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Bioinformatics. 2013 Sep 15;29(18):2355-6. doi: 10.1093/bioinformatics/btt398. Epub 2013 Jul 9.

BioSmalltalk: a pure object system and library for bioinformatics.

Author information

1
Instituto de Genética Veterinaria IGEVET, CONICET La Plata-Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata B1900AVW, CC 296 Argentina. hernan.morales@gmail.com

Abstract

SUMMARY:

We have developed BioSmalltalk, a new environment system for pure object-oriented bioinformatics programming. Adaptive end-user programming systems tend to become more important for discovering biological knowledge, as is demonstrated by the emergence of open-source programming toolkits for bioinformatics in the past years. Our software is intended to bridge the gap between bioscientists and rapid software prototyping while preserving the possibility of scaling to whole-system biology applications. BioSmalltalk performs better in terms of execution time and memory usage than Biopython and BioPerl for some classical situations.

AVAILABILITY:

BioSmalltalk is cross-platform and freely available (MIT license) through the Google Project Hosting at http://code.google.com/p/biosmalltalk

CONTACT:

hernan.morales@gmail.com

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
23842806
DOI:
10.1093/bioinformatics/btt398
[Indexed for MEDLINE]

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