques, and 4) repair specifications to cover gaps in software. The working party interpreted the topic broadly as the data processing professional's, rather than the end-user's, view of and relationship with CAFS. This report is the result of the working party's activities. The report content for good reasons exceeds the terms of reference in their strictest sense. For example, we examine QUERYMASTER, which is deemed to be an end-user tool by ICL, from both the DP and end-user perspectives. First, this is the only interface to CAFS in the current SV201. Secondly, it is necessary for the DP department to understand the end-user's interface to CAFS. Thirdly, the other subjects have not yet been addressed by other active working parties.

A narrow band pulsed eddy current instrument for materials testing

The principles of operation of an experimental prototype instrument known as J-SCAN are described along with the derivation of formulae for the rapid calculation of normalized impedances; the structure of the instrument; relevant probe design parameters; digital quantization errors; and approaches for the optimization of single frequency operation. An eddy current probe is used As the inductance element of a passive tuned-circuit which is repeatedly excited with short impulses. Each impulse excites an oscillation which is subject to decay dependent upon the values of the tuned-circuit components: resistance, inductance and capacitance. Changing conditions under the probe that affect the resistance and inductance of this circuit will thus be detected through changes in the transient response. These changes in transient response, oscillation frequency and rate of decay, are digitized, and then normalized values for probe resistance and inductance changes are calculated immediately in a micro processor. This approach coupled with a minimum analogue processing and maximum of digital processing has advantages compared with the conventional approaches to eddy current instruments. In particular there are: the absence of an out of balance condition and the flexibility and stability of digital data processing.

The state of veterinary epidemiology and economics

Recent developments in the fields of veterinary epidemiology and economics are critically reviewed and assessed. The impacts of recent technological developments in diagnosis, genetic characterisation, data processing and statistical analysis are evaluated. It is concluded that the acquisition and availability of data remains the principal constraint to the application of available techniques in veterinary epidemiology and economics, especially at population level. As more commercial producers use computerised management systems, the availability of data for analysis within herds is improving. However, consistency of recording and diagnosis remains problematic. Recent trends to the development of national livestock databases intended to provide reassurance to consumers of the safety and traceability of livestock products are potentially valuable sources of data that could lead to much more effective application of veterinary epidemiology and economics. These opportunities will be greatly enhanced if data from different sources, such as movement recording, official animal health programmes, quality assurance schemes, production recording and breed societies can be integrated. However, in order to realise such integrated databases, it will be necessary to provide absolute control of user access to guarantee data security and confidentiality. The potential applications of integrated livestock databases in analysis, modelling, decision-support, and providing management information for veterinary services and livestock producers are discussed. (c) 2004 Elsevier B.V. All rights reserved.

Hydroponic isotope labelling of entire plants (HILEP) for quantitative plant proteomics; an oxidative stress case study

Hydroponic isotope labelling of entire plants (HILEP) is a cost-effective method enabling metabolic labelling of whole and mature plants with a stable isotope such as N-15. By utilising hydroponic media that contain N-15 inorganic salts as the sole nitrogen source, near to 100% N-15-labelling of proteins can be achieved. In this study, it is shown that HILEP, in combination with mass spectrometry, is suitable for relative protein quantitation of seven week-old Arabidopsis plants submitted to oxidative stress. Protein extracts from pooled N-14- and N-15-hydroponically grown plants were fractionated by SDS-PAGE, digested and analysed by liquid chromatography electrospray ionisation tandem mass spectrometry (LC-ESI-MS/MS). Proteins were identified and the spectra of N-14/N-15 peptide pairs were extracted using their m/z chromatographic retention time, isotopic distributions, and the m/z difference between the N-14 and N-15 peptides. Relative amounts were calculated as the ratio of the sum of the peak areas of the two distinct N-14 and N-15 peptide isotope envelopes. Using Mascot and the open source trans-proteomic pipeline (TPP), the data processing was automated for global proteome quantitation down to the isoform level by extracting isoform specific peptides. With this combination of metabolic labelling and mass spectrometry it was possible to show differential protein expression in the apoplast of plants submitted to oxidative stress. Moreover, it was possible to discriminate between differentially expressed isoforms belonging to the same protein family, such as isoforms of xylanases and pathogen-related glucanases (PR 2). (C) 2008 Elsevier Ltd. All rights reserved.

A novel method for measuring lag times in division of individual bacterial cells using image analysis

A method is presented for determining the time to first division of individual bacterial cells growing on agar media. Bacteria were inoculated onto agar-coated slides and viewed by phase-contrast microscopy. Digital images of the growing bacteria were captured at intervals and the time to first division estimated by calculating the "box area ratio". This is the area of the smallest rectangle that can be drawn around an object, divided by the area of the object itself. The box area ratios of cells were found to increase suddenly during growth at a time that correlated with cell division as estimated by visual inspection of the digital images. This was caused by a change in the orientation of the two daughter cells that occurred when sufficient flexibility arose at their point of attachment. This method was used successfully to generate lag time distributions for populations of Escherichia coli, Listeria monocytogenes and Pseudomonas aeruginosa, but did not work with the coccoid organism Staphylococcus aureus. This method provides an objective measure of the time to first cell division, whilst automation of the data processing allows a large number of cells to be examined per experiment. (c) 2005 Elsevier B.V. All rights reserved.

