https://github.com/x-jiang-bioe/sb2l

Translates the biological models written in SBML into LaTeX code to be compiled and read by human eye
https://github.com/x-jiang-bioe/sb2l

converter latex sbml

Last synced: 2 days ago
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Translates the biological models written in SBML into LaTeX code to be compiled and read by human eye

• Host: GitHub
• URL: https://github.com/x-jiang-bioe/sb2l
• Owner: X-Jiang-bioe
• License: mit
• Created: 2019-10-11T22:48:07.000Z (over 5 years ago)
• Default Branch: master
• Last Pushed: 2020-01-11T23:30:12.000Z (about 5 years ago)
• Last Synced: 2025-01-17T13:17:22.355Z (12 days ago)
• Topics: converter, latex, sbml
• Language: Python
• Size: 124 KB
• Stars: 1
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# 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.s2string(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: