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
.dat and can be edited using any text
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.
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 //.
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.