BioPatML : pattern sharing for the genomic sciences

Computational biology increasingly demands the sharing of sophisticated data and annotations between research groups. Web 2.0 style sharing and publication requires that biological systems be described in well-defined, yet flexible and extensible formats which enhance exchange and re-use. In contrast to many of the standards for exchange in the genomic sciences, descriptions of biological sequences show a great diversity in format and function, impeding the definition and exchange of sequence patterns. In this presentation, we introduce BioPatML, an XML-based pattern description language that supports a wide range of patterns and allows the construction of complex, hierarchically structured patterns and pattern libraries. BioPatML unifies the diversity of current pattern description languages and fills a gap in the set of XML-based description languages for biological systems. We discuss the structure and elements of the language, and demonstrate its advantages on a series of applications, showing lightweight integration between the BioPatML parser and search engine, and the SilverGene genome browser. We conclude by describing our site to enable large scale pattern sharing, and our efforts to seed this repository.

Economic issues in funding and supplying public sector information

In May 2005, a research team began to investigate whether designing and implementing a whole-of-government information licensing framework was possible. This framework was needed to administer copyright in relation to information produced by the government and to deal properly with privately-owned copyright on which government works often rely. The outcome so far is the design of the Government Information Licensing Framework (GILF) and its gradual uptake within a number of Commonwealth and State government agencies. However, licensing is part of a larger issue in managing public sector information (PSI); and it has important parallels with the management of libraries and public archives. Among other things, managing the retention and supply of PSI requires an ability to search and locate information, ability to give public access to the information legally, and an ability to administer charges for supplying information wherever it is required by law. The aim here is to provide a summary overview of pricing principles as they relate to the supply of PSI.

Development of a colorimetric assay for heparanase activity suitable for kinetic analysis and inhibitor screening

The role that heparanase plays during metastasis and angiogenesis in tumors makes it an attractive target for cancer therapeutics. Despite this enzyme’s significance, most of the assays developed to measure its activity are complex. Moreover, they usually rely on labeling variable preparations of the natural substrate heparan sulfate, making comparisons across studies precarious. To overcome these problems, we have developed a convenient assay based on the cleavage of the synthetic heparin oligosaccharide fondaparinux. The assay measures the appearance of the disaccharide product of heparanase-catalyzed fondaparinux cleavage colorimetrically using the tetrazolium salt WST-1. Because this assay has a homogeneous substrate with a single point of cleavage, the kinetics of the enzyme can be reliably characterized, giving a Km of 46 μM and a kcat of 3.5 s−1 with fondaparinux as substrate. The inhibition of heparanase by the published inhibitor, PI-88, was also studied, and a Ki of 7.9 nM was determined. The simplicity and robustness of this method, should, not only greatly assist routine assay of heparanase activity but also could be adapted for high-throughput screening of compound libraries, with the data generated being directly comparable across studies.

Community information literacy : developing an Australian research agenda

The majority of information literacy (IL) research has been con ducted within the confi nes of educational or workplace settings. Little to no research has explored IL in community contexts. This paper will consider the current state of IL research within the community setting. The paper uses three re cent IL studies as a vehicle for developing an Australian com munity IL research agenda. Three observations are made about community information literacy (CIL) and CIL research: (i) it is multi- and inter-disciplinary; (ii) it has a learning lens; and (iii) it has a pluralistic approach. The CIL research agenda should be seen as practical and real – it is about real people, doing real things in real life contexts. To achieve this we must bring to gether a research community that is ready to cross boundar ies and forge relationships with other groups. In addition a coherent and structured research agenda should be established.

