In the recent years, Bioinformatics and computational biology are two of some important and active research disciplines. Finding insights into biology, information technology tools in the form of programming languages suitable for biology along with data mining tools and techniques are deployed. The open source programming languages used in bioinformatics are informally called Bio* projects. This work explores the performances of BioPerl, Biojava, BioPython, BioRuby, BioSmalltalk under Bio* projects for executing bioinformatics tasks.

Bioinformatics, Bio* projects , BioPerl, Biojava, BioPython, BioRuby, BioSmalltalk

[1] James Tisdall, Beginning Perl for Bioinformatics, First Edition, O’Reilly, October 2001, ISBN: 0-596-00080-4
[2] Jason E.Stajich, Hilmar Lapp, “Open Source tools and toolkits for bioinformatics: significance, and where are we?”, Briefings in Bioinformatics, Oxford University Press, Vol. 7 No. 3, Pp. 287-296, 2006
[3] Dat Tran, Christopher Dubay, Paul Gorman, William Hersh, “Applying Task Analysis to Describe & Facilitate Bioinformatics Tasks”, MEDINFO, 2004, M. Fieschi et al. (Eds), Amsterdam: IOS Press, IMIA
[4] Lutz Prechelt, “An empirical Comparison of C, C++, Java, Perl, Python, Rexx and Tcl for a search/string-processing program”, University at Karlsruhe, Technical Report 2000-5, March 10, 2000
[5] Mathieu Fourment, Michael R Gillings, “A comparison of common programming languages used in bioinformatics”, BMC Bioinformatics, 9:82, 2008
[6] Open Source Initiative, http://www.opensource.org/, accessed December, 2014
[7] Open Bioinformatics Foundation, http://www.open-bio.org/, accessed December, 2014
[8] M. Rahmania, D. Bastola, L. Najjar, “Comparative Analysis of Software Repository Metrics in BioPerl, BioJava and BioRuby”, International Conference on Computational Science, ICCS 2012, Procedia Computer Science 9 ( 2012 ) 518 – 521, 1877-0509, Published by Elsevier Ltd.
[9] T. Ryu, “Benchmarking of BioPerl, Perl, BioJava, Java, BioPython, and Python for primitive bioinformatics tasks and choosing a suitable language”, International Journal of Contents, Vol.5, No.2, June 2000
[10] Hernán F. Morales, Guillermo Giovambattista, “BioSmalltalk: A pure object system and library for bioinformatics”, Bioinformatics Application Note, Oxford University Press, vol. 29, No. 18, Pp. 2355-2356, 2013
[11] K. Cara Woodwark, “Meeting Review: The Bioinformatics Open Source Conference 2001 (BOSC 2001)”, Comparative and Functional Genomics, 2001; 2: 327–329
[12] BioPerl Web Information, http://bioperl.org, accessed December, 2014
[13] The Open Source Network, http://openhub.net, accessed December, 2014
[14] BioPerl Web Information, http://www.biopython.org, accessed December, 2014
[15] Ruby Programming Language, http://www.ruby-lang.org, accessed December, 2014
[16] IEEE Spectrum, http://spectrum.ieee.org/ns/IEEE_TPL/methods.html, accessed December, 2014
[17] Wiki Definition of Google Trends, http://en.wikipedia.org/wiki/Google_Trends, accessed December, 2014
[18] Hyunyoung Choi, Hal Varian “Predicting the Present with Google Trends”, Google Inc, April 10, 2009
[19] Liguo Yu, Stephen R. Schach, Kai Chen, “Measuring the Maintainability of Open-Source Software”, 0-7803-9508-5/05, IEEE
[20] Wiki Definition of Open Source Community Support, http://en.wikipedia.org/wiki/Open-source_movement, accessed December, 2014
[21] Carsten Kolassa, Dirk Riehle, Michel A. Salim, “The Empirical Commit Frequency Distribution of Open Source Projects”, ACM 978-1-4503-1852-5/13/08
[22] Carsten Kolassa, Dirk Riehle, Michel A. Salim, “A Model of the Commit Size Distribution of Open Source”, Proceedings of the 39th International Conference on Current Trends in Theory and Practice of Computer Science (SOFSEM 2013), LNCS 7741. Page 52-66. Springer Verlag, 2013