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.
Wednesday, 30 October 2013
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.
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:
http://www.youtube.com/watch? v=g8z2yFDYwHI
The video is about 3.5 minutes long and can be found here:
http://www.youtube.com/watch?
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:
- 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.
- Users can view what would happen to the bird’s habitat between 2015 and 2085 in Australia’s projected future climate.
- 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 http://tropicaldatahub.org/goto/edgar.
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: http://www.youtube.com/watch?v=szl61Eerfpo
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: http://www.illawarramercury.com.au/story/1121741/uni-builds-web-dashboard-to-monitor-data/?cs=300
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.
Media coverage of the launch: http://www.illawarramercury.com.au/story/1121741/uni-builds-web-dashboard-to-monitor-data/?cs=300
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.
ANDS Applications Project Blogs/Sites
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Final Product Post - 1. Introductory Product Information The web services developed as part of this project have been extensions to product known as the Biocache. This tool is u...12 years ago
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Indices of access to services and infrastructure for North West of Melbourne - As part of an agreement among City of Melbourne, AURIN and CSDILA, we will soon implement an additional tool in the North West Melbourne integration portal...10 years ago
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Bio-IT World Asia 2013 - A Genomics Virtual Lab for Cancer Research - The Cancer Genomics Linkage Application has been presented at Bio-IT World Asia 201311 years ago
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What technology is Terra Nova built with and where can I see the code? - Terra Nova was funded by the Australian National Data Service. As part of this funding the code is publicly accessible and available for reuse. All source...11 years ago
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ANDS User Acceptance Testing of ePiSaT Version 1.0 - The user acceptance testing was conducted once the ePiSaT Software was released to the public via github. Each tester was selected for their specialist exp...11 years ago
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Announcing Edgar - Here’s Edgar! tropicaldatahub.org/goto/edgar Edgar is a web based mapping tool looking at Australia’s birds, and climate change. We think Edgar is pretty...12 years ago
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Final reporting for ANDS and technical reflections -- Part 2. - Continuing our technical reflections on this project, I will wrap up with some speculation on how we think the infrastructure will evolve over the next 12 ...11 years ago
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Final Product - 1. Introductory Product Information *1.1 Name of the product* The intention of the ANDS-funded Marine Virtual laboratory Information System (MARVLIS) ...11 years ago
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POSTool - Winner of 2 Parks and Leisure Australia (WA) Awards of Excellence. - On Thursday the 8th of May at the South Perth Community Hall, Parks and Leisure Australia (WA) presented the 2014 Awards of Excellence. POSTool was nomin...10 years ago
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Final product - The AP11 project (Proteomic-genomic Nexus) has reached end of development and we are happy to announce the proteomic-genomic nexus tools are available fo...11 years ago
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Introductory Product Information - Introductory Product InformationName The Scientific Workflow and Integration Software for Health (SWISH) and the Extreme Weather Events Database (EWEBD)...11 years ago
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Semaphore: The video - And now in glorious technicolour, Semaphore: the video! Thanks to the researchers and developers who took time out to feature in this clip. We hope that it...11 years ago
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Final Product - SEQuITOR - IntroductionThe SEQITOR (*S*outh *E*ast *Qu*eensland *I*ntegrated *T*errestrial to *O*ceans *R*esearch) project harnesses investments and innovations in o...10 years ago
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The Proteome Browser - A Software Resource for the Chromosome-Centric Human Proteome Project - The Proteome Browser is a web-based portal to the human proteome developed to support the efforts of the Australian/New Zealand consortium in the Chromoso...11 years ago
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TissueStack Features - 8 - TissueStack has a simple external query interface that allows other applications and researchers to integrate the data in the application to their own syst...12 years ago
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