Supplementary Information : Hogan, Holland, Holloway, Petit and Read : Read Classification for Next Generation Sequencing, ESANN 2013, April 2013

This item provides supplementary materials for the paper mentioned in the title, specifically a range of organisms used in the study. The full abstract for the main paper is as follows: Next Generation Sequencing (NGS) technologies have revolutionised molecular biology, allowing clinical sequencing to become a matter of routine. NGS data sets consist of short sequence reads obtained from the machine, given context and meaning through downstream assembly and annotation. For these techniques to operate successfully, the collected reads must be consistent with the assumed species or species group, and not corrupted in some way. The common bacterium Staphylococcus aureus may cause severe and life-threatening infections in humans,with some strains exhibiting antibiotic resistance. In this paper, we apply an SVM classifier to the important problem of distinguishing S. aureus sequencing projects from alternative pathogens, including closely related Staphylococci. Using a sequence k-mer representation, we achieve precision and recall above 95%, implicating features with important functional associations.

Why stagnant? behind the scenes in Indonesia’s reformed state asset management policies

This study seeks to answer the question of “why is policy innovation in Indonesia, in particular reformed state asset management laws and regulations, stagnant?” through an empirical and qualitative approach, identifying and exploring potential impeding influences to the full and equal implementation of said laws and regulations. The policies and regulations governing the practice of state asset management has emerged as an urgent question among many countries worldwide (Conway, 2006; Dow, Gillies, Nichols, & Polen, 2006; Kaganova, McKellar, & Peterson, 2006; McKellar, 2006b) for there is heightened awareness of the complex and crucial role that state assets play in public service provision. Indonesia is an example of such country, introducing a ‘big-bang’ reform in state asset management laws, policies, regulations, and technical guidelines. Two main reasons propelled said policy innovation: a) world-wide common challenges in state asset management practices - such as incomplete information system, accountability, and governance adherence/conceptualisation (Kaganova, McKellar and Peterson 2006); and b) unfavourable state assets audit results in all regional governments across Indonesia. The latter reasoning is emphasised, as the Indonesian government admits to past neglect in ensuring efficiency and best practice in its state asset management practices. Prior to reform there was euphoria of building and developing state assets and public infrastructure to support government programs of the day. Although this euphoria resulted in high growth within Indonesia, there seems to be little attention paid to how state assets bought/built is managed. Up until 2003-2004 state asset management is considered to be minimal; inventory of assets is done manually, there is incomplete public sector accounting standards, and incomplete financial reporting standards (Hadiyanto 2009). During that time transparency, accountability, and maintenance state assets was not the main focus, be it by the government or the society itself (Hadiyanto 2009). Indonesia exemplified its enthusiasm in reforming state asset management policies and practices through the establishment of the Directorate General of State Assets in 2006. The Directorate General of State Assets have stressed the new direction that it is taking state asset management laws and policies through the introduction of Republic of Indonesia Law Number 38 Year 2008, which is an amended regulation overruling Republic of Indonesia Law Number 6 Year 2006 on Central/Regional Government State Asset Management (Hadiyanto, 2009c). Law number 38/2008 aims to further exemplify good governance principles and puts forward a ‘the highest and best use of assets’ principle in state asset management (Hadiyanto, 2009a). The methodology of this study is that of qualitative case study approach, with a triangulated data collection method of document analysis (all relevant state asset management laws, regulations, policies, technical guidelines, and external audit reports), semi-structured interviews, and on-site observation. Empirical data of this study involved a sample of four Indonesian regional governments and 70 interviews, performed during January-July 2010. The analytical approach of this study is that of thematic analysis, in an effort to identify common influences and/or challenges to policy innovation within Indonesia. Based on the empirical data of this study specific impeding influences to state asset management reform is explored, answering the question why innovative policy implementation is stagnant. An in-depth analysis of each influencing factors to state asset management reform, and the attached interviewee’s opinions for each factor, suggests the potential of an ‘excuse rhetoric’; whereby the influencing factors identified are a smoke-screen, or are myths that public policy makers and implementers believe in; as a means to explain innovative policy stagnancy. This study offers insights to Indonesian policy makers interested in ensuring the conceptualisation and full implementation of innovative policies, particularly, although not limited to, within the context of state asset management practices.

Goodbye TAIS and thanks for all the information

The Therapeutic Advice and Information Service was funded by the National Prescribing Service to provide a national drug information service for health professionals working in the community. For ten years the service achieved high levels of client satisfaction, and reached its contracted target of 6000 enquiries about medicines per year, however the service ceased on 30 June 2010.