OTHR impulsive interference suppression in strong clutter background

External interferences can severely degrade the performance of an Over-the-horizon radar (OTHR), so suppression of external interferences in strong clutter environment is the prerequisite for the target detection. The traditional suppression solutions usually began with clutter suppression in either time or frequency domain, followed by the interference detection and suppression. Based on this traditional solution, this paper proposes a method characterized by joint clutter suppression and interference detection: by analyzing eigenvalues in a short-time moving window centered at different time position, Clutter is suppressed by discarding the maximum three eigenvalues at every time position and meanwhile detection is achieved by analyzing the remained eigenvalues at different position. Then, restoration is achieved by forward-backward linear prediction using interference-free data surrounding the interference position. In the numeric computation, the eigenvalue decomposition (EVD) is replaced by values decomposition (SVD) based on the equivalence of these two processing. Data processing and experimental results show its efficiency of noise floor falling down about 10-20 dB.

The Heliospheric Imagers onboard the STEREO mission

Mounted on the sides of two widely separated spacecraft, the two Heliospheric Imager (HI) instruments onboard NASA’s STEREO mission view, for the first time, the space between the Sun and Earth. These instruments are wide-angle visible-light imagers that incorporate sufficient baffling to eliminate scattered light to the extent that the passage of solar coronal mass ejections (CMEs) through the heliosphere can be detected. Each HI instrument comprises two cameras, HI-1 and HI-2, which have 20° and 70° fields of view and are off-pointed from the Sun direction by 14.0° and 53.7°, respectively, with their optical axes aligned in the ecliptic plane. This arrangement provides coverage over solar elongation angles from 4.0° to 88.7° at the viewpoints of the two spacecraft, thereby allowing the observation of Earth-directed CMEs along the Sun – Earth line to the vicinity of the Earth and beyond. Given the two separated platforms, this also presents the first opportunity to view the structure and evolution of CMEs in three dimensions. The STEREO spacecraft were launched from Cape Canaveral Air Force Base in late October 2006, and the HI instruments have been performing scientific observations since early 2007. The design, development, manufacture, and calibration of these unique instruments are reviewed in this paper. Mission operations, including the initial commissioning phase and the science operations phase, are described. Data processing and analysis procedures are briefly discussed, and ground-test results and in-orbit observations are used to demonstrate that the performance of the instruments meets the original scientific requirements.

Detecting intraday periodicities with application to high frequency exchange rates

Many recent papers have documented periodicities in returns, return volatility, bid–ask spreads and trading volume, in both equity and foreign exchange markets. We propose and employ a new test for detecting subtle periodicities in time series data based on a signal coherence function. The technique is applied to a set of seven half-hourly exchange rate series. Overall, we find the signal coherence to be maximal at the 8-h and 12-h frequencies. Retaining only the most coherent frequencies for each series, we implement a trading rule that is based on these observed periodicities. Our results demonstrate in all cases except one that, in gross terms, the rules can generate returns that are considerably greater than those of a buy-and-hold strategy, although they cannot retain their profitability net of transactions costs. We conjecture that this methodology could constitute an important tool for financial market researchers which will enable them to detect, quantify and rank the various periodic components in financial data better.

Fully automated software solution for protein quantitation by global metabolic labeling with stable isotopes

Metabolic stable isotope labeling is increasingly employed for accurate protein (and metabolite) quantitation using mass spectrometry (MS). It provides sample-specific isotopologues that can be used to facilitate comparative analysis of two or more samples. Stable Isotope Labeling by Amino acids in Cell culture (SILAC) has been used for almost a decade in proteomic research and analytical software solutions have been established that provide an easy and integrated workflow for elucidating sample abundance ratios for most MS data formats. While SILAC is a discrete labeling method using specific amino acids, global metabolic stable isotope labeling using isotopes such as (15)N labels the entire element content of the sample, i.e. for (15)N the entire peptide backbone in addition to all nitrogen-containing side chains. Although global metabolic labeling can deliver advantages with regard to isotope incorporation and costs, the requirements for data analysis are more demanding because, for instance for polypeptides, the mass difference introduced by the label depends on the amino acid composition. Consequently, there has been less progress on the automation of the data processing and mining steps for this type of protein quantitation. Here, we present a new integrated software solution for the quantitative analysis of protein expression in differential samples and show the benefits of high-resolution MS data in quantitative proteomic analyses.

Boundary-layer friction in midlatitude cyclone

Results from an idealized three-dimensional baroclinic life-cycle model are interpreted in a potential vorticity (PV) framework to identify the physical mechanisms by which frictional processes acting in the atmospheric boundary layer modify and reduce the baroclinic development of a midlatitude storm. Considering a life cycle where the only non-conservative process acting is boundary-layer friction, the rate of change of depth-averaged PV within the boundary layer is governed by frictional generation of PV and the flux of PV into the free troposphere. Frictional generation of PV has two contributions: Ekman generation, which is directly analogous to the well-known Ekman-pumping mechanism for barotropic vortices, and baroclinic generation, which depends on the turning of the wind in the boundary layer and low-level horizontal temperature gradients. It is usually assumed, at least implicitly, that an Ekman process of negative PV generation is the mechanism whereby friction reduces the strength and growth rates of baroclinic systems. Although there is evidence for this mechanism, it is shown that baroclinic generation of PV dominates, producing positive PV anomalies downstream of the low centre, close to developing warm and cold fronts. These PV anomalies are advected by the large-scale warm conveyor belt flow upwards and polewards, fluxed into the troposphere near the warm front, and then advected westwards relative to the system. The result is a thin band of positive PV in the lower troposphere above the surface low centre. This PV is shown to be associated with a positive static stability anomaly, which Rossby edge wave theory suggests reduces the strength of the coupling between the upper- and lower-level PV anomalies, thereby reducing the rate of baroclinic development. This mechanism, which is a result of the baroclinic dynamics in the frontal regions, is in marked contrast with simple barotropic spin-down ideas. Finally we note the implications of these frictionally generated PV anomalies for cyclone forecasting.