Blast atlas: a virtual observatory for genomes

Following the completion of the draft Human Genome in 2001, genomic sequence data is becoming available at an accelerating rate, fueled by advances in sequencing and computational technology. Meanwhile, large collections of astronomical and geospatial data have allowed the creation of virtual observatories, accessible throughout the world and requiring only commodity hardware. Through a combination of advances in data management, data mining and visualization, this infrastructure enables the development of new scientific and educational applications as diverse as galaxy classification and real-time tracking of earthquakes and volcanic plumes. In the present paper, we describe steps taken along a similar path towards a virtual observatory for genomes – an immersive three-dimensional visual navigation and query system for comparative genomic data.

How do public librarians constitute information literacy?

To date, much work has been done to examine the ways in which information literacy – a way of thinking about, existing alongside and working with information- functions in an academic setting. However, its role in the non-academic library professions has been largely ignored. Given that the public librarian is responsible for designing and delivering services and programmes aimed at supporting the information literacy needs of the community-at-large there is great value to be had from examining the ways in which public libraries understand and experience IL. The research described in this paper investigates, through the use of phenomenography; the ways in which public librarians understand and experience the concept of Information Literacy.

Reading nineteenth century schoolbooks online : user behavior in a digitized special collection

Special collections, because of the issues associated with conservation and use, a feature they share with archives, tend to be the most digitized areas in libraries. The Nineteenth Century Schoolbooks collection is a collection of 9000 rarely held nineteenth-century schoolbooks that were painstakingly collected over a lifetime of work by Prof. John A. Nietz, and donated to the Hillman Library at the University of Pittsburgh in 1958, which has since grown to 15,000. About 140 of these texts are completely digitized and showcased in a publicly accessible website through the University of Pittsburgh’s Library, along with a searchable bibliography of the entire collection, which expanded the awareness of this collection and its user base to beyond the academic community. The URL for the website is http://digital.library.pitt.edu/nietz/. The collection is a rich resource for researchers studying the intellectual, educational, and textbook publishing history of the United States. In this study, we examined several existing records collected by the Digital Research Library at the University of Pittsburgh in order to determine the identity and searching behaviors of the users of this collection. Some of the records examined include: 1) The results of a 3-month long user survey, 2) User access statistics including search queries for a period of one year, a year after the digitized collection became publicly available in 2001, and 3) E-mail input received by the website over 4 years from 2000-2004. The results of the study demonstrate the differences in online retrieval strategies used by academic researchers and historians, archivists, avocationists, and the general public, and the importance of facilitating the discovery of digitized special collections through the use of electronic finding aids and an interactive interface with detailed metadata.

Librarians without borders

The establishment of libraries in developing countries presents its unique infrastructure, cultural, financial and training challenges... which stimulate inventive solutions. Many benefits, including skill refinement, deep engagement with culture and tourism, flow from the practice of such outward-looking professionalism. 'Librarians Without Borders, Australia' is proposed as a means of providing support for such ventures.

Practical introduction to development of sage applications

Throughout this workshop session we have looked at various configurations of Sage as well as using the Sage UI to run Sage applications (e.g. the image viewer). More advanced usage of Sage has been demonstrated using a Sage compatible version of Paraview highlighting the potential of parallel rendering. The aim of this tutorial session is to give a practical introduction to developing visual content for a tiled display using the Sage libraries. After completing this tutorial you should have the basic tools required to develop your own custom Sage applications. This tutorial is designed for software developers and intermediate programming knowledge is assumed, along with some introductory OpenGL . You will be required to write small portions of C/C++ code to complete this worksheet. However if you do not feel comfortable writing code (or have never written in C or C++), we will be on hand throughout this session so feel free to ask for some help. We have a number of machines in this lab running a VNC client to a virtual machine running Fedora 12. You should all be able to log in with the username “escience”, and password “escience10”. Some of the commands in this worksheet require you to run them as the root user, so note the password as you may need to use it a few times. If you need to access the Internet, then use the username “qpsf01”, password “escience10”