Ontology-based feature modeling for construction information extraction from a building information model

A building information model (BIM) provides a rich representation of a building's design. However, there are many challenges in getting construction-specific information from a BIM, limiting the usability of BIM for construction and other downstream processes. This paper describes a novel approach that utilizes ontology-based feature modeling, automatic feature extraction based on ifcXML, and query processing to extract information relevant to construction practitioners from a given BIM. The feature ontology generically represents construction-specific information that is useful for a broad range of construction management functions. The software prototype uses the ontology to transform the designer-focused BIM into a construction-specific feature-based model (FBM). The formal query methods operate on the FBM to further help construction users to quickly extract the necessary information from a BIM. Our tests demonstrate that this approach provides a richer representation of construction-specific information compared to existing BIM tools.

Querying a building information model for construction-specific spatial information

The design and construction community has shown increasing interest in adopting building information models (BIMs). The richness of information provided by BIMs has the potential to streamline the design and construction processes by enabling enhanced communication, coordination, automation and analysis. However, there are many challenges in extracting construction-specific information out of BIMs. In most cases, construction practitioners have to manually identify the required information, which is inefficient and prone to error, particularly for complex, large-scale projects. This paper describes the process and methods we have formalized to partially automate the extraction and querying of construction-specific information from a BIM. We describe methods for analyzing a BIM to query for spatial information that is relevant for construction practitioners, and that is typically represented implicitly in a BIM. Our approach integrates ifcXML data and other spatial data to develop a richer model for construction users. We employ custom 2D topological XQuery predicates to answer a variety of spatial queries. The validation results demonstrate that this approach provides a richer representation of construction-specific information compared to existing BIM tools.

Crowdsourcing information systems : definition, typology and design

Crowdsourcing has become a popular approach for capitalizing on the potential of large and open crowds of people external to the organization. While crowdsourcing as a phenomenon is studied in a variety of fields, research mostly focuses on isolated aspects and little is known about the integrated design of crowdsourcing efforts. We introduce a socio-technical systems perspective on crowdsourcing, which provides a deeper understanding of the components and relationships in crowdsourcing systems. By considering the function of crowdsourcing systems within their organizational context, we develop a typology of four distinct system archetypes. We analyze the characteristics of each type and derive a number of design requirements for the respective system components. The paper lays a foundation for IS-based crowdsourcing research, channels related academic work, and helps guiding the study and design of crowdsourcing information systems.

Open source information retrieval : a report on the SIGIR 2012 workshop

On August 16, 2012 the SIGIR 2012 Workshop on Open Source Information Retrieval was held as part of the SIGIR 2012 conference in Portland, Oregon, USA. There were 2 invited talks, one from industry and one from academia. There were 6 full papers and 6 short papers presented as well as demonstrations of 4 open source tools. Finally there was a lively discussion on future directions for the open source Information Retrieval community. This contribution discusses the events of the workshop and outlines future directions for the community.

An innovative information gathering and data analysis platform for railway level crossing safety data

This paper describes an innovative platform that facilitates the collection of objective safety data around occurrences at railway level crossings using data sources including forward-facing video, telemetry from trains and geo-referenced asset and survey data. This platform is being developed with support by the Australian rail industry and the Cooperative Research Centre for Rail Innovation. The paper provides a description of the underlying accident causation model, the development methodology and refinement process as well as a description of the data collection platform. The paper concludes with a brief discussion of benefits this project is expected to provide the Australian rail industry.

Link discovery for Chinese/English cross-language web information retrieval

Nowadays people heavily rely on the Internet for information and knowledge. Wikipedia is an online multilingual encyclopaedia that contains a very large number of detailed articles covering most written languages. It is often considered to be a treasury of human knowledge. It includes extensive hypertext links between documents of the same language for easy navigation. However, the pages in different languages are rarely cross-linked except for direct equivalent pages on the same subject in different languages. This could pose serious difficulties to users seeking information or knowledge from different lingual sources, or where there is no equivalent page in one language or another. In this thesis, a new information retrieval task—cross-lingual link discovery (CLLD) is proposed to tackle the problem of the lack of cross-lingual anchored links in a knowledge base such as Wikipedia. In contrast to traditional information retrieval tasks, cross language link discovery algorithms actively recommend a set of meaningful anchors in a source document and establish links to documents in an alternative language. In other words, cross-lingual link discovery is a way of automatically finding hypertext links between documents in different languages, which is particularly helpful for knowledge discovery in different language domains. This study is specifically focused on Chinese / English link discovery (C/ELD). Chinese / English link discovery is a special case of cross-lingual link discovery task. It involves tasks including natural language processing (NLP), cross-lingual information retrieval (CLIR) and cross-lingual link discovery. To justify the effectiveness of CLLD, a standard evaluation framework is also proposed. The evaluation framework includes topics, document collections, a gold standard dataset, evaluation metrics, and toolkits for run pooling, link assessment and system evaluation. With the evaluation framework, performance of CLLD approaches and systems can be quantified. This thesis contributes to the research on natural language processing and cross-lingual information retrieval in CLLD: 1) a new simple, but effective Chinese segmentation method, n-gram mutual information, is presented for determining the boundaries of Chinese text; 2) a voting mechanism of name entity translation is demonstrated for achieving a high precision of English / Chinese machine translation; 3) a link mining approach that mines the existing link structure for anchor probabilities achieves encouraging results in suggesting cross-lingual Chinese / English links in Wikipedia. This approach was examined in the experiments for better, automatic generation of cross-lingual links that were carried out as part of the study. The overall major contribution of this thesis is the provision of a standard evaluation framework for cross-lingual link discovery research. It is important in CLLD evaluation to have this framework which helps in benchmarking the performance of various CLLD systems and in identifying good CLLD realisation approaches. The evaluation methods and the evaluation framework described in this thesis have been utilised to quantify the system performance in the NTCIR-9 Crosslink task which is the first information retrieval track of this kind.

