Grid warehousing of molecular dynamics protein unfolding data

With the increasing awareness of protein folding disorders, the explosion of genomic information, and the need for efficient ways to predict protein structure, protein folding and unfolding has become a central issue in molecular sciences research. Molecular dynamics computer simulations are increasingly employed to understand the folding and unfolding of proteins. Running protein unfolding simulations is computationally expensive and finding ways to enhance performance is a grid issue on its own. However, more and more groups run such simulations and generate a myriad of data, which raises new challenges in managing and analyzing these data. Because the vast range of proteins researchers want to study and simulate, the computational effort needed to generate data, the large data volumes involved, and the different types of analyses scientists need to perform, it is desirable to provide a public repository allowing researchers to pool and share protein unfolding data. This paper describes efforts to provide a grid-enabled data warehouse for protein unfolding data. We outline the challenge and present first results in the design and implementation of the data warehouse.

The benefits of a compute cluster approach to high spatial resolution biodiversity richness modelling: projecting the impact of climate change on Mediterranean flora

High spatial resolution environmental data gives us a better understanding of the environmental factors affecting plant distributions at fine spatial scales. However, large environmental datasets dramatically increase compute times and output species model size stimulating the need for an alternative computing solution. Cluster computing offers such a solution, by allowing both multiple plant species Environmental Niche Models (ENMs) and individual tiles of high spatial resolution models to be computed concurrently on the same compute cluster. We apply our methodology to a case study of 4,209 species of Mediterranean flora (around 17% of species believed present in the biome). We demonstrate a 16 times speed-up of ENM computation time when 16 CPUs were used on the compute cluster. Our custom Java ‘Merge’ and ‘Downsize’ programs reduce ENM output files sizes by 94%. The median 0.98 test AUC score of species ENMs is aided by various species occurrence data filtering techniques. Finally, by calculating the percentage change of individual grid cell values, we map the projected percentages of plant species vulnerable to climate change in the Mediterranean region between 1950–2000 and 2020.

Beyond the computer: changing medium from digital to physical

How can organizations use digital infrastructure to realise physical outcomes? The design and construction of London Heathrow Terminal 5 is analysed to build new theoretical understanding of visualization and materialization practices in the transition from digital design to physical realisation. In the project studied, an integrated software solution is introduced as an infrastructure for delivery. The analyses articulate the work done to maintain this digital infrastructure and also to move designs beyond the closed world of the computer to a physical reality. In changing medium, engineers use heterogeneous trials to interrogate and address the limitations of an integrated digital model. The paper explains why such trials, which involve the reconciliation of digital and physical data through parallel and iterative forms of work, provide a robust practice for realizing goals that have physical outcomes. It argues that this practice is temporally different from, and at times in conflict with, building a comprehensive dataset within the digital medium. The paper concludes by discussing the implications for organizations that use digital infrastructures in seeking to accomplish goals in digital and physical media.

Acceptable use policy and employee computer usage: case of Sri Lankan software development industry

Organizations introduce acceptable use policies to deter employee computer misuse. Despite the controlling, monitoring and other forms of interventions employed, some employees misuse the organizational computers to carry out their personal work such as sending emails, surfing internet, chatting, playing games etc. These activities not only waste productive time of employees but also bring a risk to the organization. A questionnaire was administrated to a random sample of employees selected from large and medium scale software development organizations, which measured the work computer misuse levels and the factors that influence such behavior. The presence of guidelines provided no evidence of significant effect on the level of employee computer misuse. Not having access to Internet /email away from work and organizational settings were identified to be the most significant influences of work computer misuse.

Description and process evaluation of pharmacists’ interventions in a pharmacist-led information technology-enabled multicentre cluster randomised controlled trial for reducing medication errors in general practice (PINCER trial)

Objective To undertake a process evaluation of pharmacists' recommendations arising in the context of a complex IT-enabled pharmacist-delivered randomised controlled trial (PINCER trial) to reduce the risk of hazardous medicines management in general practices. Methods PINCER pharmacists manually recorded patients’ demographics, details of interventions recommended, actions undertaken by practice staff and time taken to manage individual cases of hazardous medicines management. Data were coded and double entered into SPSS v15, and then summarised using percentages for categorical data (with 95% CI) and, as appropriate, means (SD) or medians (IQR) for continuous data. Key findings Pharmacists spent a median of 20 minutes (IQR 10, 30) reviewing medical records, recommending interventions and completing actions in each case of hazardous medicines management. Pharmacists judged 72% (95%CI 70, 74) (1463/2026) of cases of hazardous medicines management to be clinically relevant. Pharmacists recommended 2105 interventions in 74% (95%CI 73, 76) (1516/2038) of cases and 1685 actions were taken in 61% (95%CI 59, 63) (1246/2038) of cases; 66% (95%CI 64, 68) (1383/2105) of interventions recommended by pharmacists were completed and 5% (95%CI 4, 6) (104/2105) of recommendations were accepted by general practitioners (GPs), but not completed at the end of the pharmacists’ placement; the remaining recommendations were rejected or considered not relevant by GPs. Conclusions The outcome measures were used to target pharmacist activity in general practice towards patients at risk from hazardous medicines management. Recommendations from trained PINCER pharmacists were found to be broadly acceptable to GPs and led to ameliorative action in the majority of cases. It seems likely that the approach used by the PINCER pharmacists could be employed by other practice pharmacists following appropriate training.