Ebook readers : separating the hype from the reality

Academic libraries have been acquiring ebooks for their collections for a number of years, but the uptake by some users has been curtailed by the limitations of screen reading on a traditional PC or laptop. Ebook readers promise to take us into a new phase of ebook development. Innovations include: wireless connectivity, electronic paper, increased battery life, and customisable displays. The recent rapid take-up of ebook readers in the United States, particularly Amazon’s Kindle, suggests that they may about to gain mass-market acceptance. A bewildering number of ebook readers are being promoted by companies eager to gain market share. In addition, each month seems to bring a new ebook reader or a new model of an existing device. Library administrators are faced with the challenge of separating the hype from the reality and deciding when the time is right to invest in and support these new technologies. The Library at QUT, in particular the QUT Library Ebook Reference Group (ERG) has been closely following developments in ebooks and ebook reader technologies. During mid 2010 QUT Library undertook a trial of a range of ebook readers available to Australian consumers. Each of the ebook readers acquired was evaluated by members of the QUT Library ERG and two student focus groups. Major criteria for evaluation included usability, functionality, accessibility and compatibility with QUT Library’s existing ebook collection. The two student focus groups evaluated the ebook readers mostly according to the criteria of usability and functionality. This paper will discuss these evaluations and outline a recommendation about which type (or types) of ebook readers could be acquired and made available for lending to students.

Australian Library and Information Studies (LIS) researchers' ranking of LIS journals

The paper describes the processes and the outcomes of the ranking of LIS journal titles by Australia’s LIS researchers during 2007-8, firstly through the Australian federal government’s Research Quality Framework (RQF) process and then its replacement, the Excellence in Research for Australia (ERA) initiative. The requirement to rank the journals titles used came from discussions held at the RQF panel meeting held in February 2007 in Canberra, Australia. While it was recognised that the Web of Science (formerly ISI) journal impact approach of journal acceptance for measures of research quality and impact might not work for LIS, it was apparent that this model would be the default if no other ranking of journal titles became apparent. Although an increasing number of LIS and related discipline journals were appearing in the Web of Science listed rankings, the number was few and it was thus decided by the Australian LIS research community to undertake the ranking exercise.

A Python package for Bayesian estimation using Markov Chain Monte Carlo

Markov chain Monte Carlo (MCMC) estimation provides a solution to the complex integration problems that are faced in the Bayesian analysis of statistical problems. The implementation of MCMC algorithms is, however, code intensive and time consuming. We have developed a Python package, which is called PyMCMC, that aids in the construction of MCMC samplers and helps to substantially reduce the likelihood of coding error, as well as aid in the minimisation of repetitive code. PyMCMC contains classes for Gibbs, Metropolis Hastings, independent Metropolis Hastings, random walk Metropolis Hastings, orientational bias Monte Carlo and slice samplers as well as specific modules for common models such as a module for Bayesian regression analysis. PyMCMC is straightforward to optimise, taking advantage of the Python libraries Numpy and Scipy, as well as being readily extensible with C or Fortran.

Correlates of Pedometer Use: Results from a Community-based Physical Activity Intervention Trial (10,000 Steps Rockhampton)

Background Pedometers have become common place in physical activity promotion, yet little information exists on who is using them. The multi-strategy, community-based 10,000 Steps Rockhampton physical activity intervention trial provided an opportunity to examine correlates of pedometer use at the population level. Methods Pedometer use was promoted across all intervention strategies including: local media, pedometer loan schemes through general practice, other health professionals and libraries, direct mail posted to dog owners, walking trail signage, and workplace competitions. Data on pedometer use were collected during the 2-year follow-up telephone interviews from random population samples in Rockhampton, Australia, and a matched comparison community (Mackay). Logistic regression analyses were used to determine the independent influence of interpersonal characteristics and program exposure variables on pedometer use. Results Data from 2478 participants indicated that 18.1% of Rockhampton and 5.6% of Mackay participants used a pedometer in the previous 18-months. Rockhampton pedometer users (n = 222) were more likely to be female (OR = 1.59, 95% CI: 1.11, 2.23), aged 45 or older (OR = 1.69, 95% CI: 1.16, 2.46) and to have higher levels of education (university degree OR = 4.23, 95% CI: 1.86, 9.6). Respondents with a BMI > 30 were more likely to report using a pedometer (OR = 1.68, 95% CI: 1.11, 2.54) than those in the healthy weight range. Compared with those in full-time paid work, respondents in 'home duties' were significantly less likely to report pedometer use (OR = 0.18, 95% CI: 0.06, 0.53). Exposure to individual program components, in particular seeing 10,000 Steps street signage and walking trails or visiting the website, was also significantly associated with greater pedometer use. Conclusion Pedometer use varies between population subgroups, and alternate strategies need to be investigated to engage men, people with lower levels of education and those in full-time 'home duties', when using pedometers in community-based physical activity promotion initiatives.

