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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.
CaSQ is provided as a Python3 package, you can install it from the https://github.com/sybila/casq-fork.git.
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, [email protected] GPLv3.
Convert CellDesigner models to partially specified Boolean networks in .aeon format.
Copyright (C) 2024, [email protected] 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)