Under collaboration with CoastalCOMS and the Gold Coast City Council, the JCU eResearch Centre developed an online environment for keeping the public informed about coastline changes.
The beaches are an integral part of the Gold Coast, its economy, and the lifestyle of its citizens. More than ever, with the ever-present effects of weather and other factors causing changes to the beaches, the public needs to be informed and wants to be kept up-to-date.
The JCU eResearch Centre worked with CoastalCOMS in its efforts for delivering a monitoring portal for the Northern Beaches and Palm Beach on the Gold Coast. In doing so, the portal delivered the ability for users to contribute photographs about beach changes, see the latest information about coastline positions, and see live camera vision. The site aimed to make the public become more knowledgeable about the changes that affect them, and leverage CoastalCOMS various technologies to do so.
The resulting site was completed in early 2010 and is fully operational. The site makes use of the flexibility of Plone, an open source CMS, and delivers the ability of easily creating content through-the-web, whilst associating content with geographical coordinates. This special feature combines with OpenLayers, a free and open source mapping framework, to deliver geographical content into users' browsers. The result is that site administrators are able to upload a report, such as a PDF, associate this with a set of coordinates, and then have the content display on a map for users to see.
eGRS, James Cook University's e-Graduate Research School portal, was a collaborative effort to deliver a secure content environment for students at JCU.
The JCU eResearch Centre developed eGRS through working on the ARCHER project, in order to provide students and academics with a secure environment to collaborate on documents relevant to their research. The site is powered by the open-source Plone Content Management System (CMS), which offers customisability and flexibility for GRS requirements. Once completed, site members, which automatically include honours and postgraduate research students, and academic staff, were given access to an online collaborative space where they can store and share work.
Within eGRS, students are able to:
- Upload draft chapters of their theses, documents, data, photos and more
- Store uploaded documents and data securely for their private use
- Share information with specific people such as supervisors
- View a large reservoir of information about writing theses, research skills and dealing with supervisors
- Quickly and easily search for the information they need, thanks to LiveSearch
Furthermore, students decide who can view their work and add comments or changes.
The eResearch Centre continues to work with GRS staff on improving this extremely useful service for staff and students alike.
Structural biology research places significant demands upon computing and informatics infrastructure.
The beginning stages of protein production, crystallisation and X-ray data collection require simple yet powerful solutions to data management, annotation, target tracking and remote experiment monitoring. The latter stages of structure elucidation are computationally demanding and require user-friendly tools to harness available high-performance computing resources. We are collaborating with the team at Monash University to address these challenges, specifically using the ARCHER toolkit.
The JCU ARCHER team has recently launched a customised collaborative workspace for the crystallography team at Monash based on the open source Content Management System (CMS), Plone.
It features a web portal, and provides a customisable environment that gives users access to running experiments (including latest CCD and microscope images), lab environment as well as access to experiments and their data. Comprehensive data searching as well as file uploads and downloads are also supported. Data stores from different sites can be federated to provide a single virtual data repository, and a security and right management capability are now being implemented. We are also working on extensions aimed at providing data processing and structure elucidation functionality direct from the portal.
The CIMA is being used to provide a scalable and extensible basis for the cyberinfrastructure, and X-ray diffraction is targeted as an ideal development domain. Australian research is enhancing the CIMA model to enable federated Grid storage via SRB, and the use of the Kepler workflow system.
The goal of the Digital History Project is to video record and present the life histories of elders of the Gugu Badhun people, and other non-indigenous people associated with the Upper Burdekin area of North Queensland.
The video annotation tool was created as a ‘proof of concept’ application as part of the ARCHER project. The application is a lightweight, simple, web-based video annotation system. Through the use of this software, members of this community are able to easily annotate portions of their history. The application:
- Allows digital videos to be uploaded to a secure Storage Resource Broker (SRB) storage centre
- Allows metadata to be attached to video files
- Provides a search engine capable of searching both metadata and annotations stored in SRB for each video
- Provides a set of links describing videos which meet the search criteria
The project aims to have a database of video and audio interviews both with the Gugu Badhun people and some of the pastoralist families that ran the cattle stations on Gugu Badhun country west and North West of Townsville, in Queesnland. The information will be stored digitally, indexed and readily retrievable.
Video Annotation Software (Mattotea)
Mattotea is a production-ready version of video annotation software with significant add-ins in terms of usability and functionality, offering researchers minimum-to-no impact on staff operations whilst delivering a tool that allows efficiency in work processes.
- Storage of video segments in a managed set of Information Technology Infrastructure allowing multiple file types,
- Providing a tool to annotate video segments with an intuitive interface,
- Providing a web interface to allow viewing & editing annotations either collaboratively or administratively only,
- Allowing description metadata to have variable titles and to allow content to be written into to allow the content management functionality.
- Play, upload and remove videos, supporting multiple file formats:
- FLV7 video
- FLV8 video,
- H.264 video ,
- Youtube video (In progress),
- MP3 audio ,
- AAC audio,
- Add descriptive meta data, including having the ability for templates in metadata headings
- Add annotations, including start time, end time, title, arbitrary text, and comments on annotations
Mattotea can be utilised as a stand alone product or an implemented product into Plone offering additional functionality.
Through the development of Mattotea as a plone product we are able to make use of the following:
- Shibboleth authentication, federating access control to the Plone CMS,
- Integration with SRB allowing access to the files and annotations through other services,
- Access to annotate not only SRB objects but Plone objects as well.
QFAB, the Queensland Facility for Advanced Bioinformatics, requested the provision of collaboration tools and a data management solution for the National Breast Cancer Foundation, an important client.
The National Breast Cancer Foundation is a group of clinical cancer researchers who are dispersed across Australia, but work closely together on various collaborative projects. Whilst each group possesses specialist skills in different areas of cancer research, a multidisciplinary approach aims to provide new and innovative derivations of Breast Cancer pathways.
The solution, developed by the JCU eResearch team, was to use , an open source Content Management System (CMS), to provide research groups with a low cost, secure, and customisable solution for collaboration and data management. The software aimed to provide the ability for communication between members of research groups, their funding partners, and both international and national collaborators. The online CMS provided a means to capture, interrogate and manage data used in related research, including text-based documents, statistical information, images, and laboratory information.
In addition to project members, the collaborative workspace solution integrated support for access by external funding partners as well. A separate category of users was defined to enable funding partners to access private areas where project reports and financial information could be disseminated and monitored. Hence, limited subsets of information could easily be shared with external users without needing to extract data from the system.
In utilising Plone as the basis for this project, the project aimed to deliver access to all these types of data in a single secured environment. Plone's flexibility, security, and open source nature provided the perfect building blocks to successfully complete this project.