A constructivist approach to media literacy education: The role of the library

An informed citizenry is essential to the effective functioning of democracy. In most modern liberal democracies, citizens have traditionally looked to the media as the primary source of information about socio-political matters. In our increasingly mediated world, it is critical that audiences be able to effectively and accurately use the media to meet their information needs. Media literacy, the ability to access, understand, evaluate and create media content is therefore a vital skill for a healthy democracy. The past three decades have seen the rapid expansion of the information environment, particularly through Internet technologies. It is obvious that media usage patterns have changed dramatically as a result. Blogs and websites are now popular sources of news and information, and are for some sections of the population likely to be the first, and possibly only, information source accessed when information is required. What are the implications for media literacy in such a diverse and changing information environment? The Alexandria Manifesto stresses the link between libraries, a well informed citizenry and effective governance, so how do these changes impact on libraries? This paper considers the role libraries can play in developing media literate communities, and explores the ways in which traditional media literacy training may be expanded to better equip citizens for new media technologies. Drawing on original empirical research, this paper highlights a key shortcoming of existing media literacy approaches: that of overlooking the importance of needs identification as an initial step in media selection. Self-awareness of one’s actual information need is not automatic, as can be witnessed daily at reference desks in libraries the world over. Citizens very often do not know what it is that they need when it comes to information. Without this knowledge, selecting the most appropriate information source from the vast range available becomes an uncertain, possibly even random, enterprise. Incorporating reference interview-type training into media literacy education, whereby the individual will develop the skills to interrogate themselves regarding their underlying information needs, will enhance media literacy approaches. This increased focus on the needs of the individual will also push media literacy education into a more constructivist methodology. The paper also stresses the importance of media literacy training for adults. Media literacy education received in school or even university cannot be expected to retain its relevance over time in our rapidly evolving information environment. Further, constructivist teaching approaches highlight the importance of context to the learning process, thus it may be more effective to offer media literacy education relating to news media use to adults, whilst school-based approaches focus on types of media more relevant to young people, such as entertainment media. Librarians are ideally placed to offer such community-based media literacy education for adults. They already understand, through their training and practice of the reference interview, how to identify underlying information needs. Further, libraries are placed within community contexts, where the everyday practice of media literacy occurs. The Alexandria Manifesto stresses the link between libraries, a well informed citizenry and effective governance. It is clear that libraries have a role to play in fostering media literacy within their communities.

"I'm thinking 'bout moving in"... An examination of the issues impacting on the recruitment of secondary school graduates to the library and information profession

In recent years concern has been expressed internationally about the future of the library and information services (LIS) profession: recruitment and retention, changing skill sets and declining numbers of people choosing librarianship as a career are all factors contributing to an uncertain future. One area yet explored in any depth is the topic of why LIS studies are not perceived, let alone promoted, as a good first professional qualification for high school graduates. This paper considers the professional literature that examines the uptake of librarianship as a first qualification by school leavers and discusses, in the context of the Australian library sector, the role of professional associations, library schools, National and State Libraries, as well as individual libraries and librarians. Examples of best practice are presented to highlight the opportunities for inspiring and motivating students through well structured and stimulating work experience programs. The topic is relevant to all librarians who are interested in the future of the LIS profession. It is argued that the focus of the present conference on ‘moving up’ and ‘moving on’ can only have real significance when the profession has a more complete understanding of the barriers to and the opportunities for ‘moving in’.

The strategic and operational dimensions of staff training and professional development for information professionals : what neXus2 has revealed

The paper seeks to continue the debate about the need for professionals in the library and information services (LIS) sector to continually engage in career-long learning to sustain and develop their knowledge and skills in a dynamic industry. Aims: The neXus2 workforce study has been funded by the ALIA and the consortium of National and State Libraries Australasia (NSLA). It builds on earlier research work (the neXus census) that looked at the demographic, educational and career perspectives of individual library and information professions, to critically examine institutional policies and practices associated with the LIS workforce. The research aims to develop a clearer understanding of the issues impacting on workforce sustainability, workforce capability and workforce optimisation. Methods: The research methodology involved an extensive online survey conducted in March 2008 which collected data on organisational and general staffing; recruitment and retention; staff development and continuing professional education; and succession planning. Encouragement to participate was provided by key industry groups, including academic, public, health, law and government library and information agencies, with the result that around 150 institutions completed the questionnaire. Results: The paper will specifically discuss the research findings relating to training and professional development, to measure the scope and distribution of training activities across the workforce, to consider the interrelationship between the strategic and operational dimensions of staff development in individual institutions and to analyse the common and distinctive factors evident in the different sectors of the profession. Conclusion: The neXus2 project has successfully engaged LIS institutions in the collection of complex industry data that is relevant to the future education and workforce strategies for all areas of the profession. Cross-sector forums such as Information Online 2009 offer the opportunity for stimulating professional dialogue on the key issues.

