Difference between revisions of "Team:Valencia UPV/Modeling"

 
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<li><a href="https://2015.igem.org/Team:Valencia_UPV/Modeling/DetModel" class="button">Deterministic model</a></li>
 
<li><a href="https://2015.igem.org/Team:Valencia_UPV/Modeling/DetModel" class="button">Deterministic model</a></li>
 
<li><a href="https://2015.igem.org/Team:Valencia_UPV/Modeling/Simulations" class="button">Simulations</a></li>
 
<li><a href="https://2015.igem.org/Team:Valencia_UPV/Modeling/Simulations" class="button">Simulations</a></li>
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<li><a href="https://2015.igem.org/Team:Valencia_UPV/Modeling/AlaDNA2.0" class="button">AladDNA 2.0</a></li>
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<li><a href="https://2015.igem.org/Team:Valencia_UPV/Modeling/AlaDNA2.0" class="button">Light control</a></li>
 
<li style="margin-top: 1.2em;"><a href="https://2015.igem.org/Team:Valencia_UPV/Modeling/Conclusions" class="button">Conclusions</a></li>
 
<li style="margin-top: 1.2em;"><a href="https://2015.igem.org/Team:Valencia_UPV/Modeling/Conclusions" class="button">Conclusions</a></li>
 
</ul>
 
</ul>
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<p>When new things are created, there is no clue about its behavior, which causes uncertainty. This is the reason why modeling has become a significant part of any project.               </p>
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<p>Whereas great inventors of History had to decide if their imaginations worth it or not in order to work on them, we rely on Modeling. Still implausible ideas being represented by equations, can transform imagination in reality, as it happened with AladDNA. Using knowledge from Biology and Engineering, biological processes already known become pieces of a puzzle which results in innovative designs that perform new functions. Modeling AladDNA has not only confirmed that our idea is feasible, it has also undressed its mechanism. Whereas wet lab experiments need inexistent time to depict our system’s performance, Modeling has been a headstone of our project, allowing us to know with depth the behavior of the circuit and becoming deadlines in feasible dates.</p>
  
 
<p>We started by figuring out how it should work in a tree diagram, keeping the idea simple:</p>
 
<p>We started by figuring out how it should work in a tree diagram, keeping the idea simple:</p>
  
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<div style="float:left"><img style="width:30em" src=https://static.igem.org/mediawiki/2015/9/9a/Valencia_upv_overviewcircuito.png></div><br/>
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<p><div style="text-align:center;"><img style="width:30em" src=https://static.igem.org/mediawiki/2015/6/64/UPV_fotobomb.png></div></p>
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<p>Basically, our aim is the biological design of a decoder that only expresses the codified genetic information when, where and which is desired by the user. The biological components that allow us this implementation in living organisms are two switches, two recombinases and a library of different binding domains. All those elements have been coordinated in this cascade of three different levels.</p>
 
<p>Basically, our aim is the biological design of a decoder that only expresses the codified genetic information when, where and which is desired by the user. The biological components that allow us this implementation in living organisms are two switches, two recombinases and a library of different binding domains. All those elements have been coordinated in this cascade of three different levels.</p>
 
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<div style="float:right"><a href="https://2015.igem.org/Team:Valencia_UPV/Modeling/DetModel"><img style="width: 13em;margin-left: 1em;" src=https://static.igem.org/mediawiki/2015/3/3c/Valencia_upv_overviewdetmodel.png></a></div>
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<div style="float:right"><img style="width: 13em;margin-left: 1em;" src=https://static.igem.org/mediawiki/2015/3/3c/Valencia_upv_overviewdetmodel.png></div>
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<p>Our deterministic model uses mathematical information contained in its equations, in order to provide results that depict the behavior of our device. After deterministic model, it is time to test our biological machine in different conditions. <div style="float:left"><img src=https://static.igem.org/mediawiki/2015/d/db/Valencia_upv_overviewsimulations.png></div> As organisms are supposed to be in a closed device, environmental variability was not the critical point. We have analyzed the influence of different color combinations of light, duration of those, numbers of gene copies and values of tetramerization. </p>
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<p>Our deterministic model uses mathematical information contained in its equations, in order to provide results that depict the behavior of our device. After deterministic model, it is time to test our biological machine in different conditions. <div style="float:left"><a href="https://2015.igem.org/Team:Valencia_UPV/Modeling/Simulations"><img src=https://static.igem.org/mediawiki/2015/d/db/Valencia_upv_overviewsimulations.png></a></div> As organisms are supposed to be in a closed device, environmental variability was not the critical point. We have analyzed the influence of different color combinations of light, duration of those, numbers of gene copies and values of tetramerization. </p>
  
 
<p>One of the main points when innovative devices are being tested, is “how”. How does AladDNA behave? This is the main question that we want to answer with our modeling task.</p>
 
