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as submitted to the BacHBerry project
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675 changes: 675 additions & 0 deletions LICENSE.txt

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<!DOCTYPE html><html><head><meta charset="utf-8"><title>Untitled Document.md</title><style></style></head><body id="preview">
<h1><a id="OptPipe__a_Pipeline_for_Optimizing_Metabolic_Engineering_Targets_0"></a>OptPipe - a Pipeline for Optimizing Metabolic Engineering Targets</h1>
<hr>
<p>This software contains up-to date standardized methods for the optimization of metabolic engineering targets in genome-scale metabolic networks. This software was developed in the frame of the
<a href="http://www.bachberry.eu/">BaCHBerry</a> project (European Union FP7- 613793)</p>
<p>The code was written by Ana Vila Santa and András Hartmann under the supervision of Susana Vinga.</p>
<h1><a id="License_7"></a>License</h1>
<hr>
<p>© 2015 - 2016 <a href="mailto:susanavinga@tecnico.ulisboa.pt">Susana Vinga</a>, <a href="mailto:andras.hartmann@gmail.com">András Hartmann</a> and <a href="mailto:vilasanta.ana@gmail.com">Ana Vila Santa</a></p>
<p>OptPipe is a free software: you can redistribute it and/or modify
it under the terms of the GNU Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.</p>
<p>This code is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU Public License for more details.</p>
<p>You should have received a copy of the GNU Public License
along with this code. If not, see <a href="http://www.gnu.org/licenses/">http://www.gnu.org/licenses/</a></p>
<h1><a id="Contents_24"></a>Contents</h1>
<hr>
<table>
<thead>
<tr>
<th></th>
<th></th>
<th></th>
</tr>
</thead>
<tbody>
<tr>
<td>common_functions</td>
<td>:</td>
<td>Folder for the common function shared by the methods</td>
</tr>
<tr>
<td>examples</td>
<td>:</td>
<td>Folder for working examples including models</td>
</tr>
<tr>
<td>external</td>
<td>:</td>
<td>Folder containing external libraries and toolboxes</td>
</tr>
<tr>
<td>methods</td>
<td>:</td>
<td>Folder containing the methods</td>
</tr>
<tr>
<td>installPipeline.m</td>
<td>:</td>
<td>Install script</td>
</tr>
<tr>
<td>LICENSE.txt</td>
<td>:</td>
<td>License file (GPL v3)</td>
</tr>
<tr>
<td>README.md</td>
<td>:</td>
<td>This file</td>
</tr>
</tbody>
</table>
<h1><a id="Install_37"></a>Install</h1>
<hr>
<h2><a id="Prerequisites_39"></a>Prerequisites</h2>
<p>You will need:</p>
<ul>
<li><a href="http://www.mathworks.com/products/matlab">MATLAB</a> software for scientific computiong version 7.14 or later
<ul>
<li>Parallel toolbox (optional, but highly recommended in order to shorten running time)</li>
</ul>
</li>
<li><a href="http://opencobra.github.io/cobratoolbox/">COBRA toolbox</a> from the openCOBRA project (an actual snapshot of is attached as external library)</li>
<li><a href="http://sbml.org/Software/SBMLToolbox">SBML toolbox</a> (an actual snapshot of is attached as external library)</li>
<li><a href="http://www.gurobi.com/">gurobi</a> optimization software installed for MATLAB (free for academic users)</li>
</ul>
<h1><a id="Installation_47"></a>Installation</h1>
<p>Place the content of the package in a separate folder, start MATLAB.
Within the MATLAB shell go to the init folder and run the init script</p>
<pre><code class="language-matlab">&gt;&gt; cd <span class="hljs-string">'&lt;code folder&gt;/init'</span>
&gt;&gt; initPipeline
</code></pre>

</body></html>
65 changes: 65 additions & 0 deletions README.md
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# OptPipe - a Pipeline for Optimizing Metabolic Engineering Targets
---
This software contains up-to date standardized methods for the optimization of metabolic engineering targets in genome-scale metabolic networks. This software was developed in the frame of the
[BaCHBerry] project (European Union FP7- 613793)

The code was written by Ana Vila Santa and András Hartmann under the supervision of Susana Vinga.

# License
---
© 2015 - 2016 [Susana Vinga], [András Hartmann] and [Ana Vila Santa]

OptPipe is a free software: you can redistribute it and/or modify
it under the terms of the GNU Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This code is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU Public License for more details.

You should have received a copy of the GNU Public License
along with this code. If not, see http://www.gnu.org/licenses/

# Contents
---

| | | |
|--------------------|-|------------------------------------------------------|
|common_functions |:| Folder for the common function shared by the methods|
|examples |:| Folder for working examples including models|
|external |:| Folder containing external libraries and toolboxes|
|methods |:| Folder containing the methods|
|installPipeline.m |:| Install script|
|LICENSE.txt |:| License file (GPL v3)|
|README.md |:| This file|

# Install
---
## Prerequisites
You will need:
- [MATLAB] software for scientific computiong version 7.14 or later
- Parallel toolbox (optional, but highly recommended in order to shorten running time)
- [COBRA toolbox] from the openCOBRA project (an actual snapshot of is attached as external library)
- [SBML toolbox] (an actual snapshot of is attached as external library)
- [gurobi] optimization software installed for MATLAB (free for academic users)

# Installation
Place the content of the package in a separate folder, start MATLAB.
Within the MATLAB shell go to the init folder and run the init script
```matlab
>> cd '<code folder>/init'
>> initPipeline
```

[BaCHBerry]: <http://www.bachberry.eu/>

[MATLAB]: <http://www.mathworks.com/products/matlab>
[COBRA toolbox]: <http://opencobra.github.io/cobratoolbox/>
[SBML toolbox]: <http://sbml.org/Software/SBMLToolbox>
[gurobi]: <http://www.gurobi.com/>

[Susana Vinga]: <mailto:susanavinga@tecnico.ulisboa.pt>
[András Hartmann]: <mailto:andras.hartmann@gmail.com>
[Ana Vila Santa]: <mailto:vilasanta.ana@gmail.com>
14 changes: 14 additions & 0 deletions common_functions/AddSinkToModel.m
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function [new_model_r] = AddSinkToModel(new_model)
%function [new_model_r] = AddSinkToModel(new_model)
%Adds Malonyl-CoA sink and export reactions
% Deplicated, should be deleted

new_model_r = addReaction( new_model,'malonylCoA_export',{'malcoa[c]','malcoa[e]'},[-1 1]);

new_model_r = addReaction( new_model_r,'sink_malonylCoA',{'malcoa[e]'},[-1]);

new_model_r = changeRxnBounds( new_model_r, {'sink_malonylCoA'}, [0], 'l');
new_model_r = changeRxnBounds( new_model_r, {'sink_malonylCoA'}, [1000], 'u');

end

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