Team:TU Delft-Leiden/Modeling/CodeRepository

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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

Flux Balance Analysis

FBA Constructed Model

Comparison with and without EET

FBA

FBA Uptake without EET

Robustness Analysis EET

Robustness Analysis Uptake

FVA

Phase Plane Analysis FBA

Phase Plane Analysis FVA


EET Complex Assembly

EET Pathway Assembly

EET Pathway Assembly Solver

EET Pathway Assembly (Simple)

EET Pathway Assembly Solver (Simple)

EET Pathway Assembly Solver (Simple) for varying d-ALA concentration


Landmine Module

Standard Activation

Cooperative Activation

Promoter Model Fitter

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