NET-file Format
From BioNetWiki
The network file (NET-file) produced by the generate_network function contains all of the blocks in the original BNGL-file plus species, reactions, and groups that contains the network elements produced by network generation. Each block begins with a "begin x" command and ends with an "end x" command, where x is one of the block names. Any characters outside of the blocks are ignored and can be used for comments. Within each block, each entry is listed on a separate line and spaces or tabs are used to separate the entry columns.
species
The syntax for each species line is
index species_string concentration
where index is an integer giving the index of each species, starting from 1. The species_string is the full BNG string describing the graph representing the species, including all molecules, components, and edges. concentration is an integer or real number giving the initial concentration of the species.
reactions
The syntax for each reaction line is
index reactant_list product_list [modifier*]rate_law
where the brackets indicate that the rate constant modifier, which multiplies the rate constant, is option (default is 1). The reactant and product lists are comma delimited lists (no spaces allowed) referring to species by index. The rate_law is either the name of a parameter, in which case the formula used to compute the reaction rate is simply parameter*[r_1]*...*[r_N], where [r_i] is the concentration of the ith reactant. Additional rate_laws can be used, each of which has the syntax type(param1,...,paramN), as discussed in the Tutorial.
An example reaction is
1 1,7 8 2*kp1
which specifies that species 1 and 7 undergo a bimolecular association to produce species 8 with an elementary rate law governed by the rate constant 2*kp1.
groups
The species (and weights) selected by an observable are output in the groups block of the NET file. Each groups line has the syntax
index group_name species_list
where the species list is a comma-separated list of species indices optionally multiplied by the a multiplicative factor
[factor*]index
An example groups entry is
1 R_phos 2,3,5,2*6
The value of the R_phos observables is R_phos= [Species2] + [Species3] + [Species5] + 2*[Species6].
