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Team:UNAM-Genomics Mexico/Modeling
From 2011.igem.org
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First off, we wanted to understand how the exogenous hydrogen pathway would interact with the endogenous nitrogen pathway. We therefore began by performing Flux Balance Analysis on a metabolic reconstruction of our chassis. All the details are [[Team:UNAM-Genomics_Mexico/Modeling/FBA|here]]. | First off, we wanted to understand how the exogenous hydrogen pathway would interact with the endogenous nitrogen pathway. We therefore began by performing Flux Balance Analysis on a metabolic reconstruction of our chassis. All the details are [[Team:UNAM-Genomics_Mexico/Modeling/FBA|here]]. | ||
| - | + | ==GT== | |
Then, we began wondering what would happen if our hydrogen pathway was incompatible with the nitrogen pathway. If both pathways were unable to co-exist in the same chassis, why not put each in a chassis and place both chassis in the plant? We approached this scenario using Game Theory. All the details are [[Team:UNAM-Genomics_Mexico/Modeling/GT|here]]. | Then, we began wondering what would happen if our hydrogen pathway was incompatible with the nitrogen pathway. If both pathways were unable to co-exist in the same chassis, why not put each in a chassis and place both chassis in the plant? We approached this scenario using Game Theory. All the details are [[Team:UNAM-Genomics_Mexico/Modeling/GT|here]]. | ||
| - | + | ==Markov== | |
Next, we decided to model our plasmid's stability. Lacking experimental values, we chose to develop an "explicative" model instead of a "predicitve" model based on the data we had. We fitted our data into a very simple Markov Chain model. All the details are [[Team:UNAM-Genomics_Mexico/Modeling/MM|here]]. | Next, we decided to model our plasmid's stability. Lacking experimental values, we chose to develop an "explicative" model instead of a "predicitve" model based on the data we had. We fitted our data into a very simple Markov Chain model. All the details are [[Team:UNAM-Genomics_Mexico/Modeling/MM|here]]. | ||
| - | + | ==Extreme Pathways== | |
Since we had some time to spare, we tried testing the hypthesis that our exogenous pathway was expanding the realm of steady state solutions for our transgenic chassis. We decided to test this our via Extreme Pathway calculation. All the details are [[Team:UNAM-Genomics_Mexico/Modeling/ExtremePathways|here]]. | Since we had some time to spare, we tried testing the hypthesis that our exogenous pathway was expanding the realm of steady state solutions for our transgenic chassis. We decided to test this our via Extreme Pathway calculation. All the details are [[Team:UNAM-Genomics_Mexico/Modeling/ExtremePathways|here]]. | ||
| - | + | ==CA== | |
| - | Finally, we began wondering if we could construct in silico representations of our chassis, and if their simulation would fit the Game Theory framework we had set. Since traditional Cellular Automata require a particular set of rules that seemed too simplistic for our intents (rule 110 looked promising though...). We opted to construct the automaton using the ''very best modeling software in possible existance'': kappa. All the | + | Finally, we began wondering if we could construct in silico representations of our chassis, and if their simulation would fit the Game Theory framework we had set. Since traditional Cellular Automata require a particular set of rules that seemed too simplistic for our intents (rule 110 looked promising though...). We opted to construct the automaton using the ''very best modeling software in possible existance'': kappa. All the details are [[Team:UNAM-Genomics_Mexico/Modeling/CA|here]]. |
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Latest revision as of 23:01, 28 September 2011
Contents |
Modeling
Hello, and welcome to the Modeling mini-portal. If you find yourself in this page, odds are high you know more or less what the project is about: producing hydrogen while fixing atmospheric nitrogen in a plant symbiont. So while my teammates have been working on the wetlab, the modeling section set out on the quest to explore how the system reacted. However, we got slightly carried away...
FBA
First off, we wanted to understand how the exogenous hydrogen pathway would interact with the endogenous nitrogen pathway. We therefore began by performing Flux Balance Analysis on a metabolic reconstruction of our chassis. All the details are here.
GT
Then, we began wondering what would happen if our hydrogen pathway was incompatible with the nitrogen pathway. If both pathways were unable to co-exist in the same chassis, why not put each in a chassis and place both chassis in the plant? We approached this scenario using Game Theory. All the details are here.
Markov
Next, we decided to model our plasmid's stability. Lacking experimental values, we chose to develop an "explicative" model instead of a "predicitve" model based on the data we had. We fitted our data into a very simple Markov Chain model. All the details are here.
Extreme Pathways
Since we had some time to spare, we tried testing the hypthesis that our exogenous pathway was expanding the realm of steady state solutions for our transgenic chassis. We decided to test this our via Extreme Pathway calculation. All the details are here.
CA
Finally, we began wondering if we could construct in silico representations of our chassis, and if their simulation would fit the Game Theory framework we had set. Since traditional Cellular Automata require a particular set of rules that seemed too simplistic for our intents (rule 110 looked promising though...). We opted to construct the automaton using the very best modeling software in possible existance: kappa. All the details are here.
