Title: BioInt: an integrative biological object-oriented application framework and interpreter

Authors: Sanket Desai; Prasad Burra

Addresses: School of Biotechnology, IGNOU - International Institute of Information Technology, Center of Excellence for Advanced Research and Education, P-14, Rajiv Gandhi Infotech Park, Phase-1, Hinjewadi, Pune, India ' School of Biotechnology, IGNOU - International Institute of Information Technology, Center of Excellence for Advanced Research and Education, P-14, Rajiv Gandhi Infotech Park, Phase-1, Hinjewadi, Pune, India

Abstract: BioInt, a biological programming application framework and interpreter, is an attempt to equip the researchers with seamless integration, efficient extraction and effortless analysis of the data from various biological databases and algorithms. Based on the type of biological data, algorithms and related functionalities, a biology-specific framework was developed which has nine modules. The modules are a compilation of numerous reusable BioADTs. This software ecosystem containing more than 450 biological objects underneath the interpreter makes it flexible, integrative and comprehensive. Similar to Python, BioInt eliminates the compilation and linking steps cutting the time significantly. The researcher can write the scripts using available BioADTs (following C++ syntax) and execute them interactively or use as a command line application. It has features that enable automation, extension of the framework with new/external BioADTs/libraries and deployment of complex work flows.

Keywords: biological programming; application framework; C++; interpreter; object-oriented design; abstract data type; workflow system; biological scripting; software engineering; software ecosystem; data mining; curation; annotation; biological algorithms; bioinformatics.

DOI: 10.1504/IJBRA.2015.069195

International Journal of Bioinformatics Research and Applications, 2015 Vol.11 No.3, pp.247 - 256

Received: 29 Oct 2013
Accepted: 03 Apr 2014
Published online: 05 May 2015 *

Full-text access for editors Full-text access for subscribers Purchase this article Comment on this article