dBabel: Cross-Language Interface Platform

Publication: dBabel: Programming Language Interoperability In Distributed Computing Environments, Poster, Pacific Symposium of Biocomputing, 2010

Kshitij Marwah (Harvard Medical School and MIT CSAIL) , Anshuman Aggarwal, Marco Ramoni and Gil Alterovitz

Open science promises increased productivity via communication and collabroation in what is now a global research community. Bioinformatics and biocomputing open science research is unique in that it joins many disciplines together. Current programming models for cross-language use (e.g. swig, http://www.swig.org/) assume one high level language for prototyping and one low level for optimized code. This works well in that there is a team of scientists who typically use one language, say Matlab, and want to interface with C for speed. The assumption here is that all of the scientists share a common language- Matlab in this case. However, in bioinformatics and biocomputing open science endeavors, the situation is different. By its nature, it involves interdisciplinary work between biologists, mathematicians, engineers, and computer scientists. Each comes with their own language. But, perhaps more importantly, each knows and can access vast libraries of code within his/her specialty's community (written in their native language). Bioinformatics and biocomputing seeks to integrate knowledge, methods, and data from different disciplines. In addition, some specialties use one platform (e.g. Mac OS X) while others use different systems (e.g. PC Windows terminal, UNIX server for calculations). This project facilitates this process through design and implementation of a system that allows for communications between languages and different platforms. The result is dBabel : Cross-language Interface Platform.

The software can be downloaded from http://bcl.med.harvard.edu/proj/dbabel .