sb2l

Description

Translates biological models written in SBML into LaTeX code to be compiled and read by human eye

Dependencies

The current version runs 1.3.1 version of PyLaTeX

Either Tellurium or python-libsbml is also required

For PDF creation functionality, either latexmk or pdflatex needs to be installed on the computer

Installation

pip install sb2l

How to Use

The following structure gives a LaTeX string that can be copied to a online compiler like Overleaf:

import sb2l
latexStr = sb2l.s2string(sbmlStringOrFile)

If using with Tellurium or Antimony:

import sb2l
latexStr = sb2l.s2latex(model_name.getSBML())

For making PDF files (The filepath must NOT have a .pdf or .tex suffix)

import sb2l
filepath = "/Users/Username/Desktop/theDesiredNameOfFile" #[NOTICE: no ".anything"]
sb2l.s2pdf(sbmlStringOrFile, file_path = filepath);

The same structure can be used to generate a .tex file if used with sb2l.s2latex

To generate the PDF file and open with the default PDF reader

import sb2l
filepath = "/Users/Username/Desktop/theDesiredNameOfFile" #[NOTICE: no ".anything"]
sb2l.s2open(sbmlStringOrFile, file_path = filepath);

License

MIT License

Copyright (c) 2019

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: