Monday, 13 April 2015

Get back to the community

 It is well known in the ANDS community that ANDS aims to make data reusable by more researchers more often. All projects funded under the ANDS applications program have demonstrated by making data available to researchers; by combing, cleaning and integrating data from a myriad of data sources, and by visualising data for easier exploration; researchers can do a range of things they could not do before or do their existing research in a more efficient way. An outcome of the application program is to advance in science and technology through sharing and reusing data.

Advance in research and science will consequently benefit to the society. Some contributions require more effort and thus benefit will be shown in a longer term. For example, the output from the Cancer Genomics Linkage Application, the Proteomic-Genomic Nexus, the Proteome Browser, the Xglom - Multimodal Kidney Image Analysis and TissueStack are contributing to internationally coordinated efforts in studying human genetics disease and finding treatments for patients who suffer from pancreatic cancer or  kidney disease. Advances in these fields will lead to improvement of our quality life. The projects Soils to Satellites, Ecosystem Production in Space and Time, Climate Change Adaptation Information Hub will contribute to the understanding of our environments, thus we can act accordingly to make our environment sustainable.

Some ANDS applications projects directly benefit a range of government agencies and the public in the short term. For example, the project Positive Places: spatial analysis of public open space  has created a first-of-its-kind, web-based geospatial tool.  The project director Fiona Bull commented that: The tool can be used by the general public to look up their nearest parks or check if the park they intend to go to has facilities like toilets and barbecues. More importantly it can be used by planners to ensure we preserve and optimise our green spaces.

Wednesday, 30 October 2013

Sustainability of ANDS Applications Projects

Recently, ANDS has congratulated a number of applications projects for their successfully completion. Yet, to many projects, the end of the ANDS project is just the beginning.  After having delivered their software  related deliverables and announced TissueStack 1.1 in April, the  TissueStack development team has had consequent releases of TissueStack 1.2 in August and TissueStack 1.3 in October. Moreover the team, together with their collaborators, has won an ARC linkage grant (2013-2015) for further research and development of the TissueStack.

A number of other projects have also laid out possible future developments. For example, the launch of the  POS (Public Open Space) portal  at a Parks and Leisure Australia workshop has attracted a lot of interests, the team has been considering possible future development of bringing in new datasets into the portals and enhancing the existing functionality of the portal to satisfy information need of stakeholders and end users.

The applications projects  have been driven by research communities and end users. The projects have adopted a similar agile software development process: researchers identify gaps between their research need for data and the use of existing available data,  development team work closely with researchers to elicit their needs and to have researchers evaluate each implementation in regular sprints. In many projects, researchers actively gather requirements from their research community,  sometimes, they have to give way of their own needs to a genuine need in a research community. This genuine involvement of research communities ensure software sustainability and a long term funding future.

Sunday, 22 September 2013

The Proteome Browser

ANDS has recently congratulated Monash University on the successful completion of the "Human Chr7 Proteomics Integration Project".  The congratulation message provides links to various project information sources, such as the online application portal "The Proteome Browser (TPB)",  the project Wiki, and source code deposit. Apart from these links,  this article ("The Proteome Browser Web Portal") published  by Journal of Proteome Research (2013, 12(1):172-8)  provides concise information about the project's background and the application's data structure, software design and  user interface.

The project was a response to a Human Proteome Organization (HUPO) initiative that aims to catalogue the protein information arising from the plethora of worldwide proteomic based studies. The project took a gene- or chromosome-centric approach (C-HPP), and aimed to link the proteome with the underlying genome. The project has implemented Phase 1 with ANDS funding.  The resulting tool TPB from Phase I  applies traffic light to indicate presence of each gene in a selected Chromosome; four data sources are used to decide a gene's presence.  The project is continuing Phase 2 to integrate potentially 4 additional data sources.  Future work  may also include an extension of TPB that will enable registered users to  add  their own data and analyse user-defined gene sets.

Like many applications projects, the close involvement of researchers in the software development process contributed greatly to the project's success.  I joined the project as an ANDS CLO at a late stage in the project, after the departure of my ex-colleague Dr. Jeff Christiansen.  In the last  2 or 3 project sprints I attended, I was impressed by how deeply researchers were engaged in the development process. For example, in a sprint about user interface testing and analysis,  the researchers asked their national and international colleagues to test the user interface and they paid attention to every interface design detail - even a symbol's position or a display color.

If you are interested in the presence of genes in a particular Chromosome, you can use TPB to check it out.

Tuesday, 26 March 2013

Even more about Edgar

Thanks to my colleague Simon Pockley, you can now view a second video on Edgar, in which Professor Stephen Garnett from Charles Darwin University gives an example of the complex questions and issues that Edgar can help answer. 

The video is about 3.5 minutes long and can be found here:

Monday, 25 February 2013

More about Edgar

One of the projects previously mentioned on this Blog is Edgar, a web based mapping tool looking at where Australia’s birds occur today, and what the impact climate change on their habitats might be. Edgar has three main functions:
  1. Users can view where a specific bird has been observed, where it lives today, and what areas would represent a suitable habitat for the bird. The occurrence data underlying Edgar are provided via live web services by the Atlas of Living Australia.
  2. Users can view what would happen to the bird’s habitat between 2015 and 2085 in Australia’s projected future climate.
  3.  Birdwatchers and experts can correct and classify bird observations, thereby helping to improve the underlying data. These corrections and classifications are sent back to the bird occurrence records data base, held by the Atlas of Living Australia.

This project is now finished, and you can access the software at

ANDS has published a short video in which Jeremy VanderWal (James Cook University) and Stephen Garnett (Charles Darwin University) talk about what you can do with Edgar. You can view the video here:

Wednesday, 23 January 2013

Launch of the SMART Infrastructure Dashboard

The ANDS-funded SMART Infrastructure Dashboard under development at the University of Wollongong’s SMART Infrastructure Facility was officially launched on 9 November 2012, at the “Culture of Innovation” Symposium, part of the new Illawarra Futures Symposium Series, which was held on 8-9 November 2012 at the University of Wollongong’s Innovation Campus.

The SMART Infrastructure Dashboard provides visual, graphical and geospatial data analysis capabilities using publicly available infrastructure utility data. This information, crossed with relevant regional, state and national-level figures from demographics and economics, constitutes a robust foundation for powerful infrastructure analytics. The dashboard acts as a customer centric portal providing easy, transparent and intuitive access to primary data and information creating a better understanding of the complex relationship between infrastructure operations and uses across major utilities. It offers a flexible collaborative platform to local planners, researchers, business analysts and citizens.

Professor Pascal Perez presented the SMART Infrastructure Dashboard to an audience representing a number of Illawarra Businesses, federal and state government agencies, local councils, as well as the University of Wollongong. His presentation included a series of scenarios illustrating how the dashboard could help service providers and consumers make more informed decisions. A lively Q&A session followed, with a number of councils interested in getting involved and providing their data.

Media coverage of the launch:

If you would like more information about the SMART Infrastructure Dashboard, please contact Neil Webster, Projects Manager, SMART Infrastructure Facility on +61 2 4221 4716 or webster <at> uow <dot> edu <dot> au.

Thursday, 15 November 2012

The Proteome Browser mentioned in WIRED

The Proteome Browser being developed by the AP32 team at Monash University for the global proteomics community has been mentioned in an article about the Human Proteome in "The WIRED World in 2013" - a 'what's hot in 2013' special issue from WIRED magazine:

The full issue is:

• downloadable from within the Wired UK app on iTunes/Kindle/Android
• downloadable from
• on sale in shops now

ANDS Applications Project Blogs/Sites