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Beyond standardization: dynamic software infrastructures for systems biology.

Morris A Swertz1, Ritsert C Jansen

  • 1Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, NL-9751 NN Haren, The Netherlands.

Nature Reviews. Genetics
|February 14, 2007
PubMed
Summary
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Systems biology software development is slow. A minimal computer language and generator tool can rapidly create customized software infrastructures, meeting biologists' specific needs for better systems biology research.

Area of Science:

  • Systems biology
  • Bioinformatics
  • Computational biology

Background:

  • Systems biology research progress is limited by the slow development of adaptable software infrastructure.
  • Current software lacks mechanisms to support the specific variations inherent in diverse biological systems.
  • Interoperability between laboratories is crucial but hindered by non-standardized tools.

Purpose of the Study:

  • To address the bottleneck in systems biology software development.
  • To propose a novel approach for creating customized and standardized software infrastructures.
  • To enable seamless integration of research from different laboratories.

Main Methods:

  • Development of a minimal computer language tailored for biological systems.

Related Experiment Videos

  • Creation of a software generator tool utilizing this language.
  • Design of infrastructure adaptable to specific biological system variations.

    • Main Results:

    • The proposed minimal language and generator tool enable rapid production of customized software infrastructures.
    • The approach facilitates the creation of software that accommodates biological system specifics.
    • Demonstrated potential for enhanced interoperability and standardization in systems biology.

    Conclusions:

    • A minimal computer language and generator tool offer a viable solution to accelerate systems biology software development.
    • This approach can provide systems biologists with the adaptable and integrated infrastructure they require.
    • Overcoming current limitations will significantly advance the field of systems biology.