Grid computing solutions for distributed repositories of protein folding and unfolding simulations

The P-found protein folding and unfolding simulation repository is designed to allow scientists to perform analyses across large, distributed simulation data sets. There are two storage components in P-found: a primary repository of simulation data and a data warehouse. Here we demonstrate how grid technologies can support multiple, distributed P-found installations. In particular we look at two aspects, first how grid data management technologies can be used to access the distributed data warehouses; and secondly, how the grid can be used to transfer analysis programs to the primary repositories --- this is an important and challenging aspect of P-found because the data volumes involved are too large to be centralised. The grid technologies we are developing with the P-found system will allow new large data sets of protein folding simulations to be accessed and analysed in novel ways, with significant potential for enabling new scientific discoveries.

P-found: grid-enabling distributed repositories of protein folding and unfolding simulations for data mining

The P-found protein folding and unfolding simulation repository is designed to allow scientists to perform data mining and other analyses across large, distributed simulation data sets. There are two storage components in P-found: a primary repository of simulation data that is used to populate the second component, and a data warehouse that contains important molecular properties. These properties may be used for data mining studies. Here we demonstrate how grid technologies can support multiple, distributed P-found installations. In particular, we look at two aspects: firstly, how grid data management technologies can be used to access the distributed data warehouses; and secondly, how the grid can be used to transfer analysis programs to the primary repositories — this is an important and challenging aspect of P-found, due to the large data volumes involved and the desire of scientists to maintain control of their own data. The grid technologies we are developing with the P-found system will allow new large data sets of protein folding simulations to be accessed and analysed in novel ways, with significant potential for enabling scientific discovery.

A ‘Boscastle-type’ quasi-stationary convective system over the UK Southwest Peninsula

An investigation is presented of a quasi-stationary convective system (QSCS) which occurred over the UK Southwest Peninsula on 21 July 2010. This system was remarkably similar in its location and structure to one which caused devastating flash flooding in the coastal village of Boscastle, Cornwall on 16 August 2004. However, in the 2010 case rainfall accumulations were around four times smaller and no flooding was recorded. The more extreme nature of the Boscastle case is shown to be related to three factors: (1) higher rain rates, associated with a warmer and moister tropospheric column and deeper convective clouds; (2) a more stationary system, due to slower evolution of the large-scale flow; and (3) distribution of the heaviest precipitation over fewer river catchments. Overall, however, the synoptic setting of the two events was broadly similar, suggesting that such conditions favour the development of QSCSs over the Southwest Peninsula. A numerical simulation of the July 2010 event was performed using a 1.5-km grid length configuration of the Met Office Unified Model. This reveals that convection was repeatedly initiated through lifting of low-level air parcels along a quasi-stationary coastal convergence line. Sensitivity tests are used to show that this convergence line was a sea breeze front which temporarily stalled along the coastline due to the retarding influence of an offshore-directed background wind component. Several deficiencies are noted in the 1.5-km model’s representation of the storm system, including delayed convective initiation; however, significant improvements are observed when the grid length is reduced to 500 m. These result in part from an improved representation of the convergence line, which enhances the associated low-level ascent allowing air parcels to more readily reach their level of free convection. The implications of this finding for forecasting convective precipitation are discussed.

Perceived helplessness is associated with individual differences in the central motor output system

Learned helplessness is a maladaptive response to uncontrollable stress characterized by impaired motor escape responses, reduced motivation and learning deficits. There are important individual differences in the likelihood of becoming helpless following exposure to uncontrollable stress but little is known about the neural mechanisms underlying these individual differences. Here we used structural MRI to measure gray and white matter in individuals with chronic pain, a population at high risk for helplessness due to prolonged exposure to a poorly controlled stressor (pain). Given that self-reported helplessness is predictive of treatment outcomes in chronic pain, understanding such differences might provide valuable clinical insight. We found that the magnitude of self-reported helplessness correlated with cortical thickness in the supplementary motor area (SMA) and midcingulate cortex, regions implicated in cognitive aspects of motor behavior. We then examined the white matter connectivity of these regions and found that fractional anisotropy of connected white matter tracts along the corticospinal tract was associated with helplessness and mediated the relationship between SMA cortical thickness and helplessness. These data provide novel evidence that links individual differences in the motor output pathway with perceived helplessness over a chronic and poorly controlled stressor.

Statistical computations with AstroGrid and the Grid

We outline our first steps towards marrying two new and emerging technologies; the Virtual Observatory (e.g, Astro- Grid) and the computational grid. We discuss the construction of VOTechBroker, which is a modular software tool designed to abstract the tasks of submission and management of a large number of computational jobs to a distributed computer system. The broker will also interact with the AstroGrid workflow and MySpace environments. We present our planned usage of the VOTechBroker in computing a huge number of n–point correlation functions from the SDSS, as well as fitting over a million CMBfast models to the WMAP data.

