Class library ranlip for multivariate nonuniform random variate generation

This paper describes generation of nonuniform random variates from Lipschitz-continuous densities using acceptance/rejection, and the class library _ranlip which implements this method. It is assumed that the required distribution has Lipschitz-continuous density, which is either given analytically or as a black box. The algorithm builds a piecewise constant upper approximation to the density (the hat function), using a large number of its values and subdivision of the domain into hyperrectangles. The class library _ranlip provides very competitive preprocessing and generation times, and yields small rejection constant, which is a measure of efficiency of the generation step. It exhibits good performance for up to five variables, and provides the user with a black box nonuniform random variate generator for a large class of distributions, in particular, multimodal distributions. It will be valuable for researchers who frequently face the task of sampling from unusual distributions, for which specialized random variate generators are not available.

Deakin University Library : an active partner in the implementation of the new generation e-learning platform Desire2Learn

Deakin University has a long association with e-learning platforms, utilising the functionality of various Learning Management Systems (LMS) over a period of years. Transforming learning and teaching is a key priority of the University and moving to a new generation e-learning platform that supports engaging learning experiences through quality course design is a strategic imperative.

In 2010 Deakin University selected Desire2Learn as its replacement LMS, an innovative platform that offers next generation functionality. The University is investing significant resources in 2011 to implement the new system. The Library is harnessing the opportunity to embed search and discovery and information access throughout the LMS, including presence at the highest level of navigation. A Library widget providing students with clear pathways and immediate access to key library collections, services and features is being developed by the Library in conjunction with the Faculties‟ academic champions and educational developers. Liaison Librarians are negotiating with academic staff to create context-specific pathways, to utilise Desire2Learn Web2.0 capabilities and to imbed more personalised resources and LibGuides aligned with units of study. This is happening at a time when libraries are introducing new approaches to information discovery.

This paper describes Deakin University Library‟s journey in partnering with academic staff and others across the University to implement Desire2Learn as a vital new e-learning platform. It reports on many outcomes including: value created by embedding quality information in learner-centred course delivery; increased awareness of library subscription resources when accessible within students‟ workspace; strong and continuing relationships built with academic staff; enhanced Library staff engagement with flexible learning principles and new technologies. The question of where embedding information access in online courses and units fits with the Library‟s exploration of web scale solutions is also touched upon. And finally, an insight into how recent research undertaken by Deakin University Library has influenced our approach to information discovery solutions suggests an opportunity for many more questions to be explored.

Case comment: Cubillo and Gunner V The Commonwealth: a denial of the stolen generation?

In the recent Australian decision in Cubillo and Gunner v The Commonwealth ( ‘Cubillo 3’ ), the Full Court of the Federal Court dismissed an appeal by the Aboriginal claimants seeking damages for, inter alia, their removal from their families and detention at certain Aboriginal institutions. The removal and detention of the plaintiffs was held to be lawful in the earlier determination of O’Loughlin J because it was, inter alia, believed to be in the [then] child’s best interests and, as the plaintiffs bore the onus of proof, they had failed to show that they were taken without the consent of their parents/guardians. This decision was based upon the factual finding that ‘at the relevant times, there was no general policy in force in the Northern Territory supporting the indiscriminate removal and detention of part-Aboriginal children, irrespective of the personal circumstances of each child’. The Full Court did not comment on O’Loughlin J’s assertion that the policy of removing part-Aboriginal children, as asserted by the plaintiffs, could not be maintained. Moreover, the Full Court in fact joined O’Loughlin J in trying to distance their findings from the broader issue of the legal rights of members of the Stolen Generation, emphasising that they were only concerned with the particular circumstances of the two plaintiffs/appellants. This case comment is not aimed at evaluating the specific legal issues raised by the plaintiffs’ claims in this case or reviewing the history of the Stolen Generation, but rather seeks to examine O’Loughlin J’s comment as to the absence of a policy of indiscriminate removal and detention of part-Aboriginal children in a bid to determine the parameters intended by the court. It will be seen that, at its broadest, the statement is quite inflammatory and may be seen as a denial of the Stolen Generation. It will be submitted that this was not intended by the court. At its narrowest, the statement is merely an assertion that the particular plaintiffs failed to prove their cases. It will be submitted that, whilst this clearly was the view of the court, O’Loughlin J’s statement does have broader implications which, it will be contended, are not warranted.

Mind the gap 2014 : research to inform the next five years of library development

Libraries have a long history of gathering evidence of performance. The results of regular client satisfaction surveys directly inform the continuous improvement of library and information services. Staff and student input is critical for improving library physical and virtual spaces, facilities and resources, and also to learn how the university community may approach information discovery into the future.

At Deakin University Library we are investigating, developing and integrating Web 2.0 applications into our service delivery. At the same time, designs for next generation physical learning spaces are being developed and implemented. These will extend the opportunities for students to contribute to a connected network of learners and teachers, to develop social networks, and to enrich experience of university life. Both the online and spaces strategies support the University’s distinctive advantage in flexible education.

