metalo 0.5.4

Metabolic analysis of Logical models extracted from maps

MetaLo is a framework for the Metabolic analysis (FBA) of Logical models extracted automatically from detailed mechanistic maps. See this published article for more details.

Install

Metalo 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 metalo

If you want to use the GUI you will need to explicitly request that feature, but it depends on wxPython which sometimes fails to build on some platformes.

$ python3 -m pip install metalo[gui]

Command-line usage

A video tutorial is available here.

Or follow the instructions:

$ metalo --help

usage: metalo [-h] [-v] [-D] [-f] [-i INIT] [-c CASQ] MAP METABOLISM

Metabolic analysis of Logical models extracted from maps. Copyright (C) 2023 [e-mail] and [e-mail]
GPLv3

positional arguments:
MAP                   CellDesigner file containing the mechanistic map
METABOLISM            MitoCore style metabolic model

options:
-h, --help            show this help message and exit
-v, --version         show program's version number and exit
-D, --debug           display some debug information
-f, --fva             run FVA to get interval of values
-i INIT, --init INIT  CSV file with forced initial values for the Logic model
-c CASQ, --casq CASQ  Additional arguments for CaSQ like -u, -d or -r

Or run metalo with no arguments to launch the GUI, if it is installed.