Team:UNAM-Genomics Mexico/Modeling

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=Modeling=
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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...
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==FBA==
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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]].
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==GT==
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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]].
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<li class="istylei0"><a class="istylei0" href="https://2011.igem.org/Team:UNAM-Genomics_Mexico">H2 Homepage</a></li>
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<li class="istylei0"><a class="istylei0" href="https://2011.igem.org/Team:UNAM-Genomics_Mexico/Project"><span>Project</span><![if gt IE 6]></a><![endif]><!--[if lte IE 6]><table><tr><td><![endif]-->
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<li><a href="https://2011.igem.org/User:Jurquiza">Uriel</a></li>
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<li><a href="https://2011.igem.org/User:Nandomgu">Nando</a></li>
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<li><a href="#">Paz</a></li>
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<li><a href="https://2011.igem.org/User:Fibonacci_Lopez">Fabricio</a></li>
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<li><a href="https://2011.igem.org/User:Hmedina">Hector</a></li>
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<li><a href="https://2011.igem.org/User:Dgarcia">Daniela</a></li>
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<li><a href="https://2011.igem.org/User:Khronus">Daniel</a></li>
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<li><a href="https://2011.igem.org/User:Melissam">Melissita</a></li>
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<li><a href="https://2011.igem.org/User:Alecanda">Aaron</a></li>
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<li><a href="https://2011.igem.org/User:Atrevino">Abiel</a></li>
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<li><a href="https://2011.igem.org/User:Meli_arr">Meli</a></li>
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<li><a href="https://2011.igem.org/User:Paedugar">Pae</a></li>
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<li><a href="https://2011.igem.org/User:Vladimir">Vladimir</a></li>
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<li><a href="https://2011.igem.org/User:Gustavoruiz">Gustavo</a></li>
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<li><a href="https://2011.igem.org/User:Palatris">Pato</a></li>
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<li><a href="https://2011.igem.org/User:Hamarillo">Helena</a></li>
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<li><a href="https://2011.igem.org/User:Paxiveri">Paloma</a></li>
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<li><a href="https://2011.igem.org/User:Nalvarez">Nataly</a></li>
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<li><a href="https://2011.igem.org/User:Misticastillo">Misti</a></li>
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<li><a href="https://2011.igem.org/User:AraceliAM">Araceli</a></li>
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<li><a href="https://2011.igem.org/User:Ocarrillo">Omar</a></li>
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==Markov==
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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]].
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==Extreme Pathways==
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<p>Inside the <a class="model" href=""><i>Phaseolus vulgaris</i></a> root nodules, <a class="model" href=""><i>Rhizobium etli</i></a>
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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]].
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enjoys a protected niche. However the protection provided by the plant is given solely in exchange for the nitrous compounds
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produced by the bacteria. For this it is very important to understand how <a class="model" href="">hydrogen production</a>
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will affect <a class="model" href="">nitrogen fixation</a> in the bacteria. That is the question we aim to answer with our
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==CA==
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modeling efforts.</p>
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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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<p><i>R. elti</i>'s metabolism inside the nodule is fairly constant. This homeostatic state is one of the assumptions done when
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modeling metabolism with <a class="model" href="">Flux Balance Analysis</a>. We have deffined three main metabolic
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compartments: <a class="model" href="">cytosol</a>, <a class="model" href="">periplasm</a> and  
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Latest revision as of 23:01, 28 September 2011

UNAM-Genomics_Mexico


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.

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