Difference between revisions of "Team:USP-Brazil/Simulations"

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           <div class="mod-content simulacoes">
 
           <div class="mod-content simulacoes">
 
             <h2><a name="simu">Simulations</a></h2>
 
             <h2><a name="simu">Simulations</a></h2>
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             <p>Lorem ipsum dolor sit amet, consectetur adipiscing elit. Donec interdum lacinia posuere. Sed nunc felis, consequat a tincidunt eu, lacinia id nisi. Praesent eget erat consequat, ultrices justo nec, eleifend ex. Donec iaculis turpis id augue molestie, in venenatis enim pellentesque. Etiam quis semper diam, sit amet rhoncus libero. Vivamus pulvinar bibendum lacus, at iaculis enim tempor semper. In ac enim libero. Mauris at porta mi, in euismod arcu.
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             <p>Now, based on our equations, we can run simulations to estimate αY, the parameter of interest of our model. For that, we decided to try to find the maximum αY that will, according to our model, fit the EC50 time and the maximum value of ρ.
 
             </p>
 
             </p>
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             <p>Lorem ipsum dolor sit amet, consectetur adipiscing elit. Donec interdum lacinia posuere. Sed nunc felis, consequat a tincidunt eu, lacinia id nisi. Praesent eget erat consequat, ultrices justo nec, eleifend ex. Donec iaculis turpis id augue molestie, in venenatis enim pellentesque. Etiam quis semper diam, sit amet rhoncus libero. Vivamus pulvinar bibendum lacus, at iaculis enim tempor semper. In ac enim libero. Mauris at porta mi, in euismod arcu.
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             <p>For that, we must assume a new assumption: That all the proteins in the systems (synthetases, receptors and reporters) are approximately equal, therefore we can say that their production and degradation rates are the same, if not explicitly given a value.
 
             </p>
 
             </p>
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             <p>Lorem ipsum dolor sit amet, consectetur adipiscing elit. Donec interdum lacinia posuere. Sed nunc felis, consequat a tincidunt eu, lacinia id nisi. Praesent eget erat consequat, ultrices justo nec, eleifend ex. Donec iaculis turpis id augue molestie, in venenatis enim pellentesque. Etiam quis semper diam, sit amet rhoncus libero. Vivamus pulvinar bibendum lacus, at iaculis enim tempor semper. In ac enim libero. Mauris at porta mi, in euismod arcu.
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             <p>At first, we defined our parameters based on literature values. (To know precisely the parameters used in the runs, see the table at the end of the page).
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            </p>
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            <p>After establishing the parameters of interest, we created an algorithm that will receive the EC50 time (tEC50) and the maximum ρ (MAX) and return the values of αY. The algorithm is resumed at the flowchart below:
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            </p>
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            <center><img src="" style="width:90%"></center>
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            <p>In this flow chart, we can see the process of the algorithm's workings. Where a parallelogram represents the initial data, round rectangles represent processes and diamonds represent decision processes. Af is used as αY and ε is a small increase. From that, we’ve been able to, comparing to our data and using some literature data as proxy, estimate the alphas!
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            </p>
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            <p>However, to do a proper comparison, we’ve set up a relative measure, we decided to call λ. Is a very simple proposal:
 
             </p>
 
             </p>
 
           </div>
 
           </div>

Revision as of 19:38, 17 October 2018

Wiki - iGEM Brazil

Simulations

Now, based on our equations, we can run simulations to estimate αY, the parameter of interest of our model. For that, we decided to try to find the maximum αY that will, according to our model, fit the EC50 time and the maximum value of ρ.

For that, we must assume a new assumption: That all the proteins in the systems (synthetases, receptors and reporters) are approximately equal, therefore we can say that their production and degradation rates are the same, if not explicitly given a value.

At first, we defined our parameters based on literature values. (To know precisely the parameters used in the runs, see the table at the end of the page).

After establishing the parameters of interest, we created an algorithm that will receive the EC50 time (tEC50) and the maximum ρ (MAX) and return the values of αY. The algorithm is resumed at the flowchart below:

In this flow chart, we can see the process of the algorithm's workings. Where a parallelogram represents the initial data, round rectangles represent processes and diamonds represent decision processes. Af is used as αY and ε is a small increase. From that, we’ve been able to, comparing to our data and using some literature data as proxy, estimate the alphas!

However, to do a proper comparison, we’ve set up a relative measure, we decided to call λ. Is a very simple proposal: