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
Example:
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