Team:TU Delft-Leiden/Modeling/CodeRepository

From 2014.igem.org

(Difference between revisions)

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

@@ Line 17: / Line 17: @@
 <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/2014/5/51/Delft2014_StandardActivation.m">Standard Activation</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/2014/8/84/Delft2014_CooperativeActivation.m">Cooperative Activation</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/f/f8/Delft2014_PromoterModel.m">Promoter Model Fitter</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://2014.igem.org/File:FBA_constructed_model.zip">FBA Constructed Model</a></p>
+<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://2014.igem.org/File:Comp_with_without_EET.m">Comparison with and without EET</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://2014.igem.org/File:FBA.m">FBA</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://2014.igem.org/File:FBA_Uptake_without_EET.m">FBA Uptake without EET</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://2014.igem.org/File:FVA.m">FVA</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://2014.igem.org/File:Phase_Plane_Analysis.m">Phase Plane Analysis FBA</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://2014.igem.org/File:Phase_Plane_Analysis_Min_Max.m">Phase Plane Analysis FVA</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://2014.igem.org/File:Robustness_Analysis_EET.m">Robustness Analysis EET</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://2014.igem.org/File:Robustness_Analysis_Uptake.m">Robustness Analysis Uptake</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>
 <br>
 <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>Curli Module</h3>
+<h3>Landmine Module</h3>
-<br>
-<br>
+<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>