Massively parallel sequencing and analysis of expressed sequence tags in a successful invasive plant

Background Invasive species pose a significant threat to global economies, agriculture and biodiversity. Despite progress towards understanding the ecological factors associated with plant invasions, limited genomic resources have made it difficult to elucidate the evolutionary and genetic factors responsible for invasiveness. This study presents the first expressed sequence tag (EST) collection for Senecio madagascariensis, a globally invasive plant species. Methods We used pyrosequencing of one normalized and two subtractive libraries, derived from one native and one invasive population, to generate an EST collection. ESTs were assembled into contigs, annotated by BLAST comparison with the NCBI non-redundant protein database and assigned gene ontology (GO) terms from the Plant GO Slim ontologies. Key Results Assembly of the 221 746 sequence reads resulted in 12 442 contigs. Over 50 % (6183) of 12 442 contigs showed significant homology to proteins in the NCBI database, representing approx. 4800 independent transcripts. The molecular transducer GO term was significantly over-represented in the native (South African) subtractive library compared with the invasive (Australian) library. Based on NCBI BLAST hits and literature searches, 40 % of the molecular transducer genes identified in the South African subtractive library are likely to be involved in response to biotic stimuli, such as fungal, bacterial and viral pathogens. Conclusions This EST collection is the first representation of the S. madagascariensis transcriptome and provides an important resource for the discovery of candidate genes associated with plant invasiveness. The over-representation of molecular transducer genes associated with defence responses in the native subtractive library provides preliminary support for aspects of the enemy release and evolution of increased competitive ability hypotheses in this successful invasive. This study highlights the contribution of next-generation sequencing to better understanding the molecular mechanisms underlying ecological hypotheses that are important in successful plant invasions.

Health Librarianship Workforce and Education : Research to plan the future. Final Report.

In late 2009, Health Libraries Australia (HLA) received a small grant to undertake a national research project to determine the future requirements for health librarians in the workforce in Australia and develop a structured, modular education framework (post-graduate qualification and continuing professional development structure) to meet these requirements. The main objective was to consider the education and professional development framework that would ensure that health librarians have a clearly defined scope of practice and the specific competency based knowledge and skills that enable them to contribute to the design and delivery of high quality health services in this country. The final report presents a detailed discussion of the changing Australian healthcare environment and the resulting impact on the health library sector, as well as an overview of international trends in health libraries and the implications for Australian health librarianship education. The research methodology is outlined, followed by an analysis of the findings from the two surveys with health librarians and health library managers and the semi-structured interviews conducted with employers. The Medical Library Association (MLA) in the United States had developed a policy document detailing the competencies required by health librarians. It was found that the MLA competencies represented an accepted professional framework of skills which could be used objectively in the survey instrument to measure the areas of professional knowledge and responsibilities that were relevant in the current workplace, and to identify how these requirements might change in the next three to five years. The research results underscore the imperative for health librarians to engage in regular, relevant professional development activities that will enable them to stay abreast with the rapid contextual changes impacting on their practice. In order to be accepted as key members of the multi-disciplinary health professional team, it is strongly believed that health librarians should commit to establishing the mechanisms for specialist certification maintained through compulsory CPD in an ongoing three-year cycle of revalidation. This development would align ALIA and health librarians with other health sector professional associations which are responsible for the self regulation of entry to and continuation in their profession.

Information literacy research : dimensions of the emerging collective consciousness

Information literacy researchers are beginning to develop a collective consciousness, a consciousness that represents the newly appearing territory of information literacy research. This paper analyses the information literacy research territory as it is represented by the emerging collective consciousness of information literacy researchers. Five dimensions of the collective consciousness are proposed: 1) the sectoral location of the research, 2) ways of seeing information literacy, 3) ‘what’ is being investigated; that is the research object, 4) ‘how’ the object is being investigated; that is the research approaches and paradigms, and 5) disciplinary influences. These dimensions are used to: 1) reveal the character of the information literacy research territory which is in early stages of construction; 2) show how different kinds of research approaches can shed different kinds of light on the object of research; and 3) demonstrate how the five dimensions work together in the development of new studies.