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.

Determination of tube theory parameters using a simple grid model as an example

Although the tube theory is successful in describing entangled polymers qualitatively, a more quantitative description requires precise and consistent definitions of its parameters. Here we investigate the simplest model of entangled polymers, namely a single Rouse chain in a cubic lattice of line obstacles, and illustrate the typical problems and uncertainties of the tube theory. In particular we show that in general one needs 3 entanglement related parameters, but only 2 combinations of them are relevant for the long-time dynamics. Conversely, the plateau modulus can not be determined from these two parameters and requires a more detailed model of entanglements with explicit entanglement forces, such as the slipsprings model. It is shown that for the grid model the Rouse time within the tube is larger than the Rouse time of the free chain, in contrast to what the standard tube theory assumes.

Mutual dependency grid for stakeholder mapping: a component-based approach to supply chain participant analysis

Stakeholder analysis plays a critical role in business analysis. However, the majority of the stakeholder identification and analysis methods focus on the activities and processes and ignore the artefacts being processed by human beings. By focusing on the outputs of the organisation, an artefact-centric view helps create a network of artefacts, and a component-based structure of the organisation and its supply chain participants. Since the relationship is based on the components, i.e. after the stakeholders are identified, the interdependency between stakeholders and the focal organisation can be measured. Each stakeholder is associated with two types of dependency, namely the stakeholder’s dependency on the focal organisation and the focal organisation’s dependency on the stakeholder. We identify three factors for each type of dependency and propose the equations that calculate the dependency indexes. Once both types of the dependency indexes are calculated, each stakeholder can be placed and categorised into one of the four groups, namely critical stakeholder, mutual benefits stakeholder, replaceable stakeholder, and easy care stakeholder. The mutual dependency grid and the dependency gap analysis, which further investigates the priority of each stakeholder by calculating the weighted dependency gap between the focal organisation and the stakeholder, subsequently help the focal organisation to better understand its stakeholders and manage its stakeholder relationships.

A fast two-grid and finite section method for a class of integral equations on the real line with application to an acoustic scattering problem in the half-plane

We consider the numerical treatment of second kind integral equations on the real line of the form ∅(s) = ∫_(-∞)^(+∞)▒〖κ(s-t)z(t)ϕ(t)dt,s=R〗 (abbreviated ϕ= ψ+K_z ϕ) in which K ϵ L_1 (R), z ϵ L_∞ (R) and ψ ϵ BC(R), the space of bounded continuous functions on R, are assumed known and ϕ ϵ BC(R) is to be determined. We first derive sharp error estimates for the finite section approximation (reducing the range of integration to [-A, A]) via bounds on (1-K_z )^(-1)as an operator on spaces of weighted continuous functions. Numerical solution by a simple discrete collocation method on a uniform grid on R is then analysed: in the case when z is compactly supported this leads to a coefficient matrix which allows a rapid matrix-vector multiply via the FFT. To utilise this possibility we propose a modified two-grid iteration, a feature of which is that the coarse grid matrix is approximated by a banded matrix, and analyse convergence and computational cost. In cases where z is not compactly supported a combined finite section and two-grid algorithm can be applied and we extend the analysis to this case. As an application we consider acoustic scattering in the half-plane with a Robin or impedance boundary condition which we formulate as a boundary integral equation of the class studied. Our final result is that if z (related to the boundary impedance in the application) takes values in an appropriate compact subset Q of the complex plane, then the difference between ϕ(s)and its finite section approximation computed numerically using the iterative scheme proposed is ≤C_1 [kh log⁡〖(1⁄kh)+(1-Θ)^((-1)⁄2) (kA)^((-1)⁄2) 〗 ] in the interval [-ΘA,ΘA](Θ<1) for kh sufficiently small, where k is the wavenumber and h the grid spacing. Moreover this numerical approximation can be computed in ≤C_2 N log⁡N operations, where N = 2A/h is the number of degrees of freedom. The values of the constants C1 and C2 depend only on the set Q and not on the wavenumber k or the support of z.

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: 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.

Non-orthogonal version of the arbitrary polygonal C-grid and a new diamond grid

Quasi-uniform grids of the sphere have become popular recently since they avoid parallel scaling bottle- necks associated with the poles of latitude–longitude grids. However quasi-uniform grids of the sphere are often non- orthogonal. A version of the C-grid for arbitrary non- orthogonal grids is presented which gives some of the mimetic properties of the orthogonal C-grid. Exact energy conservation is sacrificed for improved accuracy and the re- sulting scheme numerically conserves energy and potential enstrophy well. The non-orthogonal nature means that the scheme can be used on a cubed sphere. The advantage of the cubed sphere is that it does not admit the computa- tional modes of the hexagonal or triangular C-grids. On var- ious shallow-water test cases, the non-orthogonal scheme on a cubed sphere has accuracy less than or equal to the orthog- onal scheme on an orthogonal hexagonal icosahedron. A new diamond grid is presented consisting of quasi- uniform quadrilaterals which is more nearly orthogonal than the equal-angle cubed sphere but with otherwise similar properties. It performs better than the cubed sphere in ev- ery way and should be used instead in codes which allow a flexible grid structure.

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.

GRID and docking analyses reveal a molecular basis for flavonoid inhibition of src-family kinase activity

Flavonoids reduce cardiovascular disease risk through anti-inflammatory, anti-coagulant and anti-platelet actions. One key flavonoid inhibitory mechanism is blocking kinase activity that drives these processes. Flavonoids attenuate activities of kinases including phosphoinositide-3-kinase (PI3K), Fyn, Lyn, Src, Syk, PKC, PIM1/2, ERK, JNK, and PKA. X-ray crystallographic analyses of kinase-flavonoid complexes show that flavonoid ring systems and their hydroxyl substitutions are important structural features for their binding to kinases. A clearer understanding of structural interactions of flavonoids with kinases is necessary to allow construction of more potent and selective counterparts. We examined flavonoid (quercetin, apigenin and catechin) interactions with Src-family kinases (Lyn, Fyn and Hck) applying the Sybyl docking algorithm and GRID. A homology model (Lyn) was used in our analyses to demonstrate that high quality predicted kinase structures are suitable for flavonoid computational studies. Our docking results revealed potential hydrogen bond contacts between flavonoid hydroxyls and kinase catalytic site residues. Identification of plausible contacts indicated that quercetin formed the most energetically stable interactions, apigenin lacked hydroxyl groups necessary for important contacts, and the non-planar structure of catechin could not support predicted hydrogen bonding patterns. GRID analysis using a hydroxyl functional group supported docking results. Based on these findings, we predicted that quercetin would inhibit activities of Src-family kinases with greater potency than apigenin and catechin. We validated this prediction using in vitro kinase assays. We conclude that our study can be used as a basis to construct virtual flavonoid interaction libraries to guide drug discovery using these compounds as molecular templates.