3.2. Syntax of GNA initial conditions

The initial conditions file specifies the initial domain(s), and hence initial qualitative state(s), from which the genetic regulatory network is to be simulated. Initial conditions files have the extension.dat and can be edited using any text editor.

3.2.1. Syntactic conventions

Terminals are written in bold, whereas non-terminals are written in italics. Furthermore,

| separates alternatives;
(...) delimitates a block composed of several alternatives;
[...] delimitates an optional block;
[...]^* denotes a block repeated any (possibly 0) number of times;
[...]⁺denotes a block repeated at least once.

3.2.2. BNF of an initial conditions file

The BNF definition of the syntax of the GNA initial conditions is shown below. The axiom is initial-conditions.

Comments can be inserted into the files. The syntax of comments follows the rules for comments in languages like C: multi-line comments are placed between /* and */, while single-line comments are placed after characters //.

3.2.3. Additional constraints

In the above syntax, for each of the alternative initial-condition expressions, the first idf is a state or input variable and the second idf either the box parameter, the zero parameter, or one of the threshold parameters of the variable. Initial conditions come in pairs for each variable, the first one giving its lower bound, the second one its upper bound. For the lower bound, the operator must be >=, if the right-hand side parameter is a zero parameter, and >, if it is a threshold parameter. For the upper bound, the operator must be <=, if the right-hand side parameter is a box parameter, and <, if it is a threshold parameter. The order of the threshold parameters, zero parameters, and box parameters given in the model file must be respected. Examples of initial conditions files can be consulted in the samples directory of the GNA distribution.