An ensemble method for predicting subnuclear localizations from primary protein structures

Background Predicting protein subnuclear localization is a challenging problem. Some previous works based on non-sequence information including Gene Ontology annotations and kernel fusion have respective limitations. The aim of this work is twofold: one is to propose a novel individual feature extraction method; another is to develop an ensemble method to improve prediction performance using comprehensive information represented in the form of high dimensional feature vector obtained by 11 feature extraction methods. Methodology/Principal Findings A novel two-stage multiclass support vector machine is proposed to predict protein subnuclear localizations. It only considers those feature extraction methods based on amino acid classifications and physicochemical properties. In order to speed up our system, an automatic search method for the kernel parameter is used. The prediction performance of our method is evaluated on four datasets: Lei dataset, multi-localization dataset, SNL9 dataset and a new independent dataset. The overall accuracy of prediction for 6 localizations on Lei dataset is 75.2% and that for 9 localizations on SNL9 dataset is 72.1% in the leave-one-out cross validation, 71.7% for the multi-localization dataset and 69.8% for the new independent dataset, respectively. Comparisons with those existing methods show that our method performs better for both single-localization and multi-localization proteins and achieves more balanced sensitivities and specificities on large-size and small-size subcellular localizations. The overall accuracy improvements are 4.0% and 4.7% for single-localization proteins and 6.5% for multi-localization proteins. The reliability and stability of our classification model are further confirmed by permutation analysis. Conclusions It can be concluded that our method is effective and valuable for predicting protein subnuclear localizations. A web server has been designed to implement the proposed method. It is freely available at http://bioinformatics.awowshop.com/snlpr​ed_page.php.

Multi-level knowledge transfer in software development outsourcing projects : the agency theory view

In recent years, software development outsourcing has become even more complex. Outsourcing partner have begun‘re- outsourcing’ components of their projects to other outsourcing companies to minimize cost and gain efficiencies, creating a multi-level hierarchy of outsourcing. This research in progress paper presents preliminary findings of a study designed to understand knowledge transfer effectiveness of multi-level software development outsourcing projects. We conceptualize the SD-outsourcing entities using the Agency Theory. This study conceptualizes, operationalises and validates the concept of Knowledge Transfer as a three-phase multidimensional formative index of 1) Domain knowledge, 2) Communication behaviors, and 3) Clarity of requirements. Data analysis identified substantial, significant differences between the Principal and the Agent on two of the three constructs. Using Agency Theory, supported by preliminary findings, the paper also provides prescriptive guidelines of reducing the friction between the Principal and the Agent in multi-level software outsourcing.

Groundwater visualisation system (GVS) : a software framework for integrated display and interrogation of conceptual hydrogeological models, data and time-series animation

