All tools support the -hoption, which will list a short description of the tool, and all available options.
fmllint checks if a file conforms to the fml syntax. To execute it simply run:
fmllint -i file.fml.
Update the FluxML Level of an fml file. To update a file from level 1 to 2 run:
fmlupdate -i level1_file.fml -o level2_file.fml -l 2
Converts a file from the old tabular ftbl format to fml. There are many options available but the basic usage is:
ftbl2fml -i ftbl_file.csv -o fml_file.fml
Converts sbml files to fml files and vice versa. Note that the atom mapping is lost, when converting an fml file to an sbml file!
sbml2fml -i model.xml -o model.fml
fml2sbml -i model.fml -o model.yml
Prints some statistical information about the network, ie number of:
- metabolites
- reactions
- atoms
- isotopomers
- cumomers (in unreduced network)
- cumomers per level of the cascade
The call is simply fmlstats -i file.fml
Multiplies a network once per configuration.
multiply_fml -i model_with_n_configurations.fml -o model_with_n_fold_network.fml
tools to set inputs (i.e. substrates) parameters (i.e. free fluxes and poolsizes) and measurements to a fml file. Their syntax is identical:
setXXX -i original.fml -C data.csv -o modified.fml