Towards Ubiquitous Bio-Information Computing: Data protocols, middleware, and Web services for heterogeneous biological information integration and retrieval

Biological information computing is rapidly advancing from homogeneous data computation to large-scale heterogeneous data computation. However, the development of data specification protocols, software middleware, and Web services, which support large-scale heterogeneous data exchange, integration, and computation, generally falls behind data expansion rates and bioinformatics demands. The Ubiquitous Bio-Inforniation Computing (UBIC2) project aims to disseminate software packages to assist the development of heterogeneous bio-information computing applications that are interoperable and may run distributedly. UBIC2 lays down the software architecture for integrating, retrieving, and manipulating heterogeneous biological information so that data behave like being stored in a unified database. UBIC2 programming library implements the software architecture and provides application programming interfaces (APIs) to facilitate the development of heterogeneous bio-information computing applications. To achieve interoperability, UBIC2 Web services use XML-based data communication means, which allow distributed applications to consume heterogeneous bio-information regardless of platforms. The documents and software package of UBIC2 are available at http://www.ubic2.org.