GNA format

This format defines the representation of a model through the use of piecewise-linear differential equations (PLDEs). For each variable, the domain partitions must be defined by the threshold-parameters, as well as the synthesis and degradation parameters (synthesis-parameters and degradation-parameters). The rules afecting the system are then given by a set of inequality constraints on the parameters.

See http://ibis.inrialpes.fr/people/dejong/GNA/user/ch02.html

Sample

state-variable: geneB
  zero-parameter: zero_geneB
  box-parameter: max_geneB
  threshold-parameters: t1_geneB
  synthesis-parameters: k1_geneB
  degradation-parameters: g_geneB
  state-equation:
    d/dt geneB = k1_geneB * s-(geneA,t1_geneA)
        - g_geneB * geneB
  parameter-inequalities:
    zero_geneB < t1_geneB < k1_geneB / g_geneB < max_geneB
state-variable: geneA
  zero-parameter: zero_geneA
  box-parameter: max_geneA
  threshold-parameters: t1_geneA
  synthesis-parameters: k_geneA, k1_geneA
  degradation-parameters: g_geneA
  state-equation:
    d/dt geneA = k_geneA
        - g_geneA * geneA
  parameter-inequalities:
    zero_geneA < k_geneA / g_geneA < t1_geneA < k1_geneA / g_geneA < max_geneA