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Team:KULeuven/Software/Simbiology2LaTeX
From 2008.igem.org
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== Introduction == | == Introduction == | ||
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We've written a small toolbox to convert the information in the Matlab Simbiology models to LaTeX-code. This code can be easily converted to a pdf-file with various open source programs (e.g. [http://www.texniccenter.org/index.php?id=20 TeXnicCenter for Windows]). The idea for this toolbox is based on the plugin [http://systems-biology.org/cd/plugins.html Squeezer] for CellDesigner. | We've written a small toolbox to convert the information in the Matlab Simbiology models to LaTeX-code. This code can be easily converted to a pdf-file with various open source programs (e.g. [http://www.texniccenter.org/index.php?id=20 TeXnicCenter for Windows]). The idea for this toolbox is based on the plugin [http://systems-biology.org/cd/plugins.html Squeezer] for CellDesigner. | ||
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*The formatted equations are sometimes too long. | *The formatted equations are sometimes too long. | ||
*There can only be one model in the project file. The first model will always the chosen one. | *There can only be one model in the project file. The first model will always the chosen one. | ||
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| + | == Remarks == | ||
| + | |||
| + | <html><center><div style="float:center;background:#5cc7dd;width:600px;height:170px" > | ||
| + | <p> | ||
| + | The Simbiology2LaTeX Toolbox is made available for non commercial research purposes only under the GNU General Public License. However, notwithstanding any provision of the <a href="http://www.gnu.org/copyleft/gpl.html">GNU General Public License</a>, Simbiology2LaTeX Toolbox may not be used for commercial purposes without explicit written permission after contacting <a href="mailto:igem@kuleuven.be?SUBJECT=IGEM 2008:License Simbiology2LaTeX">igem@kuleuven.be</a>. | ||
| + | </p> | ||
| + | <p> When reporting results obtained by Simbiology2LaTeX Toolbox, one should refer to </p> | ||
| + | <p> <center>iGEM2008/Team:KULeuven, Maarten Breckpot <br> | ||
| + | Simbiology2LaTeX Toolbox</center> | ||
| + | </p> | ||
| + | </div></center></html> | ||
== File == | == File == | ||
Latest revision as of 15:03, 3 October 2008
Contents |
Introduction
We've written a small toolbox to convert the information in the Matlab Simbiology models to LaTeX-code. This code can be easily converted to a pdf-file with various open source programs (e.g. [http://www.texniccenter.org/index.php?id=20 TeXnicCenter for Windows]). The idea for this toolbox is based on the plugin [http://systems-biology.org/cd/plugins.html Squeezer] for CellDesigner.
The Program
GUI
The program consists of GUI as interface between the user and the converting code. You can start the program by typing "Simbiology2Latex" in the Matlab console. The GUI looks like this:
Use
Step 1
The first thing you have to do is import the model. You can do this by clicking on the "Load Project File" button or by File > Load in the menu bar. After you imported the right model, you'll see some information about your project, like the project name, the number of compartments, reactions, ...
Step 2
The second step is optional and consists of different substeps. With the button "Load Logo" you can import a logo (e.g. the team logo) that will be on the front page of your pdf-file. You can also give the name of the author, title and subtitle of the project.
A result after step 1 and 2:
Step 3
Push "RUN" to generate your TeX-file.
Step 4
Open an Editor to convert the TeX-file into a pdf-file.
Problems
- The formatted equations are sometimes too long.
- There can only be one model in the project file. The first model will always the chosen one.
Remarks
The Simbiology2LaTeX Toolbox is made available for non commercial research purposes only under the GNU General Public License. However, notwithstanding any provision of the GNU General Public License, Simbiology2LaTeX Toolbox may not be used for commercial purposes without explicit written permission after contacting igem@kuleuven.be.
When reporting results obtained by Simbiology2LaTeX Toolbox, one should refer to
Simbiology2LaTeX Toolbox
