Command-Line Interface

The command line interface enables model conversion and simple model analysis (currently only listing the stable states). The arguments start with a file from which to load the model, and end either with a target file (for model conversion) or with a specification of the analysis to perform. Between these required parts, a list of model modifiers can also be specified, allowing to save modified models or to analyse them directly. Some additional optional switches facilitate the selection of input and output formats.

The command line use of bioLQM use the following pattern:

java -jar bioLQM-${version}.jar [-if format] input_file [-m model_modifier]* ([-of format] output_file)|(-r action)

When launched without argument (or with non-recognized ones), a help message is displayed, showing the syntax and available features.

The command line arguments contain the 3 parts described below (in this order):

  • The loaded file. An import filter will be used to open this file and construct a model.

    The format can be guessed from the file extension or specified explicitly with the -if format optional argument.

  • An optional list of model modifications using the -m modifier_name [parameters] switch. All following arguments which do not start with a "-" sign will be taken as modifier parameters, except the last argument.

    Note that the -p argument shortcut can be used to apply a perturbation directly.

  • The action to perform on the resulting model: it can be saved to a file or used as input for an analysis tool.

    To export the model to a file, provide the output filename. Like when loading a model, the format can be guessed from the extension or specified with the -of format optional argument.

The -s switch is used to run bioLQM in script mode.

Examples

  • Convert a model from SBML qual to boolsim:

    java -jar bioLQM.jar model.sbml model.boolsim

  • Apply a knockout perturbation before saving the model:

    java -jar bioLQM.jar model.sbml -p A%0 modified.boolsim

  • Booleanize and save a model:

    java -jar bioLQM.jar model.sbml -m booleanize model_bool.sbml

  • More complex conversion syntax, specifying input and output formats:

    java -jar bioLQM.jar -if sbml model.xml -of ina model.pnt