BioMashups: The New World of Exploratory Bioinformatics?

Sumitomo, J; Hogan, JM; Roe, P
Sumitomo, J
Hogan, JM
Roe, P
eScience, 2008. eScience'08. IEEE Fourth International
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BioMashups: the new world of exploratory bioinformatics?
Jiro Sumitomo, James M. Hogan and Paul Roe Microsoft QUT eResearch Centre Queensland University of Technology GPO Box 2434, Brisbane, QLD, 4001 AUSTRALIA Bioinformaticians have a large range of tools and services at their disposal, each of which is useful alone, but more powerful when integrated with others to perform a more complex task. Routine workflows are a critical aspect of modern science, but the programming required to realize them may act as a barrier to free exploration. Web mashups provide one solution to this problem, rapidly combining data and services from multiple sources into a single facility through a web based application. Mashups are growing in popularity in the life sciences, but like their mainstream equivalents, BioMashups are generally written from scratch, and independently hosted. Mashups are small, focused applications with limited scope, their appeal dependent on a combination of services critical to the solution of a particular problem. The specificity of bioinformatic applications and the absence of suitable component libraries may act as barriers to mashup sharing and broader adoption. Moreover, many active biologists lack the programming skills necessary to integrate novel mashups, and greater support is necessary. Recently, a number of sophisticated frameworks for developing and hosting mashups have emerged, each markedly simplifying the mashup creation and sharing process, although these environments vary in their focus. Notable among these initiatives are Microsoft Popfly1, Google Mashups2, Yahoo Pipes3, Intel MashMaker4 and Lotus Mashups5. We believe that these frameworks may in time address some of the concerns identified above, making novel mashups accessible to less technical users. In particular, given a broad range of useful component blocks to compose, it is likely that Popfly will prove a very convenient environment for exploratory bioinformatics. To create a mashup, the author creates a wrapper around the separate tools and services to be composed. Each wrapper has an interface known to the author, and so wrapped tools and services may interact with each other. Frameworks promote a standard means of building these wrappers, supporting a common interface between different service components. Over time, adoption of suitable frameworks within the scientific community may well lead to a community based component library of some complexity. However, this adoption is dependent on a broader awareness of the capability of the mashup

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