Extreme wind storms over Europe in present and future climate: a cluster analysis approach

Boreal winter wind storm situations over Central Europe are investigated by means of an objective cluster analysis. Surface data from the NCEP-Reanalysis and ECHAM4/OPYC3-climate change GHG simulation (IS92a) are considered. To achieve an optimum separation of clusters of extreme storm conditions, 55 clusters of weather patterns are differentiated. To reduce the computational effort, a PCA is initially performed, leading to a data reduction of about 98 %. The clustering itself was computed on 3-day periods constructed with the first six PCs using "k-means" clustering algorithm. The applied method enables an evaluation of the time evolution of the synoptic developments. The climate change signal is constructed by a projection of the GCM simulation on the EOFs attained from the NCEP-Reanalysis. Consequently, the same clusters are obtained and frequency distributions can be compared. For Central Europe, four primary storm clusters are identified. These clusters feature almost 72 % of the historical extreme storms events and add only to 5 % of the total relative frequency. Moreover, they show a statistically significant signature in the associated wind fields over Europe. An increased frequency of Central European storm clusters is detected with enhanced GHG conditions, associated with an enhancement of the pressure gradient over Central Europe. Consequently, more intense wind events over Central Europe are expected. The presented algorithm will be highly valuable for the analysis of huge data amounts as is required for e.g. multi-model ensemble analysis, particularly because of the enormous data reduction.

Bigger data for Big Data: from Twitter to brain-computer interface

We are sympathetic with Bentley et al’s attempt to encompass the wisdom of crowds in a generative model, but posit that success at using Big Data will include more sensitive measurements, more and more varied sources of information, as well as build from the indirect information available through technology, from ancillary technical features to data from brain-computer interface.

Computer Theorem Proving and HoTT

Theorem-proving is a one-player game. The history of computer programs being the players goes back to 1956 and the ‘LT’ LOGIC THEORY MACHINE of Newell, Shaw and Simon. In game-playing terms, the ‘initial position’ is the core set of axioms chosen for the particular logic and the ‘moves’ are the rules of inference. Now, the Univalent Foundations Program at IAS Princeton and the resulting ‘HoTT’ book on Homotopy Type Theory have demonstrated the success of a new kind of experimental mathematics using computer theorem proving.

Effects of target expansion on selection performance in older computer users

Point and click interactions using a mouse are an integral part of computer use for current desktop systems. Compared with younger users though, older adults experience greater difficulties performing cursor positioning tasks, and this can present limitations to using a computer easily and effectively. Target expansion is a technique for improving pointing performance, where the target dynamically grows as the cursor approaches. This has the advantage that targets conserve screen real estate in their unexpanded state, yet can still provide the benefits of a larger area to click on. This paper presents two studies of target expansion with older and younger participants, involving multidirectional point-select tasks with a computer mouse. Study 1 compares static versus expanding targets, and Study 2 compares static targets with three alternative techniques for expansion. Results show that expansion can improve times by up to 14%, and reduce error rates by up to 50%. Additionally, expanding targets are beneficial even when the expansion happens late in the movement, i.e. after the cursor has reached the expanded target area or even after it has reached the original target area. Participants’ subjective feedback on the target expansion are generally favorable, and this lends further support for the technique.

WCCC 2013: the 20th World Computer Chess Championship

The 20th World Computer Chess Championship took place in Yokohama, Japan during August 2013. It was narrowly won by JUNIOR from JONNY with HIARCS, PANDIX, SHREDDER and MERLIN occupying the remaining positions. There are references to the detailed chess biographies of the engines and engine-authors in the Chessprogramming Wiki. The games, occasionally annotated, are available here.

Massive Science with VO and Grids

There is a growing need for massive computational resources for the analysis of new astronomical datasets. To tackle this problem, we present here our first steps towards marrying two new and emerging technologies; the Virtual Observatory (e.g, AstroGrid) and the computa- tional grid (e.g. TeraGrid, COSMOS etc.). 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 compu- tational jobs to a distributed computer system. The broker will also interact with the AstroGrid workflow and MySpace environments. We discuss our planned usages of the VOTechBroker in computing a huge number of n–point correlation functions from the SDSS data and mas- sive model-fitting of millions of CMBfast models to WMAP data. We also discuss other applications including the determination of the XMM Cluster Survey selection function and the construction of new WMAP maps.