Software

The complexity of biology calls for the aid of computers in a synthetic biology design process. Over the summer we have created a range of useful applications to make the life of the synthetic biologist easier.

Local MediaWiki Editor

[[Team:

DNA Template Compiler

MDL2LaTeX

[http://www.stompy.sourceforge.net StochPy] is a versatile stochastic simulation package implemented in Python for the simulation of biochemical networks. Its inherits the easy to learn model description language [http://www.stompy.sourceforge.net/html/inputfile_doc.html MDL] from its parent package [http://pysces.sourceforge.net/PySCeS PySCeS], which is a modelling environment with deterministic capabilities. By defining models in MDL and executing them through high-level commands in the Python or IPython shell, an easy-going experience is presented to the modeller in which one (almost) doesn’t need to worry about implementation details.

MDL2LaTeX is another step towards making a modeller’s life as carefree as possible. Exactly as its name implies: it converts MDL files to clean LaTeX representations, so the models can be easily integrated into reports. No more time wasted on tedious equation copying into LaTeX!

Installation

MLD2LaTeX has been tested in both Linux and Unix (Mac OS). For easy installation, first install [http://www.github.com git].

Then run:

git clone https://github.com/slagtermaarten/MDL2Latex.git

If you can’t access git, simply go to this MDL2LaTeX github page and download and extract the .zip.

Usage

Edit the

Makefile

inside of this folder and change the pscfile variable to filepath of the the .psc (MDL model) file you want to convert. Save and run

make

MDL2LaTeX (MDL-to-LaTeX) converts MDL stochastic model description files used by the stochastic simulation package [http://stompy.sourceforge.net StochPy] to LaTeX representations, so they become more human-readable and can be easily integrated into reports.

Click here for the MDL2LaTeX tool