Team:TU Delft-Leiden/Modeling/CodeRepository

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Latest revision as of 00:12, 18 October 2014

Code Repository

On this page, links to the Matlab scripts we made for our modeling efforts are given. Right clicking the link and choosing "Save link as..." allows you to save the code to your computer.

Curli Module

The curli gene and cell level code.

Find the persistence length of a curli.

Fit the density from the cell to the colony level.

Calculate if there is percolation as function of time.

Simulate an experiment on the colony level.

EET Module

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+<body>
+<div class='grid_12'>
 <h2> Code Repository </h2>
-<p>On this page, links to the matlab scripts used for our modeling efforts are given. Right clicking the link and choosing "Save link as..." allows you to save the code to your computer. </p>
+<p>
+On this page, links to the Matlab scripts we made for our modeling efforts are given. Right clicking the link and choosing "Save link as..." allows you to save the code to your computer.
+</p>
 <br>
-<h3>Landmine module</h3>
+<h3>Curli Module</h3>
+<p><a href="https://static.igem.org/mediawiki/2014/b/be/TUDelft_2014_Curli_Server_celllevel.m">The curli gene and cell level code.</a></p>
+<p><a href="https://static.igem.org/mediawiki/2014/9/90/TUDelft_2014_Colony_ComputePersistenceLength.m">Find the persistence length of a curli.</a></p>
+<p><a href="https://static.igem.org/mediawiki/2014/b/b3/TUDelft_2014_Curli_Colony_FitDensity.m">Fit the density from the cell to the colony level.</a></p>
+<p><a href="https://static.igem.org/mediawiki/2014/d/dd/TUDelft_2014_Curli_colonylevel_Light.m">Calculate if there is percolation as function of time.</a></p>
+<p><a href="https://static.igem.org/mediawiki/2014/2/2c/TUDelft_2014_Colony_Calculate_Resistance.m">Simulate an experiment on the colony level.</a></p>
+<br>
+<h3>EET Module</h3>
+<h4>Flux Balance Analysis </h4>
+<p><a href="https://static.igem.org/mediawiki/2014/0/0a/TU_Delft_2014_FBA_constructed_model.zip">FBA Constructed Model</a></p>
+<p><a href="https://static.igem.org/mediawiki/2014/f/ff/TU_Delft_2014_Comp_with_without_EET.m">Comparison with and without EET</a></p>
+<p><a href="https://static.igem.org/mediawiki/2014/0/04/TU_Delft_2014_FBA.m">FBA</a></p>
+<p><a href="https://static.igem.org/mediawiki/2014/1/11/TU_Delft_2014_FBA_Uptake_without_EET.m">FBA Uptake without EET</a></p>
+<p><a href="https://static.igem.org/mediawiki/2014/b/b9/TU_Delft_2014_Robustness_Analysis_EET.m">Robustness Analysis EET</a></p>
+<p><a href="https://static.igem.org/mediawiki/2014/5/5e/TU_Delft_2014_Robustness_Analysis_Uptake.m">Robustness Analysis Uptake</a></p>
+<p><a href="https://static.igem.org/mediawiki/2014/6/62/TU_Delft_2014_FVA.m">FVA</a></p>
+<p><a href="https://static.igem.org/mediawiki/2014/1/1f/TU_Delft_2014_Phase_Plane_Analysis.m">Phase Plane Analysis FBA</a></p>
+<p><a href="https://static.igem.org/mediawiki/2014/d/db/TU_Delft_2014_Phase_Plane_Analysis_Min_Max.m">Phase Plane Analysis FVA</a></p>
-<p><a href="https://static.igem.org/mediawiki/2014/5/51/Delft2014_StandardActivation.m">StandardActivation</a></p>
-<p><a href="https://static.igem.org/mediawiki/2014/8/84/Delft2014_CooperativeActivation.m">CooperativeActivation</a></p>
-<p><a href="https://static.igem.org/mediawiki/2014/f/f8/Delft2014_PromoterModel.m">PromoterModel</a></p>
 <br>
-<h3>EET module</h3>
+<h4>EET Complex Assembly </h4>
 <p><a href="https://static.igem.org/mediawiki/2014/6/60/Delft2014_EETpathway_assembly.m">EET Pathway Assembly</a></p>
 <p><a href="https://static.igem.org/mediawiki/2014/6/6b/Delft2014_EETPathway_assembly_solver.m">EET Pathway Assembly Solver</a></p>
 <p><a href="https://static.igem.org/mediawiki/2014/b/ba/Delft2014_EETpathway_assembly_simple.m">EET Pathway Assembly (Simple)</a></p>
 <p><a href="https://static.igem.org/mediawiki/2014/8/84/Delft2014_EETpathway_assembly_simple_solver.m">EET Pathway Assembly Solver (Simple)</a></p>
-<p><a href="https://static.igem.org/mediawiki/2014/7/7e/Delft2014_EETvsdALA.m.m">EET Pathway Assembly Solver (Simple) for varying d-ALA concentration</a></p>
+<p><a href="https://static.igem.org/mediawiki/2014/7/7e/Delft2014_EETvsdALA.m">EET Pathway Assembly Solver (Simple) for varying d-ALA concentration</a></p>
+<br>
+<h3>Landmine Module</h3>
+<p><a href="https://static.igem.org/mediawiki/2014/5/51/Delft2014_StandardActivation.m">Standard Activation</a></p>
+<p><a href="https://static.igem.org/mediawiki/2014/8/84/Delft2014_CooperativeActivation.m">Cooperative Activation</a></p>
+<p><a href="https://static.igem.org/mediawiki/2014/f/f8/Delft2014_PromoterModel.m">Promoter Model Fitter</a></p>
+</div>
+</body>
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