Management of groundwater systems requires realistic conceptual hydrogeological models as a framework for numerical simulation modelling, but also for system understanding and communicating this to stakeholders and the broader community. To help overcome these challenges we developed GVS (Groundwater Visualisation System), a stand-alone desktop software package that uses interactive 3D visualisation and animation techniques. The goal was a user-friendly groundwater management tool that could support a range of existing real-world and pre-processed data, both surface and subsurface, including geology and various types of temporal hydrological information. GVS allows these data to be integrated into a single conceptual hydrogeological model. In addition, 3D geological models produced externally using other software packages, can readily be imported into GVS models, as can outputs of simulations (e.g. piezometric surfaces) produced by software such as MODFLOW or FEFLOW. Boreholes can be integrated, showing any down-hole data and properties, including screen information, intersected geology, water level data and water chemistry. Animation is used to display spatial and temporal changes, with time-series data such as rainfall, standing water levels and electrical conductivity, displaying dynamic processes. Time and space variations can be presented using a range of contouring and colour mapping techniques, in addition to interactive plots of time-series parameters. Other types of data, for example, demographics and cultural information, can also be readily incorporated. The GVS software can execute on a standard Windows or Linux-based PC with a minimum of 2 GB RAM, and the model output is easy and inexpensive to distribute, by download or via USB/DVD/CD. Example models are described here for three groundwater systems in Queensland, northeastern Australia: two unconfined alluvial groundwater systems with intensive irrigation, the Lockyer Valley and the upper Condamine Valley, and the Surat Basin, a large sedimentary basin of confined artesian aquifers. This latter example required more detail in the hydrostratigraphy, correlation of formations with drillholes and visualisation of simulation piezometric surfaces. Both alluvial system GVS models were developed during drought conditions to support government strategies to implement groundwater management. The Surat Basin model was industry sponsored research, for coal seam gas groundwater management and community information and consultation. The “virtual” groundwater systems in these 3D GVS models can be interactively interrogated by standard functions, plus production of 2D cross-sections, data selection from the 3D scene, rear end database and plot displays. A unique feature is that GVS allows investigation of time-series data across different display modes, both 2D and 3D. GVS has been used successfully as a tool to enhance community/stakeholder understanding and knowledge of groundwater systems and is of value for training and educational purposes. Projects completed confirm that GVS provides a powerful support to management and decision making, and as a tool for interpretation of groundwater system hydrological processes. A highly effective visualisation output is the production of short videos (e.g. 2–5 min) based on sequences of camera ‘fly-throughs’ and screen images. Further work involves developing support for multi-screen displays and touch-screen technologies, distributed rendering, gestural interaction systems. To highlight the visualisation and animation capability of the GVS software, links to related multimedia hosted online sites are included in the references.

The OO files : providing online formative feedback on Contract Law learning in a narrative setting

Feedback, both formative and summative, enables students to reflect on their understandings and to restructure their thinking to develop their capabilities. It can also encourage positive motivation and help boost self-esteem. Online multiple choice questions can be an efficient and effective means of providing timely formative feedback. At the same time, locating learning in a narrative environment can facilitate engaging and effective learning experiences. Narratives can help learners to navigate through information and support cognitive and imaginative engagement. This article will discuss The 00 Files, an online suite of modules containing multiple choice questions situated in the narrative of a fictional law firm. It notes student responses to the program and discusses lessons that may be learnt from its development which may be of assistance to academics considering the development of similar programs for their courses.

The construction contract bidder homogeneity assumption : an empirical test

This paper describes an empirical study to test the proposition that all construction contract bidders are homogeneous ie. they can be treated as behaving collectively in an identical (statistical) manner. Examination of previous analyses of bidding data reveals a flaw in the method of standardising bids across different size contracts and a new procedure is proposed which involves the estimation of a contract datum. Three independent sets of bidding data were then subjected to this procedure and estimates of the necessary distributional parameters obtained. These were then tested against the bidder homogeneity assumption resulting in the conclusion that the assumption may be appropriate for a three parameter log-normal shape, but not for scale and location.

Factors affecting marketing decision making with an ethical content : collusive tendering in the construction contract market

Reports of immoral marketing practices i n the construction industry attract political, media and public but not much academic interest. This paper adopts a behavioural perspective and proposes a model for applying marketing ethics concepts and methods in the study of collusion in the construction contract market. An extensive multidisciplinary review of existing literature identified a lack of adequate conceptualisation of the mechanisms and decision making factors of collusive tendering. The process of developing the model is detailed in this paper. The objectives and methodology of the research project that tested the model are also outlined. The paper concludes with a brief note on the contributions and application of the proposed model.