<p>One of the main points when innovative devices are being tested, is “how”. How does AladDNA behave? This is the main question that we want to answer with our modeling task.</p>
  
 
<p>Take a sit and enjoy this wander in our mathematical chaos!</p>
 
<p>Take a sit and enjoy this wander in our mathematical chaos!</p>
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<script type="text/x-mathjax-config">
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    MathJax.Hub.Config({tex2jax: {inlineMath: [['$','$'], ['\\(','\\)']]}});
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</script>
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PRUEBA
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Degradations are considered as first order reactions. Production rates that gobern each process are the same for all proteins, as they are preceeded by the same promotor. However, this could be changed by using promotors with different strength. Thus, each protein could have an individualized production rate (transcription + translation).
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\begin{equation}
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[\dot{A}]=k_{P_A}\cdot[mA]-d_A[A]\longrightarrow
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\begin{bmatrix}\dot{m}A \\\dot{A} \\\end{bmatrix}=
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\begin{bmatrix}-d_{mA}& 0 \\k_{P_A}&-d_A\\\end{bmatrix}
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\begin{bmatrix}mA\\A\\\end{bmatrix}+
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\begin{bmatrix}k_{mA}c_{gA}\\0\\\end{bmatrix}\end{equation}
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\\ As genes encoding proteins A, B, C and D,  follow the same transcription pathway, we will write their equations taking A as reference.\\
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Expressing each concentration as a "x" variable:\\•
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$$[gA]=x_1 \qquad\quad [RNA_p]=x_2 \qquad\quad [gA·RNA_p]=x_3$$
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$$[mA]=x_4\qquad\quad [A]=x_5$$
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Where A is E-PIF6.
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\begin{equation}
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\dot{x_{1}}=-k_{1_{A}}\cdot x_{1} \cdot x_{2}+k_{-1_{A}}\cdot x_{3}+k_{mA}\cdot x_{3}
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\end{equation}
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$$
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\dot{x_{2}}=0 $$
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The expression above means that $[RNA_{pol}]$  inside the cell is high enough to consider it in excess.
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PRUEBA
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<ul class="actions" style="text-align:right">
 
<ul class="actions" style="text-align:right">
 
<li><a href="https://2015.igem.org/Team:Valencia_UPV/Modeling/DetModel" class="button alt">Deterministic model</a></li>
 
<li><a href="https://2015.igem.org/Team:Valencia_UPV/Modeling/DetModel" class="button alt">Deterministic model</a></li>
 
<li><a href="https://2015.igem.org/Team:Valencia_UPV/Modeling/Simulations" class="button alt">Simulations</a></li>
 
<li><a href="https://2015.igem.org/Team:Valencia_UPV/Modeling/Simulations" class="button alt">Simulations</a></li>
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<li><a href="https://2015.igem.org/Team:Valencia_UPV/Modeling/AlaDNA2.0" class="button alt">AladDNA 2.0</a></li>
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<li><a href="https://2015.igem.org/Team:Valencia_UPV/Modeling/AlaDNA2.0" class="button alt">Light control</a></li>
 
<li><a href="https://2015.igem.org/Team:Valencia_UPV/Modeling/Conclusions" class="button alt">Conclusions</a></li>
 
<li><a href="https://2015.igem.org/Team:Valencia_UPV/Modeling/Conclusions" class="button alt">Conclusions</a></li>
 
</ul>
 
</ul>

Latest revision as of 00:11, 20 November 2015

Link title Valencia UPV iGEM 2015

Overview

Whereas great inventors of History had to decide if their imaginations worth it or not in order to work on them, we rely on Modeling. Still implausible ideas being represented by equations, can transform imagination in reality, as it happened with AladDNA. Using knowledge from Biology and Engineering, biological processes already known become pieces of a puzzle which results in innovative designs that perform new functions. Modeling AladDNA has not only confirmed that our idea is feasible, it has also undressed its mechanism. Whereas wet lab experiments need inexistent time to depict our system’s performance, Modeling has been a headstone of our project, allowing us to know with depth the behavior of the circuit and becoming deadlines in feasible dates.

We started by figuring out how it should work in a tree diagram, keeping the idea simple:

Basically, our aim is the biological design of a decoder that only expresses the codified genetic information when, where and which is desired by the user. The biological components that allow us this implementation in living organisms are two switches, two recombinases and a library of different binding domains. All those elements have been coordinated in this cascade of three different levels.


Our deterministic model uses mathematical information contained in its equations, in order to provide results that depict the behavior of our device. After deterministic model, it is time to test our biological machine in different conditions.

As organisms are supposed to be in a closed device, environmental variability was not the critical point. We have analyzed the influence of different color combinations of light, duration of those, numbers of gene copies and values of tetramerization.

One of the main points when innovative devices are being tested, is “how”. How does AladDNA behave? This is the main question that we want to answer with our modeling task.

Take a sit and enjoy this wander in our mathematical chaos!