The arobase in the libr@ry : new political economies of children’s literatures and literacies

This essay--part of a special issue on the work of Gunther Kress--uses the idea of affordances and constraints to explore the (im)possibilities of new environments for engaging with literature written for children (see Kress, 2003). In particular, it examines a festival of children's literature from an Australian education context that occurs online. The festival is part of a technologically mediated library space designated by the term libr@ry (Kapitzke & Bruce, 2006). The @ symbol (French word "arobase") inserted into the word library indicates that technological mediation has a history, an established set of social practices, and a political economy, which even chatrooms with "real" authors may alter but not fully supplant.

University library virtual reference services : best practices and continuous improvement

The inclusion or not of chat services within Virtual Reference (VR) is an important topic for university libraries. Increasingly, email supported by a Frequently Asked Questions (FAQ) database is suggested in the scholarly literature as the preferred, cost-effective means for providing university VR services. This paper examines these issues and identifies some best practices for university library VR services relating to chat and email service, collaborative service provision, services staffing, and staff training. Further studies are required to more completely identify best practices for the complete range of VR services.

The right person, in the right job, with the right skills, at the right time. A workforce-planning model that goes beyond metrics

Purpose – The paper aims to describe a workforce-planning model developed in-house in an Australian university library that is based on rigorous environmental scanning of an institution, the profession and the sector. Design/methodology/approach – The paper uses a case study that describes the stages of the planning process undertaken to develop the Library’s Workforce Plan and the documentation produced. Findings – While it has been found that the process has had successful and productive outcomes, workforce planning is an ongoing process. To remain effective, the workforce plan needs to be reviewed annually in the context of the library’s overall planning program. This is imperative if the plan is to remain current and to be regarded as a living document that will continue to guide library practice. Research limitations/implications – Although a single case study, the work has been contextualized within the wider research into workforce planning. Practical implications – The paper provides a model that can easily be deployed within a library without external or specialist consultant skills, and due to its scalability can be applied at department or wider level. Originality/value – The paper identifies the trends impacting on, and the emerging opportunities for, university libraries and provides a model for workforce planning that recognizes the context and culture of the organization as key drivers in determining workforce planning. Keywords - Australia, University libraries, Academic libraries, Change management, Manpower planning Paper type - Case study

Report to the Government 2.0 Taskforce : Project 4 - Copyright Law and Intellectual Property

This report is the primary output of Project 4: Copyright and Intellectual Property, the aim of which was to produce a report considering how greater access to and use of government information could be achieved within the scope of the current copyright law. In our submission for Project 4, we undertook to address: •the policy rationales underlying copyright and how they apply in the context of materials owned, held and used by government; • the recommendations of the Copyright Law Review Committee (CLRC) in its 2005 report on Crown copyright; • the legislative and regulatory barriers to information sharing in key domains, including where legal impediments such as copyright have been relied upon (whether rightly or wrongly) to justify a refusal to provide access to government data; • copyright licensing models appropriate to government materials and examples of licensing initiatives in Australia and other relevant jurisdictions; and • issues specific to the galleries, libraries, archives and museums (“GLAM”) sector, including management of copyright in legacy materials and “orphan” works. In addressing these areas, we analysed the submissions received in response to the Government 2.0 Taskforce Issues Paper, consulted with members of the Task Force as well as several key stakeholders and considered the comments posted on the Task Force’s blog. This Project Report sets out our findings on the above issues. It puts forward recommendations for consideration by the Government 2.0 Task Force on steps that can be taken to ensure that copyright and intellectual property promote access to and use of government information.

An experiment in mixed compilation/interpretation

One of the classic forms of intermediate representation used for communication between compiler front-ends and back-ends are those based on abstract stack machines. It is possible to compile the stack machine instructions into machine code by means of an interpretive code generator, or to simulate the stack machine at runtime using an interpreter. This paper describes an approach intermediate between these two extremes. The front-end for a commercial Modula 2 compiler was ported to the "industry standard PC", and a partially compiling back-end written. The object code runs with the assistance of an interpreter, but may be linked with libraries which are fully compiled. The intent was to provide a programming environment on the PC which is identical to that of the same compilers on 32-bit UNIX machines. This objective has been met, and the compiler is available to educational institutions as free-ware. The design basis of the new compiler is described, and the performance critically evaluated.

