Taverna/myGrid: Aligning a Workflow System with the Life Sciences Community

Bioinformatics is a discipline that uses computational and mathematical techniques to store, manage, and analyze biological data in order to answer biological questions. Bioinformatics has over 850 databases [154] and numerous tools that work over those databases and local data to produce even more data themselves. In order to perform an analysis, a bioinformatician uses one or more of these resources to gather, filter, and transform data to answer a question. Thus, bioinformatics is an in silico science. The traditional bioinformatics technique of cutting and pasting between Web pages can be effective, but it is neither scalable nor does it support scientific best practice, such as record keeping. In addition, as such methods are scaled up, slips and omissions are more likely to occur. A final human factor is the tedium of such repetitive tasks [397]. Doing these tasks programmatically is an obvious solution, especially for the repetitive nature of the tasks. Some bioinformaticians have the programming skills to wrap these distributed resources. Such solutions are, however, not easy to disseminate, adapt, and verify. Moreover, one of the consequences of the autonomy of bioinformatics service providers is massive heterogeneity within those resources. The advent of Web services has brought about a major change in the availability of bioinformatics resources from Web pages and command-line programs to Web services [395], though much of the structural, value-based, and syntactic heterogeneity remains. The consequent lack of a common type system means that services are difficult to join together programmatically, and any technical solution to in silico experiments in biology has to address this issue. Many scientific computing projects within the academic community have turned to workflows as a means of orchestrating complex tasks (in silico experiments) over a distributed set of resources. Examples include DiscoveryNet [373] for molecular biology and environmental data analysis,