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.
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...10 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 ...10 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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Future Enhancements - We plan to integrate the following into the code base within the next 2 weeks: - Addition of a "Data Panel" on the left hand side of the screen, righ...12 years ago
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