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A Petri nets-based framework for whole-cell modeling.

Fei Liu1, George Assaf2, Ming Chen3

  • 1School of Software Engineering, South China University of Technology, Guangzhou 510006, China.

Bio Systems
|September 20, 2021
PubMed
Summary
This summary is machine-generated.

Whole-cell modeling, a systems biology challenge, faces hurdles in network heterogeneity, component uncertainty, and structural representation. This study introduces a Petri nets-based framework to address these challenges, offering a graphical and modular approach for constructing whole-cell models.

Keywords:
Modeling frameworkPetri netsSystems biologyWhole-cell modeling

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Area of Science:

  • Systems Biology
  • Computational Biology
  • Biophysics

Background:

  • Whole-cell modeling seeks to integrate all cellular components and processes into a single, comprehensive model.
  • It is considered a central goal and a significant challenge within the field of systems biology.
  • Such models are crucial for understanding cellular functions and predicting cellular behavior.

Purpose of the Study:

  • To analyze the key challenges and requirements associated with whole-cell modeling.
  • To explore the utility of Petri net classes in addressing these specific modeling challenges.
  • To propose a novel Petri nets-based framework for constructing whole-cell models.

Main Methods:

  • Classification of whole-cell modeling challenges into three dimensions: heterogeneous biochemical networks, component uncertainties, and cell structure representation.
  • Evaluation of different Petri net classes for their suitability in addressing each identified modeling aspect.
  • Development of a graphical, modular, and hierarchical framework based on Petri nets.

Main Results:

  • Identification of heterogeneous biochemical networks, component uncertainties, and cell structure representation as primary challenges.
  • Demonstration of how various Petri net classes can be applied to tackle these distinct aspects of whole-cell modeling.
  • Presentation of a functional Petri nets-based framework designed for whole-cell model construction.

Conclusions:

  • The proposed Petri nets-based framework effectively addresses critical requirements for whole-cell modeling.
  • This framework provides a graphical, modular, and hierarchical approach, facilitating model development.
  • The framework offers a feasible and promising strategy for the construction of complex whole-cell models.