Optional Entries
These entries are not required to fully define a scotch model. However, they may be inserted into the JSON file at various points.
Filename
The Filename field takes the full path for the location of the model's JSON file as a string :
"Filename" : "/Users/qcaudron/scotch/models/myfile.json"
When you save the model by calling model.save("/some/directory/model.json"), the Filename entry is automatically added to the JSON file. Next time, you can then call model.save() without
specifying a path, and the model will be saved with its default filename - the one you specifed last time.
If you call model.save() without a filename, and Filename is not defined in the model's optional entries, the file will be saved in the current working directory under the filename scotch_model.json.
Default algorithm
The default_algorithm field also takes a string.
"default_algorithm" : "gillespie"
Every time you call any function that invokes scotch's simulator without specifying the algorithm you want to use, then the default_algorithm is used. This entry is added to the model as soon as
the model is built - that is, as soon as the wizard finishes, or as the first step in any simulation ( as long as you aren't propagating your state space from the last simulation ). If you don't
specify a default algorithm, the default algorithm is set to gillespie. Valid entries are :
gillespietauLeap