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-information computing (UBlC²) project aims to disseminate software packages to assist the development of heterogeneous bio-information computing applications that are interoperable and may run distributedly. UBlC² 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 UBlC² are available at http://www.ubic2.org.