Table of contents
    1. 1. Primary Reading
    2. 2. Secondary Reading

    1 February 2010
    Michael Gribskov

    All biological processes are controlled by regulatory networks.  While quantitative differential equation-based models based ca be constructed for some systems, we often lack the precise quantitative information needed for such an approach.  Qualitative approaches such as Boolean networks and Petri nets rely much more on the kinds of information we can deduce from high-throughput experiments, namely which genes/proteins interact and whether their interactions are positive or negative.  The Petri net approach was originally applied to manufacturing and communication systems, but more recently has been applied to biological systems.


    Primary Reading

    Students participants should read these papers thoroughly

    • Doi, et al. Constructing Biological Pathway Models with Hybrid Functional Petri Nets, In Silico Biology 4, 271-291, 2004 [PDF]
    • Genrich et al., Executable Petri net models of the analysis of metabolic pathways, Int.J.STTT 3, 394-404, 2001. [PDF]

    Secondary Reading

    Student participants should read these, but do not have to read them as deeply

    • Goss and Peccoud, Analysis of the stabilizing effect of ROM on the genetic network controlling ColE1 plasmid replication, Pacific Symposium of Biocomputing 4, 65-76, 1999. [PDF]
    • Heiner et al., Model validation of biological pathways using Petri nets -- demonstrated for apoptosis, BioSystems 75, 15-28, 2004 [PDF]

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