Social and environmental accounting research : major contributions and future directions for developing countries

A review is provided of major contributions in social and environmental accounting literature focusing on the issues of developing countries. The review of prior research shows that the major contributions have been related to the motivations for social and environmental disclosure. However, other important research areas such as ethical/accountability issues and how to cost externalities which have already been considered within the developing country context. Contemporary social and environmental issues such as climate change and greenhouse gas emissions affecting the global community also appear to be key issues of research to scholars in both developed and developing countries. Finally, some future research directions are identified.

Perceptions of corporate social and environmental accounting and reporting practices from accountants in Bangladesh

Purpose – The aim of this study is to elicit accountants’ perceptions regarding corporate social and environmental accounting and reporting practices in a developing country such as Bangladesh. Design/methodology/approach – Members of the Institute of Chartered Accountants of Bangladesh (ICAB) were surveyed to determine their perceptions on issues pertaining to social and environmental accounting and reporting practices in Bangladesh. Findings – Whilst the findings show that accountants have positive attitudes toward corporate social and environmental accounting, progress is limited, with the absence of ICAB in making any noticeable effort to develop such practices. Research implications – Unlike prior studies, the implications of this study suggest that without international influence, it is less likely that institutional forces in Bangladesh (ICAB and the government) would be effective in dealing with social and environmental accounting and reporting issues. Originality/value – While prior studies advocate proactive roles of the accounting profession, this study argues that proactive roles are less likely to prevail in the context of Bangladesh without direct intervention from institutional and regulatory authorities in the international arena.

Designing an information accountability framework for eHealth

Information privacy is a crucial aspect of eHealth. Appropriate privacy management measures are therefore essential for its success. However, traditional measures for privacy preservation such as rigid access controls (i.e., preventive measures) are not suitable to eHealth because of the specialised and information - intensive nature of healthcare itself, and the nature of the information. Healthcare professionals (HCP) require easy, unrestricted access to as much information as possible towards making well - informed decisions. On the other end of the scale however, consumers (i.e., patients) demand control over their health information and raise concerns for privacy arising from internal activities (i.e., information use by HCPs). A proper balance of these competing concerns is vital for the implementation of successful eHealth systems. Towards reaching this balance, we propose an information accountability framework (IAF) for eHealth systems.

Engaging social customers : influencing new marketing strategies for social media information sources

A global, online quantitative study among 300 consumers of digital technology products found the most reliable information sources were friends, family or word of mouth (WOM) from someone they knew, followed by expert product reviews, and product reviews written by other consumers. The most unreliable information sources were advertising or infomercials, automated recommendations based on purchasing patterns or retailers. While a very small number of consumers evaluated products online, rating of products and online discussions were more frequent activities. The most popular social media websites for reviews were Facebook, Twitter, Amazon and e-Bay, indicating the importance of WOM in social networks and online media spaces that feature product reviews as it is the most persuasive piece of information in both online and offline social networks. These results suggest that ‘social customers’ must be considered as an integral part of a marketing strategy.

Principals, Teachers, and Student's Perception of the Information and Communication Technology in Kuwait Secondary Schools (Rhetoric and reality)

ICT integration has been advocated to provide opportunities to improve students’ achievement and engagement through transforming the educational setting. A valuable tool that contributes in enhancing and developing students’ cognitive skills for lifelong learning, ICT integration has introduced a new educational philosophy, shifting the role of students into a more central position in the pedagogical processes. Kuwait, as with many other countries, has recently planned ICT integration to develop its citizen’s capacities. This study sought to capture the principals’, teachers’, and students’ perceptions of ICT integration in pedagogical activities, as well as how ICT is being used for learning and teaching activities in three ICT leading Kuwaiti secondary schools. Interviews with principals, teachers, and students were conducted, along with an open-ended questionnaire for the teachers, researcher observations, and document analysis. The findings revealed that ICT integration in Kuwait needed to be reinforced to accomplish the ICT integration objectives. A call for further support for teachers, and a reconsideration of the ICT integration strategies were also recommended.