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.

Integrating the Climate Science Modelling Language with geospatial software and services

Much consideration is rightly given to the design of metadata models to describe data. At the other end of the data-delivery spectrum much thought has also been given to the design of geospatial delivery interfaces such as the Open Geospatial Consortium standards, Web Coverage Service (WCS), Web Map Server and Web Feature Service (WFS). Our recent experience with the Climate Science Modelling Language shows that an implementation gap exists where many challenges remain unsolved. To bridge this gap requires transposing information and data from one world view of geospatial climate data to another. Some of the issues include: the loss of information in mapping to a common information model, the need to create ‘views’ onto file-based storage, and the need to map onto an appropriate delivery interface (as with the choice between WFS and WCS for feature types with coverage-valued properties). Here we summarise the approaches we have taken in facing up to these problems.

Methodology To model the energy and greenhouse gas emissions of electronic software distributions

A new electronic software distribution (ESD) life cycle analysis (LCA)methodology and model structure were constructed to calculate energy consumption and greenhouse gas (GHG) emissions. In order to counteract the use of high level, top-down modeling efforts, and to increase result accuracy, a focus upon device details and data routes was taken. In order to compare ESD to a relevant physical distribution alternative,physical model boundaries and variables were described. The methodology was compiled from the analysis and operational data of a major online store which provides ESD and physical distribution options. The ESD method included the calculation of power consumption of data center server and networking devices. An in-depth method to calculate server efficiency and utilization was also included to account for virtualization and server efficiency features. Internet transfer power consumption was analyzed taking into account the number of data hops and networking devices used. The power consumed by online browsing and downloading was also factored into the model. The embedded CO2e of server and networking devices was proportioned to each ESD process. Three U.K.-based ESD scenarios were analyzed using the model which revealed potential CO2e savings of 83% when ESD was used over physical distribution. Results also highlighted the importance of server efficiency and utilization methods.

The impact of Group Intelligence software on enquiry-based learning

Despite the increasing use of groupware technologies in education, there is little evidence of their impact, especially within an enquiry-based learning (EBL) context. In this paper, we examine the use of a commercial standard Group Intelligence software called GroupSystems®ThinkTank. To date, ThinkTank has been adopted mainly in the USA and supports teams in generating ideas, categorising, prioritising, voting and multi-criteria decision-making and automatically generates a report at the end of each session. The software was used by students carrying out an EBL project, set by employers, for a full academic year. The criteria for assessing the impact of ThinkTank on student learning were those of creativity, participation, productivity, engagement and understanding. Data was collected throughout the year using a combination of interviews and questionnaires, and written feedback from employers. The overall findings show an increase in levels of productivity and creativity, evidence of a deeper understanding of their work but some variation in attitudes towards participation in the early stages of the project.

FACSGen 2.0 animation software: generating three-dimensional FACS-valid facial expressions for emotion research

In this article, we present FACSGen 2.0, new animation software for creating static and dynamic threedimensional facial expressions on the basis of the Facial Action Coding System (FACS). FACSGen permits total control over the action units (AUs), which can be animated at all levels of intensity and applied alone or in combination to an infinite number of faces. In two studies, we tested the validity of the software for the AU appearance defined in the FACS manual and the conveyed emotionality of FACSGen expressions. In Experiment 1, four FACS-certified coders evaluated the complete set of 35 single AUs and 54 AU combinations for AU presence or absence, appearance quality, intensity, and asymmetry. In Experiment 2, lay participants performed a recognition task on emotional expressions created with FACSGen software and rated the similarity of expressions displayed by human and FACSGen faces. Results showed good to excellent classification levels for all AUs by the four FACS coders, suggesting that the AUs are valid exemplars of FACS specifications. Lay participants’ recognition rates for nine emotions were high, and comparisons of human and FACSGen expressions were very similar. The findings demonstrate the effectiveness of the software in producing reliable and emotionally valid expressions, and suggest its application in numerous scientific areas, including perception, emotion, and clinical and euroscience research.

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.

WCSC 2013: the 3rd World Chess Software Championship

The 3rd World Chess Software Championship took place in Yokohama, Japan during August 2013. It pits chess engines against each other on a common hardware platform - in this instance, the Intel i7 2740 Ivy Bridge with 16GB RAM supporting a potential eight processing threads. It was narrowly won by HIARCS from JUNIOR and PANDIX with JONNY, SHREDDER and MERLIN taking the remaining places. Games, occasionally annotated, are available here.

Software-based study of a non-sorting method for median calculation on a set of integer numbers

This paper presents a software-based study of a hardware-based non-sorting median calculation method on a set of integer numbers. The method divides the binary representation of each integer element in the set into bit slices in order to find the element located in the middle position. The method exhibits a linear complexity order and our analysis shows that the best performance in execution time is obtained when slices of 4-bit in size are used for 8-bit and 16-bit integers, in mostly any data set size. Results suggest that software implementation of bit slice method for median calculation outperforms sorting-based methods with increasing improvement for larger data set size. For data set sizes of N > 5, our simulations show an improvement of at least 40%.