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pastboon: an R package to simulate parameterized stochastic Boolean networks.

Mohammad Taheri-Ledari1, Sayed-Amir Marashi2, Kaveh Kavousi1

  • 1Laboratory of Complex Biological Systems and Bioinformatics (CBB), Department of Bioinformatics, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, 1417614411, Iran.

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Summary
This summary is machine-generated.

This study introduces pastboon, an R package for simulating parameterized stochastic Boolean networks. It allows researchers to explore phenotypic effects of perturbations in systems biology models without needing deep knowledge of logical rules.

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Area of Science:

  • Systems Biology
  • Computational Biology
  • Network Dynamics

Background:

  • Boolean networks are powerful models for biological systems.
  • Modifying deterministic Boolean networks requires intricate knowledge of update rules, which can be challenging and may disrupt network function.
  • Parameterizing logical functions offers an alternative to directly altering update rules for influencing network behavior.

Purpose of the Study:

  • To develop an R package, pastboon, for simulating parameterized stochastic Boolean networks.
  • To provide a tool for studying the phenotypic consequences of perturbations in biological network models.
  • To facilitate systems biology research by offering a flexible approach to network behavior manipulation.

Main Methods:

  • Developed the pastboon R package.
  • Implemented three distinct parameterization methods for Boolean networks.
  • Utilized parameterized stochastic Boolean networks to simulate system dynamics.

Main Results:

  • The pastboon package enables the simulation of parameterized stochastic Boolean networks.
  • Researchers can investigate the effects of various perturbations on network behavior.
  • The package supports studying phenotypic effects in models of cellular processes.

Conclusions:

  • Parameterized Boolean networks offer a viable alternative for influencing network dynamics without altering core logical rules.
  • The pastboon package provides a valuable resource for systems biology researchers.
  • This approach aids in understanding the impact of perturbations on biological systems.