The challenge of unravelling gene function and better understand gene regulation processes in an era where exponentially growing amounts of genomic data are being deposited into the public databases, requires fast and unlimited access to tools that can, in a systematic manner, simplify the analysis of these data.
Equally important, scientists are no longer bound to work within the confinement of their own labs. The Internet has provided the means to develop systems with which it is possible to exchange results and partial analysis of data. Characterizing a gene in terms of a sequence, its translation, expression profile, function and structure requires access to widely distributed services. The integration of such services and their interoperability is now feasible using Web Services technologies.
These data and the corresponding analysis tools are mainly accessed using browser-based interfaces. When large amounts of data need to be retrieved and analysed, this often proves to be tedious and impractical. Moreover, research is rarely completed just by retrieving or analysing a particular nucleotide or protein sequence. Database information retrieval and analysis services have to be linked, so that, for example, search results from one database can be used as the base of a search in another, the results of which are then analysed. When performing these operations using a web browser, researchers are forced to repeat the troublesome tasks of searching; copying the results for subsequent searches into other database services, and again copying the results from these for further analysis.
Creating a local bioinformatics work environment is possible by downloading and installing the necessary database content and services (such as retrieval and analysis programs). This has the advantage that processes that otherwise require manual operations can be automated. However, the hidden overheads imposed by maintaining and operating such environments are, more often than not, exceed the capacity of local systems.
Programmatic Web Services technology has gained much attention as an open architecture enabling interoperability among applications across heterogeneous platforms and different networks. The European Bioinformatics Institute (EBI) has been using this technology (1
) to enhance and ease the use of the bioinformatics resources it provides (2
). Currently, the European Bioinformatics Institute provides access to more than 200 databases and to about 150 bioinformatics applications.