Ubiquitous grid resource monitoring

In any wide-area distributed system there is a need to communicate and interact with a range of networked devices and services ranging from computer-based ones (CPU, memory and disk), to network components (hubs, routers, gateways) and specialised data sources (embedded devices, sensors, data-feeds). In order for the ensemble of underlying technologies to provide an environment suitable for virtual organisations to flourish, the resources that comprise the fabric of the Grid must be monitored in a seamless manner that abstracts away from the underlying complexity. Furthermore, as various competing Grid middleware offerings are released and evolve, an independent overarching monitoring service should act as a corner stone that ties these systems together. GridRM is a standards-based approach that is independent of any given middleware and that can utilise legacy and emerging resource-monitoring technologies. The main objective of the project is to produce a standardised and extensible architecture that provides seamless mechanisms to interact with native monitoring agents across heterogeneous resources.

GridRM: an extensible resource monitoring system

GridRM is an open and extensible resource monitoring system, based on the Global Grid Forum's Grid Monitoring Architecture (GMA). GridRM is not intended to interact with applications; rather it is designed to monitor the resources that an application may use. This paper focuses on the dynamic driver infrastructure used by GridRM to interact with heterogeneous data sources, such as SNMP or Ganglia agents, and how it provides a homogeneous view of the underlying heterogeneous data. This paper discusses the local infrastructure and details work implementing and deploying a number of drivers.

GridRM: a resource monitoring architecture for the grid

Monitoring resources is an important aspect of the overall efficient usage and control of any distributed system. In this paper, we describe a generic open-source resource monitoring architecture that has been specifically designed for the Grid. The paper consists of three main sections. In the first section, we outline our motivation and briefly detail similar work in the area. In the second section, we describe the general monitoring architecture and its components. In the final section of the paper, we summarise the experiences so far and outline our future work.

Jini meets the Grid

There is an increasing interest in integrating Java-based, and in particular Jini systems, with the emerging Grid infrastructures. In this paper we explore various ways of integrating the key components of each architecture, their directory and information management services. In the first part of the paper we sketch out the Jini and Grid architectures and their services. We then review the components and services that Jini provides and compare these with those of the Grid. In the second part of the paper we critically explore four ways that Jini and the Grid could interact, here in particular we look at possible scenarios that can provide a seamless interface to a Jini environment for Grid clients and how to use Jini services from a Grid environment. In the final part of the paper we summarise our findings and report on future work being undertaken to integrate Jini and the Grid.

Coupling ensemble weather predictions based on TIGGE database with Grid-Xinanjiang model for flood forecast

The incorporation of numerical weather predictions (NWP) into a flood forecasting system can increase forecast lead times from a few hours to a few days. A single NWP forecast from a single forecast centre, however, is insufficient as it involves considerable non-predictable uncertainties and lead to a high number of false alarms. The availability of global ensemble numerical weather prediction systems through the THORPEX Interactive Grand Global Ensemble' (TIGGE) offers a new opportunity for flood forecast. The Grid-Xinanjiang distributed hydrological model, which is based on the Xinanjiang model theory and the topographical information of each grid cell extracted from the Digital Elevation Model (DEM), is coupled with ensemble weather predictions based on the TIGGE database (CMC, CMA, ECWMF, UKMO, NCEP) for flood forecast. This paper presents a case study using the coupled flood forecasting model on the Xixian catchment (a drainage area of 8826 km2) located in Henan province, China. A probabilistic discharge is provided as the end product of flood forecast. Results show that the association of the Grid-Xinanjiang model and the TIGGE database gives a promising tool for an early warning of flood events several days ahead.

Mid-Holocene land-surface conditions in northern Africa and the Arabian peninsula: a data set for the analysis of biogeophysical feedbacks in the climate system

Large changes in the extent of northern subtropical arid regions during the Holocene are attributed to orbitally forced variations in monsoon strength and have been implicated in the regulation of atmospheric trace gas concentrations on millenial timescales. Models that omit biogeophysical feedback, however, are unable to account for the full magnitude of African monsoon amplification and extension during the early to middle Holocene (˜9500–5000 years B.P.). A data set describing land-surface conditions 6000 years B.P. on a 1° × 1° grid across northern Africa and the Arabian Peninsula has been prepared from published maps and other sources of palaeoenvironmental data, with the primary aim of providing a realistic lower boundary condition for atmospheric general circulation model experiments similar to those performed in the Palaeoclimate Modelling Intercomparison Project. The data set includes information on the percentage of each grid cell occupied by specific vegetation types (steppe, savanna, xerophytic woods/scrub, tropical deciduous forest, and tropical montane evergreen forest), open water (lakes), and wetlands, plus information on the flow direction of major drainage channels for use in large-scale palaeohydrological modeling.

