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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.
CaSQ is provided as a Python3 package, you can install it from the Python package index with pip, conda or your Python package manager of choice:
$ python3 -m pip install casqJust follow the instructions:
$ casq --help
usage: casq [-h] [-v] [-D] [-c] [-s] [-r S] [-u [UPSTREAM ...]]
[-d [DOWNSTREAM ...]] [-b] [-g GRANULARITY] [-i INPUT] [-C]
[infile] [outfile]
Convert CellDesigner models to SBML-qual with a rather strict semantics.
Copyright (C) 2019, [email protected] GPLv3
positional arguments:
infile CellDesigner File
outfile SBML-Qual/BMA json File
optional arguments:
-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 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)
-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
-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)