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CaSQ converts CellDesigner models to Boolean models encoded in SBML-Qual with a rather strict semantics defined in a published article.

This extension allows also generating partially specified Boolean networks in .aeon format from CellDesigner models. Possible use in AEON tool for further analyses.

Install

CaSQ is provided as a Python3 package, you can install it from the https://github.com/sybila/casq-fork.git.

Command-line usage

Just follow the instructions:

$ casq --help
usage: casq [-h] [-v] [-D] [-c] [-s] [-r S] [-f FIXED] [-n] [-u [UPSTREAM ...]]
         [-d [DOWNSTREAM ...]] [-a] [-b] [-g GRANULARITY] [-i INPUT] [-C]
         [infile] [outfile]

 Convert CellDesigner models to SBML-qual with a rather strict semantics.
 Copyright (C) 2019, Sylvain.Soliman@inria.fr GPLv3.
 Convert CellDesigner models to partially specified Boolean networks in .aeon format.
 Copyright (C) 2024, xfrak@fi.muni.cz GPLv3.

 positional arguments:
     infile                CellDesigner File
     outfile               SBML-Qual/BMA json File/.aeon File

 options:
   -h, --help            show this help message and exit
   -v, --version         show program's version number and exit
   -D, --debug           Display a lot of debug information
   -c, --csv             Store the species information in a separate CSV (and .bnet) file
   -s, --sif             Store the influence information in a separate SIF file
   -r S, --remove S      Delete connected components in the resulting model if
                         their size is smaller than S. A negative
                         S leads to keep only the biggest(s) connected component(s)
   -f FIXED, --fixed FIXED
                         A CSV file containing input values or knock-ins/knock-outs,
                         one per line, with name in the
                         first column and the value in the second.
   -n, --names           Use the names as IDs in the SBML file
   -u [UPSTREAM ...], --upstream [UPSTREAM ...]
                         Only species upstream of this/these species will be kept
   -d [DOWNSTREAM ...], --downstream [DOWNSTREAM ...]
                         Only species downstream of this/these species will be kept
   -a, --aeon            Output to partially specified Boolean networks in .aeon format
   -b, --bma             Output to BMA json format
   -g GRANULARITY, --granularity GRANULARITY
                         When exporting to BMA, use this granularity
   -i INPUT, --input INPUT
                         When exporting to BMA, nodes with no input should be set to
                         this value
   -C, --colourConstant  When exporting to BMA, colour all variables pink
                         (defaults to colour by compartment)