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BioSmalltalk: a pure object system and library for bioinformatics.

Hernán F Morales¹, Guillermo Giovambattista

¹Instituto 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

Bioinformatics (Oxford, England)

|July 12, 2013

Summary

BioSmalltalk is a novel object-oriented programming system for bioinformatics. It enhances biological knowledge discovery and software prototyping for bioscientists, showing improved performance over existing toolkits.

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Area of Science:

Bioinformatics
Computational Biology
Software Engineering

Background:

Adaptive end-user programming systems are increasingly vital for biological knowledge discovery.
Open-source programming toolkits for bioinformatics have gained prominence.
Bridging the gap between bioscience research and rapid software development is crucial.

Purpose of the Study:

Introduce BioSmalltalk, a new programming environment for pure object-oriented bioinformatics.
Facilitate rapid software prototyping for biosciences.
Enable scalability to whole-system biology applications.

Main Methods:

Development of a novel object-oriented programming environment.
Comparative performance analysis against existing bioinformatics toolkits (Biopython, BioPerl).

Main Results:

BioSmalltalk demonstrates superior execution time and memory usage compared to Biopython and BioPerl in specific classical bioinformatics scenarios.
The system supports pure object-oriented programming for bioinformatics tasks.

Conclusions:

BioSmalltalk offers an effective solution for bioinformatics programming, enhancing efficiency and usability.
The system aids in discovering biological knowledge and supports the development of complex biological applications.