http://espace.library.uq.edu.au/ The University of Queensland en Fez http://blogs.law.harvard.edu/tech/rss http://espace.library.uq.edu.au/view/UQ:155362 In this paper, I discuss some of the more salient intellectual and technological dimensions of work over the past year, focused on developing an open source knowledge creation, management and publication system. In key respects, our work seeks to anticipate developments in national collaborative e-research infrastructure over the next five or so years. Especially in view of recent statements on innovation policy by the Australian government, we can expect the next five or so years will see significant advances in the development of online knowledge repositories for not only more complex kinds of quantitative research data, but also for qualitative data in rich and diverse media forms that will offer new possibilities for humanities research. We will also see improved or new middleware, allowing Australian research communities in the humanities collaboratively to create, share and interrogate new knowledge of cultural and social phenomena. However, if humanities researchers are to exploit these and other possible advances in digital research infrastructure, then what they will also need are ‘tools’ enabling the creation, reception and use of knowledge that these infrastructural advances can put into intellectual circulation. They will need the means of using networked digital technologies as primary media for research, and to publish their findings as complex multimedia artifacts. 2008-09-26T14:10:05Z Paul Turnbull og Mark Fallu http://espace.library.uq.edu.au/view/UQ:155356 CSIRO is currently working on a comprehensive e-Research strategy outlining the organisations development plans for e-Research for the next 5 years. That document will review the current global e-Science/e-Research environment and outline our ongoing participation in the global research community. The strategy will be heavily influenced by national research goals and our flagship programs and the National Collaborative Research Infrastructure Strategy (NCRIS) agenda. 2008-09-26T13:48:18Z John A. Taylor og John Zic og John Morrissey http://espace.library.uq.edu.au/view/UQ:155380 A combination of off-the-shelf open-source software and custom-built middleware is used to unite remotely sensed marine data archives operated across Australia by five different agencies and make them accessible via a common interface to a user located anywhere on the internet. The utilisation of existing storage and some state of the art fileservers with a distributed data model, makes the system low-cost, scalable and robust. The creation of a virtual national data set with automatic cataloguing enables the development of advanced data services including aggregation and spatio-temporal time series and sub-setting. Data sets are served through OPeNDAP and automatically harvested for meta-data including temporal and spatial bounds. Spatio-temporal queries made on the catalogues provide information to allow retrieval of subset data, or if many data sets are returned, the aggregation of data matching the query. The software developed to implement the system is built as a set of layers with well defined interfaces, allowing system modularisation and a range of levels of access. 2008-09-27T09:09:35Z E.A. King og P.P.Y. Mak og P.J. Turner og G.P. Smith og K.D. Suber og M.J. Paget og C. J. Jackett og P. Fearns og A.L. Rohl og F. Goessmann og L. Majewski og S. Reddy og C. Steinberg http://espace.library.uq.edu.au/view/UQ:155367 Collaboration-intensive research is increasingly becoming the norm in the humanities and social science arenas. eResearch tools such as online repositories offer researchers the opportunity to access and interact with data online. For the last 20 years video has formed an important part of humanities research, although dealing with multimedia in an online setting has proven difficult with existing tools. File size limitations, lack of interoperability with existing security systems, and the inability to include rich supportive detail regarding files have hampered the use of video. This paper describes a collaborative and data management solution for video and other files using a combination of existing tools (SRB and Plone integrated with Shibboleth) and a custom application for video upload and annotation (Mattotea). Rather than creating new proprietary systems, this development has examined the reuse of existing technologies with the addition of custom extensions to provide fullfeatured access to research data. 2008-09-26T14:23:46Z Dianna Hardy og Matthew Morgan og Ian Atkinson og Sue McGinty og Yvonne Cadet-James og Agnes Hannan og Robert James http://espace.library.uq.edu.au/view/UQ:155728 This video, produced on behalf of the Australian Department of Innovation, Industry, Science and Research, features researchers explaining the importance of eResearch to their work. The video was originally shown at the opening of the eResearch Australasia 2008 conference on 29 September. 