fMRI evidence for the involvement of the procedural memory system in morphological processing of a second language

Behavioural evidence suggests that English regular past tense forms are automatically decomposed into their stem and affix (played  = play+ed) based on an implicit linguistic rule, which does not apply to the idiosyncratically formed irregular forms (kept). Additionally, regular, but not irregular inflections, are thought to be processed through the procedural memory system (left inferior frontal gyrus, basal ganglia, cerebellum). It has been suggested that this distinction does not to apply to second language (L2) learners of English; however, this has not been tested at the brain level. This fMRI study used a masked-priming task with regular and irregular prime-target pairs (played-play/kept-keep) to investigate morphological processing in native and highly proficient late L2 English speakers. No between-groups differences were revealed. Compared to irregular pairs, regular pairs activated the pars opercularis, bilateral caudate nucleus and the right cerebellum, which are part of the procedural memory network and have been connected with the processing of morphologically complex forms. Our study is the first to provide evidence for native-like involvement of the procedural memory system in processing of regular past tense by late L2 learners of English.

Cost function for sub-agent elements in multi-agent energy management system

Distributed generation plays a key role in reducing CO2 emissions and losses in transmission of power. However, due to the nature of renewable resources, distributed generation requires suitable control strategies to assure reliability and optimality for the grid. Multi-agent systems are perfect candidates for providing distributed control of distributed generation stations as well as providing reliability and flexibility for the grid integration. The proposed multi-agent energy management system consists of single-type agents who control one or more gird entities, which are represented as generic sub-agent elements. The agent applies one control algorithm across all elements and uses a cost function to evaluate the suitability of the element as a supplier. The behavior set by the agent's user defines which parameters of an element have greater weight in the cost function, which allows the user to specify the preference on suppliers dynamically. This study shows the ability of the multi-agent energy management system to select suppliers according to the selection behavior given by the user. The optimality of the supplier for the required demand is ensured by the cost function based on the parameters of the element.

Financial implications for companies running standby generators in support of a smart grid

Integrating renewable energy into built environments requires additional attention to the balancing of supply and demand due to their intermittent nature. Demand Side Response (DSR) has the potential to make money for organisations as well as support the System Operator as the generation mix changes. There is an opportunity to increase the use of existing technologies in order to manage demand. Company-owned standby generators are a rarely used resource; their maintenance schedule often accounts for a majority of their running hours. DSR encompasses a range of technologies and organisations; Sustainability First (2012) suggest that the System Operator (SO), energy supply companies, Distribution Network Operators (DNOs), Aggregators and Customers all stand to benefit from DSR. It is therefore important to consider impact of DSR measures to each of these stakeholders. This paper assesses the financial implications of organisations using existing standby generation equipment for DSR in order to avoid peak electricity charges. It concludes that under the current GB electricity pricing structure, there are several regions where running diesel generators at peak times is financially beneficial to organisations. Issues such as fuel costs, Carbon Reduction Commitment (CRC) charges, maintenance costs and electricity prices are discussed.

A diabatically-generated potential vorticity structure near the extratropical tropopause in three simulated extratropical cyclones

The structure of near-tropopause potential vorticity (PV) acts as a primary control on the evolution of extratropical cyclones. Diabatic processes such as the latent heating found in ascending moist warm conveyor belts modify PV. A dipole in diabatically-generated PV (hereafter diabatic PV) straddling the extratropical tropopause, with the positive pole above the negative pole, was diagnosed in a recently published analysis of a simulated extratropical cyclone. This PV dipole has the potential to significantly modify the propagation of Rossby waves and the growth of baroclinically-unstable waves. This previous analysis was based on a single case study simulated with 12-km horizontal grid spacing and parameterized convection. Here, the dipole is investigated in three additional cold-season extratropical cyclones simulated in both convection-parameterizing and convection-permitting model configurations. A diabatic PV dipole across the extratropical tropopause is diagnosed in all three cases. The amplitude of the dipole saturates approximately 36 hours from the time diabatic PV is accumulated. The node elevation of the dipole varies between 2-4 PVU in the three cases, and the amplitude of the system-averaged dipole varies between 0.2-0.4 PVU. The amplitude of the negative pole is similar in the convection-parameterizing and convection-permitting simulations. The positive pole, which is generated by long-wave radiative cooling, is weak in the convection-permitting simulations due to the small domain size which limits the accumulation of diabatic tendencies within the interior of the domain. The possible correspondence between the diabatic PV dipole and the extratropical tropopause inversion layer is discussed.