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A pattern recognition application framework for biomedical datasets.

Rodrigo Vivanco1, Aleksander B Demko, Mark Jarmasz

  • 1National Research Coucil, Institute for Biodiagnostics, Canada. rodrigo.vivanco@nrc-cnrc.gc.ca

IEEE Engineering in Medicine and Biology Magazine : the Quarterly Magazine of the Engineering in Medicine & Biology Society
|April 20, 2007
PubMed
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Scopira is an open-source C++ framework for high-performance applications, particularly in biomedical data analysis. It offers subsystems, data models, and tools for efficient development and parallel algorithms, aiding prototype migration to C++.

Area of Science:

  • Computer Science
  • Bioinformatics
  • Software Engineering

Background:

  • Developing high-performance applications requires robust frameworks with efficient data handling and parallel processing capabilities.
  • Biomedical data analysis presents unique challenges demanding specialized tools for complex computations and large datasets.

Purpose of the Study:

  • To introduce Scopira, a C++ programming framework designed for high-performance application development.
  • To highlight Scopira's utility in biomedical data analysis and its extensibility through plug-in modules.
  • To provide an open-source solution for researchers to develop and adapt efficient computational tools.

Main Methods:

  • Utilizes C++ for object-oriented, efficient programming.
  • Provides subsystems for memory management, serialization, GUI, and visualization.

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  • Supports parallel algorithm implementation using Message Passing Interface (MPI).
  • Offers plug-in extensions for integrating with scripting languages like Matlab.

    • Main Results:

    • Scopira facilitates the creation of high-performance applications, especially in biomedical data analysis.
    • Enables seamless migration of prototypes to efficient C++ applications via Matlab integration.
    • The framework is available as open-source, promoting research adaptation and collaboration.
    • Successfully compiled for Linux and Windows XP, with Mac OS port in development.

    Conclusions:

    • Scopira is a versatile and efficient framework for high-performance computing in scientific research.
    • Its open-source nature and extensibility foster wider adoption and development in fields like bioinformatics.
    • Future development includes agent-based distributed programming for grid-computing and data mining applications.