Leveraging managed frameworks from modular languages

Managed execution frameworks, such as the.NET Common Language Runtime or the Java Virtual Machine, provide a rich environment for the creation of application programs. These execution environments are ideally suited for languages that depend on type-safety and the declarative control of feature access. Furthermore, such frameworks typically provide a rich collection of library primitives specialized for almost every domain of application programming. Thus, when a new language is implemented on one of these frameworks it becomes necessary to provide some kind of mapping from the new language to the libraries of the framework. The design of such mappings is challenging since the type-system of the new language may not span the domain exposed in the library application programming interfaces (APIs). The nature of these design considerations was clarified in the implementation of the Gardens Point Component Pascal (gpcp) compiler. In this paper we describe the issues, and the solutions that we settled on in this case. The problems that were solved have a wider applicability than just our example, since they arise whenever any similar language is hosted in such an environment.

The getting of wisdom : reflections of a teaching librarian

The shift in focus from teaching to learning in higher education can be paralleled in the shift from bibliographic instruction to information literacy. This move has resulted in a change of role from librarians as service providers to educators. This paper argues that in order to facilitate students' 'getting of wisdom', librarians who design and deliver information literacy programs should see themselves as teachers rather than trainers. It compares the role of the school teacher-librarian with that of the academic teaching librarian. The implications of a dominant training paradigm result in the reduction of information literacy to lower order surface learning. Support for teaching librarians is crucial in changing roles and self-image.

Rivalry within and between strategic networks : an investigation of the United States Automotive Industry

As a consequence of the increased incidence of collaborative arrangements between firms, the competitive environment characterising many industries has undergone profound change. It is suggested that rivalry is not necessarily enacted by individual firms according to the traditional mechanisms of direct confrontation in factor and product markets, but rather as collaborative orchestration between a number of participants or network members. Strategic networks are recognised as sets of firms within an industry that exhibit denser strategic linkages among themselves than other firms within the same industry. Based on this, strategic networks are determined according to evidence of strategic alliances between firms comprising the industry. As a result, a single strategic network represents a group of firms closely linked according to collaborative ties. Arguably, the collective outcome of these strategic relationships engineered between firms suggest that the collaborative benefits attributed to interorganisational relationships require closer examination in respect to their propensity to influence rivalry in intraindustry environments. Derived in large from the social sciences, network theory allows for the micro and macro examination of the opportunities and constraints inherent in the structure of relationships in strategic networks, establishing a relational approach upon which the conduct and performance of firms can be more fully understood. Research to date has yet to empirically investigate the relationship between strategic networks and rivalry. The limited research that has been completed utilising a network rationale to investigate competitive patterns in contemporary industry environments has been characterised by a failure to directly measure rivalry. Further, this prior research has typically embedded investigation in industry settings dominated by technological or regulatory imperatives, such as the microprocessor and airline industries. These industries, due to the presence of such imperatives, are arguably more inclined to support the realisation of network rivalry, through subscription to prescribed technological standards (eg., microprocessor industry) or by being bound by regulatory constraints dictating operation within particular market segments (airline industry). In order to counter these weaknesses, the proposition guiding research - Are patterns of rivalry predicted by strategic network membership? – is embedded in the United States Light Vehicles Industry, an industry not dominated by technological or regulatory imperatives. Further, rivalry is directly measured and utilised in research, thus distinguishing this investigation from prior research efforts. The timeframe of investigation is 1993 – 1999, with all research data derived from secondary sources. Strategic networks were defined within the United States Light Vehicles Industry based on evidence of horizontal strategic relationships between firms comprising the industry. The measure of rivalry used to directly ascertain the competitive patterns of industry participants was derived from the traditional Herfindahl Index, modified to account for patterns of rivalry observed at the market segment level. Statistical analyses of the strategic network and rivalry constructs found little evidence to support the contention of network rivalry; indeed, greater levels of rivalry were observed between firms comprising the same strategic network than between firms participating in opposing network structures. Based on these results, patterns of rivalry evidenced in the United States Light Vehicle Industry over the period 1993 – 1999 were not found to be predicted by strategic network membership. The findings generated by this research are in contrast to current theorising in the strategic network – rivalry realm. In this respect, these findings are surprising. The relevance of industry type, in conjunction with prevailing network methodology, provides the basis upon which these findings are contemplated. Overall, this study raises some important questions in relation to the relevancy of the network rivalry rationale, establishing a fruitful avenue for further research.