Team:Wageningen UR/notebook/journal/model

From 2014.igem.org

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All the necessary scripts for running the Genomic-Scale Metabolic Model "System Cost" can be found <a href="https://static.igem.org/mediawiki/2014/5/50/Wageningen_UR_Scripts_for_System_Cost.zip" target="blank" class="soft_link">here</a>.
All the necessary scripts for running the Genomic-Scale Metabolic Model "System Cost" can be found <a href="https://static.igem.org/mediawiki/2014/5/50/Wageningen_UR_Scripts_for_System_Cost.zip" target="blank" class="soft_link">here</a>.
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All the necessary scripts for running the Dynamic Model "Promoter Design" and "System Performance" can be found <a href="https://static.igem.org/mediawiki/2014/9/97/Wageningen_UR_modeling_Python_Code.zip" target="blank" class="soft_link">here</a>.
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<dt id="02w12"><a>Week 4</a></dt>
<dt id="02w12"><a>Week 4</a></dt>
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<p>The Toxin/anti-Toxin part of BananaGuard is added to the model. A literature research has been performed to find all the remaining unknown fungal growth inhibitor production rates. The new extended model is tested and improved to run the simulations faster. Also multiple carbon sources is now possible and it is possible to change the oxygen uptake rate.</p>
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<p>The Toxin/anti-Toxin part of BananaGuard is added to the model. A literature research has been performed to find all the remaining unknown fungal growth inhibitor production rates. The new extended model is tested and improved to run the simulations faster. Also multiple carbon sources are now possible and it is possible to change the oxygen uptake rate.</p>
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<p>The simulation with glucose and oxygen as variables could not run properly in a minimized flux model. This has been changed back to a  model with a normal structure. This fix could cause minor differences in the results but was necessary to perform this simulation. <br/>
<p>The simulation with glucose and oxygen as variables could not run properly in a minimized flux model. This has been changed back to a  model with a normal structure. This fix could cause minor differences in the results but was necessary to perform this simulation. <br/>
The only thing left to do was making the plots for the wiki’s. This is a time consuming process. In the waiting time of the simulations I focused on writing the metabolic modeling part.   
The only thing left to do was making the plots for the wiki’s. This is a time consuming process. In the waiting time of the simulations I focused on writing the metabolic modeling part.   
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Questions about the metabolic modeling part can be send to walter.dekoster@wur.nl
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<h3>Dynamic model</h3>
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The first month of iGEM was dedicated to the making of the statistical mechanics model. The experimentalists needed the optimized configuration of repressor binding sites for the Kill-switch. Most of the time spend on the model went into literature research considering the code to be fairly simple.
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The last three months were spend on building a stochastic model of BananaGuard. This model was more complex. The runtimes for a single point on the plots could sometimes take a day. For one of the results in the population dynamics the number of simulations had to be reduced to 5000.
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For reproduction  purposes 7 scripts have been added which can be used or modified to reproduce the results. Because the raw data files range from several hundred megabytes to gigabytes they could not be uploaded.
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Because there were a large amount of scripts 7 have been chosen that can be worked with as a base.
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Should there be any questions feel free to contact me or one of the iGEM team members.
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All the models are made in python, Ananconda 2.7. <br/>
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Important to note: Adding stochastisity to the equations and attempting to solve it using the standard odeint solver might cause the solver to crash.
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bob.vansluijs@wur.nl
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Latest revision as of 01:52, 18 October 2014

Wageningen UR iGEM 2014

 

 

Modelers journal


All the included pathways and metabolites used in the metabolic model can be found here.

All the necessary scripts for running the Genomic-Scale Metabolic Model "System Cost" can be found here.

All the necessary scripts for running the Dynamic Model "Promoter Design" and "System Performance" can be found here.


June

Week 4

July

Week 1
Week 2
Week 3

August

Week 1-4

September

Week 1
Week 2
Week 3
Week 4

October

Week 1
Week 2