Quasi Steady State Petri Net (QSSPN)

Dynamic simulation of genome-scale molecular interaction networks will enable the mechanistic prediction of genotype-phenotype relationships. Despite advances in quantitative biology, full parameterisation of whole-cell models is not yet possible. We formulate Quasi-steady state Petri nets (QSSPN), a novel method integrating Petri nets and constraint-based analysis to predict the feasibility of qualitative dynamic behaviours in qualitative models of gene regulation, signalling and whole-cell metabolism. In our publication (Bioinformatics (2013) 29 (24): 3181-3190.) we apply QSSPN to perform the first dynamic simulations including regulatory mechanisms and a genome scale metabolic network in human cell, using bile acid homeostasis in human hepatocytes as a case study.

Resources:

People:

  • Ciaran Fisher,  ciaran.fisher@surrey.ac.uk (hepatocyte model contact)
  • Nick Plant, n.plant@surrey.ac.uk
  • Bernadette Moore, j.b.moore@surrey.ac.uk
  • Andrzej Kierzek, a.kierzek@surrey.ac.uk (software contact)