Integration and simultaneous access to the many thousands of disparate public data sources and tools represent a significant bioinformatics challenge.  Providing a flexible mechanism for running complex queries using these resources is crucial to uncovering knowledge.  To meet this challenge we are building an integrated bioinformatics platform using Sequence Retrieval System (SRS)[1] and Storage Resource Broker (SRB)[2] as the core engines, and a web services API for ease of use.

SRS automatically downloads and indexes databanks and provides access to embedded tools.  Using internal SRS data entities, linked information from multiple data sources can be queried and retrieved in single actions.  SRB is middleware that provides a uniform interface for connecting to distributed data resources based on their attributes rather than physical locations.  Additional to the SRS databanks, the Australian mirror for the UCSC genome browser [3] has been implemented at the Institute for Molecular Bioscience and managed by Queensland Facility for Advanced Bioinformatics (QFAB), while a mirror of the Ensembl genome browser [4] is hosted at Griffith University.  Authenticated users who logon to SRB are able to access and query both genome browsers and SRS files under a single file hierarchy even though the data is distributed across several storage systems.  

A bioinformatics web services API, called Cowrie, is being developed to interface with SRS and SRB. This API enables data and tool integration, and provides accessible data services for targeted bioinformatics tasks.  Based on Cowrie, customised utility, workflow and web applications can be rapidly developed using any technology supporting web services, thus facilitating code reuse and consolidating development effort.  Such applications have at their disposal the vast array of up-to-date data and tool services maintained by QFAB and other institutions such as EBI or NCBI.

This poster presents the hardware and software components of this platform and illustrates how this architecture is beneficial in a high data and service bioinformatics environment.


References
[1] Sequence Retrieval System (SRS),  http://www.biowisdom.com 
[2] Storage Resource Broker (SRB),  http://www.sdsc.edu/srb/index.php/Main_Page
[3] Mirror of the UCSC genome browser, http://genome.qfab.org/
[4] Mirror of the Ensembl genome browser, http://ensembl.griffith.edu.au/