2008-10-14T16:47:19Z http://espace.library.uq.edu.au/view/UQ:155359 This paper documents the plight of 'average' modern researchers as they apply their academic writing skills in the new world of eResearch. We might expect researchers to have mastered some of the basic generic writing tools; an office suite with a word processor, the ability to generate charts from tables of data; a reference manager that can insert citations; and tools of their discipline like statistics packages. But the 'ordinary' researcher who tunes-in to the clamour about ideas and tools from a conference like eResearch Australia could be easily overwhelmed by the gap between the obvious potential and their own command of the technology they have to hand. Eight things to which a tuned-in researcher might aspire: (a) to share data with colleagues, (b) to collaborate on semantically rich documents which include appropriate data visualizations, (c) to blog their research as it happens, (d) to annotate data and works in progress, (e) to submit to journals, (f)to deposit appropriate copies of papers into various discipline and institutional repositories, and not just in PDF format, (g) in HTML, with rich interactivity and links to their data. They might also aspire to ensure (h) preservation of their data and their writing without accidentally choosing a doomed data format in which to store it. The question is how do we get there from here? The starting point is using Microsoft Word with references in EndNote emailed around a workgroup then sent to a publisher. The goal is to collaborate on a document which has embedded rich semantics, such as geographical data points that can be displayed on maps and overlaid with data from other sources. The document needs to be viewed on the web with interactive maps, and annotated, tagged and commented upon, as well as being distributed as a traditional paper paper and stored in the dreaded PDF file. Finally it must be automatically deposited in appropriate repositories, one of which is a publisher's review queue. Focussing on the writing process, this paper explores some of the aspirations listed above and suggests some practical advice for researchers and their support staff. There is a discussion at this point about the Integrated Content Environment – an academically focussed collaborative content management system, with integration into repository systems which can help with some of the aspirations of the modern eResearcher, but with a lot of work still to do. Other tools are also considered and found wanting. The conclusion suggests some more areas for research and development, targeted both at the Australasian context but also globally, to research funding bodies. How can our researchers get there from here? 2008-09-26T13:59:45Z Peter Sefton http://espace.library.uq.edu.au/view/UQ:155381 In this paper, we present a new framework complete with implementation, for a digital repository that will address some of the most difficult issues facing repository managers today: how to enable federated identity access, rapidly changing access control requirements, and the management of multiple metadata standards for different types of digital objects. Our work draws together leading industry standards in the area of authentication, authorization, and metadata management, and apply them in a new and innovative way to the repository landscape. As a demonstration, we apply our work to a speech annotation research project which makes use of a repository to manage its culturally sensitive data. 2008-09-27T09:17:39Z Chi Nguyen og James Dalziel og Steve Cassidy http://espace.library.uq.edu.au/view/UQ:155364 The aim of this paper is to showcase recent developments in the UK arts and humanities e-Science initiative. A specific grass-roots research agenda in arts and humanities e-Science has been developing over the past few years in the UK. In this paper, we will look at the new research questions and institutions emerging in the many e-Science grass-roots activities. 2008-09-26T14:16:55Z Tobias Blanke og Mark Hedges og Stuart Dunn http://espace.library.uq.edu.au/view/UQ:155351 Delivering bioinformatics power to life science researchers inevitably runs into problems of limited computing resources in the context of exponentially increasing data sources, access time, costs, lack of skills and, rapidly evolving technology and software tools with poorly defined standards. In this context the development of online facilities to best enable collaborative research often needs to be customized to specific project applications in close cooperation with the experimentalist users and, to be concerned with the storage and management of results to allow more consistency and traceability of results on a broad access data mining platform. Here we showcase an Internet based research platform using the PHP/MySQL paradigm for the collaborative, integrative and comparative analysis of lactation related gene sequences and gene expression experiments to support lactation research. We also illustrate how these resources are used, how they enable research by allowing meta-analysis of data and results and, how the bottom-up development of customized eResearch components can lead to the production of more generic functional software tools and eResearch environments for deployment to a larger number of biological researchers working on other bio-systems. 2008-09-26T12:22:45Z Kevin R Nicholas og Amit Kumar og Yvan Strahm og David Powell og Torsten Seemann og Kerry A. Daly og Amelia Brennan og Karensa Menzies og Julie Sharp og Matthew Digby og Christophe Lefèvre http://espace.library.uq.edu.au/view/UQ:157816 Due to the signi¯cant amount of data generated by modern medicine there is a growing reliance on tools such as data mining and knowledge discovery to help make sense and comprehend such data. The success of this process requires collaboration and interaction between such methods and medical professionals. Therefore an important question is: How can we strengthen the relationship between two traditionally separate fields (technology and medicine) in order to work simultaneously towards enhancing knowledge in modern medicine. To address this question, this study examines the application of data mining techniques to a large asthma medical dataset. A discussion introducing various methods for a smooth approach, straying from the `jack of all trades, master of none' to a modular cooperative approach for a successful outcome is pro-posed. The results of this study support the use of data mining as a useful tool and highlight the advantages on a global scale of closer relations between the two distinct fields. The exploration of CRISP methodology suggests that a `one methodology fits all approach' is not appropriate, but rather combines to create a hybrid holistic approach to data mining. 