Team:TU-Munich/Modeling/Overview

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== Modeling Overview ==
== Modeling Overview ==
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In our modeling efforts, we tried to cover a very wide range of different methods, reaching from simple and ordinary differential equations, over partial differential equations, to stochastic differential equations as well as bioinformatical methods. To gain the largest possible output, we stayed in close contact with our wetlab team, answered their design questions and fitted parameters which could then be used for implementation aspects.
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<div class="box-left overview"><html><img src="https://static.igem.org/mediawiki/2013/9/91/TUM13_modeling-1.jpg" /></html>
<div class="box-left overview"><html><img src="https://static.igem.org/mediawiki/2013/9/91/TUM13_modeling-1.jpg" /></html>
===Protein Predictions===
===Protein Predictions===
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For the immobilization of effectors on the cell membrane, we needed to design a transmembrane domain. Using several bioinformatical methods we identified the transmembrane region of the SERK receptor which we later used as starting point for our constructs. [https://2013.igem.org/Team:TU-Munich/Modeling/Protein_Predictions Read More]
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<div class="box-right overview"><html><img src="https://static.igem.org/mediawiki/2013/2/28/TUM13_modeling-2.jpg" /></html>
<div class="box-right overview"><html><img src="https://static.igem.org/mediawiki/2013/2/28/TUM13_modeling-2.jpg" /></html>
===Enzyme Kinetics===
===Enzyme Kinetics===
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Proper analysis of data is important to really understand them. For this reason we formed groups in which our wet and dry lab people came together to understand our experiments from an experimental as well as mathematical point of view.
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For an effective implementation of our filter system it is essential to analyze the enzymatic activity of our effectors. Using experimental data we fitted the respective kinetic parameters and carried out rigorous uncertainty analysis to assess the reliability of the fitted parameters. [https://2013.igem.org/Team:TU-Munich/Modeling/Enzyme Read More]
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<div class="box-left overview"><html><img src="https://static.igem.org/mediawiki/2013/b/b0/TUM13_modeling-3.jpg" /></html>
<div class="box-left overview"><html><img src="https://static.igem.org/mediawiki/2013/b/b0/TUM13_modeling-3.jpg" /></html>
===Kill Switch===
===Kill Switch===
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Especially during planing seasons, we had several different ideas in which way our moss could detect on its own that it has escaped from its appropriate environment, how the resulting signal is triggered and how it should decrease its viablility.
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During the planning stage of our project, we had several different ideas on how to efficiently implement a kill-switch in our moss. In this section of the wiki we documented our mathematical train of thought that eventually led us to our final design.<br>[https://2013.igem.org/Team:TU-Munich/Modeling/Kill_Switch Read More]
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<div class="box-right overview"><html><img src="https://static.igem.org/mediawiki/2013/2/25/TUM13_modeling-4.jpg" /></html>
<div class="box-right overview"><html><img src="https://static.igem.org/mediawiki/2013/2/25/TUM13_modeling-4.jpg" /></html>
===Filter Model===
===Filter Model===
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The filter model is aimed to simulate different remediation scenarios and should be used to calculate the perfectly fitting conditions of our Physco filter, referring to the needs of the environment.  
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The filter model is designed to simulate different remediation scenarios. It should be used to calculate the necessary amount of PhyscoFilters, referring to the environmental parameters.<br>[https://2013.igem.org/Team:TU-Munich/Modeling/Filter Read More]
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Latest revision as of 03:47, 29 October 2013


Modeling Overview

In our modeling efforts, we tried to cover a very wide range of different methods, reaching from simple and ordinary differential equations, over partial differential equations, to stochastic differential equations as well as bioinformatical methods. To gain the largest possible output, we stayed in close contact with our wetlab team, answered their design questions and fitted parameters which could then be used for implementation aspects.

Protein Predictions

For the immobilization of effectors on the cell membrane, we needed to design a transmembrane domain. Using several bioinformatical methods we identified the transmembrane region of the SERK receptor which we later used as starting point for our constructs. Read More

Enzyme Kinetics

For an effective implementation of our filter system it is essential to analyze the enzymatic activity of our effectors. Using experimental data we fitted the respective kinetic parameters and carried out rigorous uncertainty analysis to assess the reliability of the fitted parameters. Read More

Kill Switch

During the planning stage of our project, we had several different ideas on how to efficiently implement a kill-switch in our moss. In this section of the wiki we documented our mathematical train of thought that eventually led us to our final design.
Read More

Filter Model

The filter model is designed to simulate different remediation scenarios. It should be used to calculate the necessary amount of PhyscoFilters, referring to the environmental parameters.
Read More

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