This short tutorial introduces the main steps to get started with GINsim, using as illustration a simple model of the lysis-lysogeny decision in the phage lambda (as presented in Thieffry 1995):
the specification of the regulatory graph,
the simulation of this model (i.e the construction of the state transition graph),
the use of some of the available tools to analyse dynamical properties,
the definition of perturbations,
the definition of priorities,
few advanced features.
Content of this tutorial is mainly based on the chapter Chaouiya 2012, updated for GINsim-2.9 and complemented with recent advanced functionalities.
Study-case: lysis-lysogeny decision in the bacteriophage lambda
Here, we rely on the logical model presented in Thieffry 1995, which focuses on the core of the lambda regulatory network involving four main cross-regulating genes: cI coding for lambda repressor, the only gene in the lysogenic state; cro, coding for another repressor, expressed in the lytic cycle; cII, an activator of several lysogenic genes, including cI; and N, an anti-terminator factor promoting cII expression.
A more complete description of the model is available, along with the GINsim model file, in the.