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: