Qualitative and quantitative analysis of systems and synthetic biology constructs using P systems

ACS Synth Biol. 2015 Jan 16;4(1):83-92. doi: 10.1021/sb500134w. Epub 2014 Aug 14.

Abstract

Computational models are perceived as an attractive alternative to mathematical models (e.g., ordinary differential equations). These models incorporate a set of methods for specifying, modeling, testing, and simulating biological systems. In addition, they can be analyzed using algorithmic techniques (e.g., formal verification). This paper shows how formal verification is utilized in systems and synthetic biology through qualitative vs quantitative analysis. Here, we choose two well-known case studies: quorum sensing in P. aeruginosas and pulse generator. The paper reports verification analysis of two systems carried out using some model checking tools, integrated to the Infobiotics Workbench platform, where system models are based on stochastic P systems.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Artificial Cells
  • Bacteria / genetics
  • Bacteria / metabolism
  • Computer Simulation
  • Green Fluorescent Proteins / genetics
  • Models, Biological
  • Models, Statistical
  • Pseudomonas aeruginosa / metabolism
  • Quorum Sensing
  • Signal Transduction
  • Stochastic Processes
  • Synthetic Biology*
  • Systems Biology*

Substances

  • Green Fluorescent Proteins