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Team:Amsterdam/extra/software
From 2012.igem.org
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| - | < | + | <h2>Local MediaWiki Editor</h2> |
[https://github.com/mreijnders/Local-MediaWiki Click here to retrieve the Local MediaWiki Editor] | [https://github.com/mreijnders/Local-MediaWiki Click here to retrieve the Local MediaWiki Editor] | ||
| - | < | + | <h2>DNA Template Compiler</h2> |
[https://github.com/mreijnders/DNA-Template-Compiler Click here to retrieve the DNA Template Compiler] | [https://github.com/mreijnders/DNA-Template-Compiler Click here to retrieve the DNA Template Compiler] | ||
| - | < | + | <h2>MDL2LaTeX</h2> |
[[File:MDL2LaTeXlogo.png|frameless|center|400px]] | [[File:MDL2LaTeXlogo.png|frameless|center|400px]] | ||
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[https://github.com/slagtermaarten/MDL2Latex 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! | [https://github.com/slagtermaarten/MDL2Latex 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]. | MLD2LaTeX has been tested in both Linux and Unix (Mac OS). For easy installation, first install [http://www.github.com git]. | ||
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If you can’t access git, simply go to this [https://github.com/slagtermaarten/MDL2Latex MDL2LaTeX github page] and download and extract the .zip. | If you can’t access git, simply go to this [https://github.com/slagtermaarten/MDL2Latex MDL2LaTeX github page] and download and extract the .zip. | ||
| - | + | '''Usage''' | |
Edit the | Edit the | ||
Revision as of 17:58, 26 September 2012
Software
Contents |
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
Click here to retrieve the Local MediaWiki Editor
DNA Template Compiler
Click here to retrieve the 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