Connecting across continents : collaborative learning in a Web 2.0 world

Purpose – The article aims to review a university course, offered to students in both Australia and Germany, to encourage them to learn about designing, implementing, marketing and evaluating information programs and services in order to build active and engaged communities. The concepts and processes of Web 2.0 technologies come together in the learning activities, with students establishing their own personal learning networks (PLNs). Design/methodology/approach – The case study examines the principles of learning and teaching that underpin the course and presents the students' own experiences of the challenges they faced as they explored the interactive, participative and collaborative dimensions of the web. Findings – The online format of the course and the philosophy of learning through play provided students with a safe and supportive environment for them to move outside of their comfort zones, to be creative, to experiment and to develop their professional personas. Reflection on learning was a key component that stressed the value of reflective practice in assisting library and information science (LIS) professionals to adapt confidently to the rapidly changing work environment. Originality/value – This study provides insights into the opportunities for LIS courses to work across geographical boundaries, to allow students to critically appraise library practice in different contexts and to become active participants in wider professional networks.

Characteristics of Chinese drivers attending a mandatory training course following license suspension

Penalties and sanctions to deter risky/illegal behaviours are important components of traffic law enforcement. Sanctions can be applied to the vehicle (e.g., impoundment), the person (e.g., remedial programs or jail), or the licence (e.g., disqualification). For licence sanctions, some offences attract automatic suspension while others attract demerit points which can indirectly lead to licence loss. In China, a licence is suspended when a driver accrues twelve demerit points within one year. When this occurs, the person must undertake a one-week retraining course at their own expense and successfully pass an examination to become relicensed. Little is known about the effectiveness of this program. A pilot study was conducted in Zhejiang Province to examine basic information about participants of a retraining course. The aim was to gather baseline data for future comparison. Participants were recruited at a driver retraining centre in a large city in Zhejiang Province. In total, 239 suspended drivers completed an anonymous questionnaire which included demographic information, driving history, and crash involvement. Overall, 87% were male with an overall mean age of 35.02 years (SD=8.77; range 21-60 years). A large proportion (83.3%) of participants owned a vehicle. Commuting to work was reported by 64% as their main reason for driving, while 16.3% reported driving for work. Only 6.4% reported holding a licence for 1 year or less (M=8.14 years, SD=6.5, range 1-31 years) and people reported driving an average of 18.06 hours/week (SD=14.4, range 1-86 hours). This represents a relatively experienced group, especially given the increase in new drivers in China. The number of infringements reportedly received in the previous year ranged from 2 to 18 (M=4.6, SD=3.18); one third of participants reported having received 5 or more infringements. Approximately one third also reported having received infringements in the previous year but not paid them. Various strategies for avoiding penalties were reported. The most commonly reported traffic violations were: drink driving (DUI; 0.02-0.08 mg/100ml) with 61.5% reporting 1 such violation; and speeding (47.7% reported 1-10 violations). Only 2.2% of participants reported the more serious drunk driving violation (DWI; above 0.08mg/100ml). Other violations included disobeying traffic rules, using inappropriate licence, and licence plate destroyed/not displayed. Two-thirds of participants reported no crash involvement in the previous year while 14.2% reported involvement in 2-5 crashes. The relationship between infringements and crashes was limited, however there was a small, positive significant correlation between crashes and speeding infringements (r=.2, p=.004). Overall, these results indicate the need for improved compliance with the law among this sample of traffic offenders. For example, lower level drink driving (DUI) and speeding were the most commonly reported violations with some drivers having committed a large number in the previous year. It is encouraging that the more serious offence of drunk driving (DWI) was rarely reported. The effectiveness of this driver retraining program and the demerit point penalty system in China is currently unclear. Future research including driver follow up via longitudinal study is recommended to determine program effectiveness to enhance road safety in China.

ClusterEval 1.0 : Cluster quality Evaluation software

This report describes the available functionality and use of the ClusterEval evaluation software. It implements novel and standard measures for the evaluation of cluster quality. This software has been used at the INEX XML Mining track and in the MediaEval Social Event Detection task.

