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Comparing Petri net-based models of biological systems using Holmes.

Bartłomiej Szawulak1, Marcin Radom1,2, Piotr Formanowicz1

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Summary

This study introduces a new tool for comparing biological system models represented as Petri nets. The Holmes application enables formal analysis of conserved biological processes, addressing a gap in current software.

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Area of Science:

  • Systems Biology
  • Computational Biology
  • Bioinformatics

Background:

  • Systems biology requires formal models for studying biological phenomena.
  • Petri nets offer a graphical and mathematically analyzable approach to biological modeling.
  • Comparing models is crucial for identifying conserved biological processes and homologies.

Purpose of the Study:

  • To address the lack of software tools for comparing Petri net-based biological models.
  • To introduce a novel analytical tool for model comparison within the Holmes application.

Main Methods:

  • Implementation of a new analytical tool within the Holmes application.
  • Utilizing four distinct comparison methods: t-invariants, decomposition, graphlets, and branching vertices.

Main Results:

  • A new software tool for comparing Petri net models has been developed and implemented.
  • The tool supports multiple analytical approaches for model comparison, enhancing biological systems analysis.

Conclusions:

  • The developed tool facilitates the comparison of Petri net models, aiding in the discovery of conserved biological processes.
  • This advancement provides a much-needed computational resource for systems biology research.