But what of the future? How can the Library ensure that its support of research, teaching and learning aligns with changes in the behaviour and preferences of the university community in the next five years? This paper reviews Deakin University Library’s recent achievements, exposes an important gap and previews its plans to ensure its reliable support to the university community continues.

Library learning spaces in the digital age

Students describe the Library as being central to their learning, offering focus and inspiration, enabling access to information and technologies, and collaboration with peers. Deakin University Library’s building redevelopment program has been integral to the Library’s re-imagined value proposition for students learning in the digital age. The introduction of new generation library and learning spaces strengthens the University’s offer to students for a brilliant education where you are and where you want to go through premium cloud and located learning experiences that are personal, engaging and relevant.

The Library’s building projects are distinctive in terms of location and the built environment, as well as the characteristics of the university campus communities. Each progressive project has brought new aspirations and challenges. Through joint research with Deakin University’s School of Architecture and Built Environment, the Library has developed a quality framework for planning and assessing library and learning spaces.

This paper will discuss the research findings to date on the quality framework and the need to continually review and assess indicators of quality in a highly dynamic digital environment. The Library’s experiences in introducing high-end multimedia provide some insights into planning for and delivering enduring value.

The next steps in exploring the question of how library spaces assist students in achieving their learning goals are introduced.

A general method to eliminate laboratory induced recombinants during massive, parallel sequencing of cDNA library.

Massive, parallel sequencing is a potent tool for dissecting the regulation of biological processes by revealing the dynamics of the cellular RNA profile under different conditions. Similarly, massive, parallel sequencing can be used to reveal the complexity of viral quasispecies that are often found in the RNA virus infected host. However, the production of cDNA libraries for next-generation sequencing (NGS) necessitates the reverse transcription of RNA into cDNA and the amplification of the cDNA template using PCR, which may introduce artefact in the form of phantom nucleic acids species that can bias the composition and interpretation of original RNA profiles.

The development of 10 novel polymorphic microsatellite markers through next generation sequencing and a preliminary population genetic analysis for the endangered Glenelg spiny crayfish, Euastacus bispinosus

The Glenelg spiny crayfish, Euastacus bispinosus, is an iconic freshwater invertebrate of south eastern Australia and listed as 'endangered' under the Environment Protection and Biodiversity Conservation Act 1999, and 'vulnerable' under the International Union for Conservation of Nature's Red List. The species has suffered major population declines as a result of over-fishing, low environmental flows, the introduction of invasive fish species and habitat degradation. In order to develop an effective conservation strategy, patterns of gene flow, genetic structure and genetic diversity across the species distribution need to be clearly understood. In this study we develop a suite of polymorphic microsatellite markers by next generation sequencing. A total of 15 polymorphic loci were identified and 10 characterized using 22 individuals from the lower Glenelg River. We observed low to moderate genetic variation across most loci (mean number of alleles per locus = 2.80; mean expected heterozygosity = 0.36) with no evidence of individual loci deviating significantly from Hardy-Weinberg equilibrium. Marker independence was confirmed with tests for linkage disequilibrium, and analyses indicated no evidence of null alleles across loci. Individuals from two additional sites (Crawford River, Victoria; Ewens Ponds Conservation Park, South Australia) were genotyped at all 10 loci and a preliminary investigation of genetic diversity and population structure was undertaken. Analyses indicate high levels of genetic differentiation among sample locations (F ST = 0.49), while the Ewens Ponds population is genetically homogeneous, indicating a likely small founder group and ongoing inbreeding. Management actions will be needed to restore genetic diversity in this and possibly other at risk populations. These markers will provide a valuable resource for future population genetic assessments so that an effective framework can be developed for implementing conservation strategies for E. bispinosus.

Microsatellite loci and the complete mitochondrial DNA sequence characterized through next generation sequencing and de novo genome assembly for the critically endangered orange-bellied parrot, Neophema chrysogaster

A suite of polymorphic microsatellite markers and the complete mitochondrial genome sequence was developed by next generation sequencing (NGS) for the critically endangered orange-bellied parrot, Neophema chrysogaster. A total of 14 polymorphic loci were identified and characterized using DNA extractions representing 40 individuals from Melaleuca, Tasmania, sampled in 2002. We observed moderate genetic variation across most loci (mean number of alleles per locus = 2.79; mean expected heterozygosity = 0.53) with no evidence of individual loci deviating significantly from Hardy-Weinberg equilibrium. Marker independence was confirmed with tests for linkage disequilibrium, and analyses indicated no evidence of null alleles across loci. De novo and reference-based genome assemblies performed using MIRA were used to assemble the N. chrysogaster mitochondrial genome sequence with mean coverage of 116-fold (range 89 to 142-fold). The mitochondrial genome consists of 18,034 base pairs, and a typical metazoan mitochondrial gene content consisting of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a single large non-coding region (control region). The arrangement of mitochondrial genes is also typical of Avian taxa. The annotation of the mitochondrial genome and the characterization of 14 microsatellite markers provide a valuable resource for future genetic monitoring of wild and captive N. chrysogaster populations. As found previously, NGS provides a rapid, low cost and reliable method for polymorphic nuclear genetic marker development and determining complete mitochondrial genome sequences when only a fraction of a genome is sequenced.