Developing and delivering a software internationalisation subject

This paper describes the content and delivery of a software internationalisation subject (ITN677) that was developed for Master of Information Technology (MIT) students in the Faculty of Information Technology at Queensland University of Technology. This elective subject introduces students to the strategies, technologies, techniques and current development associated with this growing 'software development for the world' specialty area. Students learn what is involved in planning and managing a software internationalisation project as well as designing, building and using a software internationalisation application. Students also learn about how a software internationalisation project must fit into an over-all product localisation and globalisation that may include culturalisation, tailored system architectures, and reliance upon industry standards. In addition, students are exposed to the different software development techniques used by organizations in this arena and the perils and pitfalls of managing software internationalisation projects.

Locating packaged software in information systems research

The papers in this issue focus our attention to packaged software as an increasingly important, but still relatively poorly understood phenomena in the information systems research community. The topic is not new: Lucas et al. (1988) wrote a provocative piece focused on the issues with implementing packaged software. A decade later, Carmel (1997) argued that packaged software was both ideally suited for American entrepreneurial activity and rapidly growing. The information systems research community, however, has moved more slowly to engage this change (e.g., Sawyer, 2001). The papers in this special issue represent a significant step in better engaging the issues of packaged software relative to information systems research, and highlighting opportunities for additional relevant research.

The maintenance implications of the customization of ERP software

Enterprise resource planning (ERP) software is a dominant approach for dealing with legacy information system problems. In order to avoid invalidating maintenance and development support from the ERP vendor, most organizations reengineer their business processes in line with those implicit within the software. Regardless, some customization is typically required. This paper presents two case studies of ERP projects where customizations have been performed. The case analysis suggests that while customizations can give true organizational benefits, careful consideration is required to determine whether a customization is viable given its potential impact upon future maintenance. Copyright © 2001 John Wiley & Sons, Ltd.

Exploring subscription renewal intention of operational cloud enterprise systems - a stakeholder perspective

Retaining customers is a relevant topic throughout all service industries. However, only limited attention has been directed towards studying the antecedents of subscription renewal in the context of operational cloud enterprise systems. Cloud services have historically been offered as subscription-based services with the (theoretical) possibility of seamless service cancellation, in contrast to classical IT-Outsourcing contracts or license-based software installations of on-premise enterprise systems. In this work, we investigate the central concept of subscription renewal by focusing on different facets of IS success and their relevance for distinct employee cohorts. Analyzing inter-cohort differences has strong practical implications, as it helps IT vendors to focus on specific IT-related factors when trying to retain customers. Therefore an empirical study was undertaken. The hypotheses were developed on an individual level and tested using survey responses of IT decision makers within companies which adopted cloud enterprise systems. Gathered data was then analyzed using PLS. The results show that subscription renewal intention of the strategic cohort is mainly based on perceived system quality, whereas information quality explains most of the variance of subscription renewal in the management cohort. Beneath the cloud enterprise systems specific contributions, the work adds to the theoretical body of research related to IS success and IS continuation, as well as stakeholder perspectives.

An interpretive field study of packaged software selection processes

Packaged software is pre-built with the intention of licensing it to users in domestic settings and work organisations. This thesis focuses upon the work organisation where packaged software has been characterised as one of the latest ‘solutions’ to the problems of information systems. The study investigates the packaged software selection process that has, to date, been largely viewed as objective and rational. In contrast, this interpretive study is based on a 21⁄2 year long field study of organisational experiences with packaged software selection at T.Co, a consultancy organisation based in the United Kingdom. Emerging from the iterative process of case study and action research is an alternative theory of packaged software selection. The research argues that packaged software selection is far from the rationalistic and linear process that previous studies suggest. Instead, the study finds that aspects of the traditional process of selection incorporating the activities of gathering requirements, evaluation and selection based on ‘best fit’ may or may not take place. Furthermore, even where these aspects occur they may not have equal weight or impact upon implementation and usage as may be expected. This is due to the influence of those multiple realities which originate from the organisational and market environments within which packages are created, selected and used, the lack of homogeneity in organisational contexts and the variously interpreted characteristics of the package in question.