2008-10-23T09:16:07Z Sam Schmidt og Peter Vuillermin og Bernard Jenner og Yongli Ren og Gang Li og Yi-Ping Phoebe Chen http://espace.library.uq.edu.au/view/UQ:155348 The proceedings contains refereed papers associated with presentations, posters, and workshops at the conference. 2008-09-26T11:49:50Z http://espace.library.uq.edu.au/view/UQ:155355 Within the domains of reactive transport and structural geology, numerical simulations are often used to approximate a real-world scenario. Such simulations generally require both highly specific domain knowledge, and an in-depth knowledge of a specific numerical solver and its syntax. Additionally, these simulations often run in very specific computational environments (eg Windows pools, Linux supercomputers, Linux clusters) that themselves require a steep learning curve in terms of library and module dependencies, gaining accounts, logging in, data formatting, moving data etc. For a geologist to become fluent in all of the above areas requires a significant investment of time and effort outside of the scientific field of interest. Numerical solvers are normally specific to particular problem domains (eg 'mechanical deformation', 'fluid flow' 'chemical deposition' etc), and are usually highly complex pieces of commercial code with their own specific language and syntax. Hence changing the numerical solver (for instance to a newer code that is faster or more scale-appropriate) becomes a daunting and rarely-done task. Even within the one solver, there are often so many ways to construct simulations for the same problem that consistency and repeatability can suffer. A similar issue arises for using alternative computational resources to actually run the simulation on. The Desktop Modelling Toolkit (DMT) buffers the user from most of these issues. It is a tool that allows the user to specify certain geo-scientific problems on a conceptual level, without recourse to specific numerical idiosyncrasies of the actual solver that will run the simulation; solver-specific pseudo-code is auto-generated by the DMT. It also manages interactions with Grid-Computing resources on the user's behalf, insulating the user from the specific requirements of the computational resource that the simulation will run on. The DMT is aimed at modellers who wish to run simulations of mechanical deformation, fluid flow, thermal regimes and/or chemical interactions in the area of Earth crustal processes; however, it is foreseeable that it could be modified to suit a range of other modelling domains, such as seismic processing, magneto-tellurics etc. It provides a fast-track to setting up and running multiple simulations (often required for parameter sweeps or geological inversion techniques) and is particularly useful for training new researchers or students. Through the enforcing of consistent algorithms and coding standards, it is also an important method of ensuring experimental repeatability. 2008-09-26T13:40:39Z Gordon W. H. German http://espace.library.uq.edu.au/view/UQ:155352 Visualization has been a part of computing for a long time, however with the growth in data produced by researchers and the computing resources available visualization capability has not developed in a way that provides researchers with the ability to include visualization as part of their standard analysis of these very large datasets. To address this issue and to understand how visualization systems must adapt to meet the new needs the eResearch brings we examine the past, present and begin to look into the future at visualization systems and architectures, to aid in understanding how visualization may be used or wish to be used a scenario involving a variety of Earth Science researchers working at a variety of locations to collect data and conduct analysis is presented. Reviewing traditional visualization systems, in particular, Modular Visualization Environments and Visualization Toolkits, to understand the heritage of visualization systems and the challenges that researchers have identified face. We look at current visualization systems that begin to take advantage of grid computing technologies, including those that modify traditional systems, those that a new architectures and those that have been developed in a bespoke manner for particular eResearch projects. Whilst these current visualization systems address some of the challenges of visualization for eResearch several challenges still exist and we examine ways in which these systems need to develop into the future to meet these challenges relating to use of multiple datasets, display devices, variation in bandwidth availability, the need for interaction and the role that predictive rendering can play in this, the need for new and revised algorithms, a focus on the end to end performance of visualization pipelines and the ability to integrate in to a researchers workflow rather than be an additional activity. 2008-09-26T13:30:17Z Stuart M. Charters