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.

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