Difference between revisions of "Team:Aix-Marseille/Model"

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(Created page with our model's first iteration. Second one to come tomorrow afternoon as I get out of the lab. The esthetics also need work (I like euphemisms!))
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<title>Engineered M13 modelling</title>
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<h3>★  ALERT! </h3>
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<p>This page is used by the judges to evaluate your team for the <a href="https://2017.igem.org/Judging/Medals">medal criterion</a> or <a href="https://2017.igem.org/Judging/Awards"> award listed above</a>. </p>
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<p> Delete this box in order to be evaluated for this medal criterion and/or award. See more information at <a href="https://2017.igem.org/Judging/Pages_for_Awards"> Instructions for Pages for awards</a>.</p>
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<h1> Modeling</h1>
 
  
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<p>Mathematical models and computer simulations provide a great way to describe the function and operation of BioBrick Parts and Devices. Synthetic Biology is an engineering discipline, and part of engineering is simulation and modeling to determine the behavior of your design before you build it. Designing and simulating can be iterated many times in a computer before moving to the lab. This award is for teams who build a model of their system and use it to inform system design or simulate expected behavior in conjunction with experiments in the wetlab.</p>
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<h5>Wet- and dry-lab back and forth:</h5>
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<p>Reste à rédiger, et ça je ne peux pas le faire seul</p>
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<h5>What are we modeling?</h5>
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<p>Reste à rédiger: décrire succintement le cycle de M13, idéalement avec un schéma (je peux m'en occuper. Du schéma aussi s'il n'y a pas de graphiste dispo) </p>
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<h5>First iteration of the model:</h5>
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<h3> Gold Medal Criterion #3</h3>
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<p>We started with an excessively simple model to see wether our understanding of our system was profound enough to allow room for such simplifications. We made the following assumptions in this spirit:<br/>
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<TABLE BORDER="1">  
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To complete for the gold medal criterion #3, please describe your work on this page and fill out the description on your <a href="https://2017.igem.org/Judging/Judging_Form">judging form</a>. To achieve this medal criterion, you must convince the judges that your team has gained insight into your project from modeling. You may not convince the judges if your model does not have an effect on your project design or implementation.
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<CAPTION> Table 1: assumptions of our "simplistic" model </CAPTION>  
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<TH> Assumption </TH>
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<TH> Reasonning </TH>
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<TD> Neglecting cooperative effects </TD>
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<TD>  </TD>
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<TD> Constant rate of p5 transcription/traduction </TD>
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<TD>  </TD>
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<TD> One M13KO7 per factory cell </TD>
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<TD>  </TD>
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<TD> Phage assembly isn't a limiting factor </TD>
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<TD>  </TD>
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<TD> Neglecting stochasticity </TD>
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<TD>  </TD>
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Which led to the following model:<br/>
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<i>insérer image que j'ai dans la présentation que j'ai faite, mais en mieux dessinée / plus travaillée / classe / raccord avec le reste du thème graphique + comment je mets les images sur le site pour qu'elle s'intègrent dans le wiki? Est-ce que je les met sur internet sinon?</i><br/>
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<img src="model first iteration.jpg" alt="Simplistic model"><br/>
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Which yielded the following results:<br/>
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<i>là aussi mon graphique n'est pas adapté esthétiquement</i><br/>
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<img src=" " alt=" "><br/>
 
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<h5>Second iteration:</h5>
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Please see the <a href="https://2017.igem.org/Judging/Medals"> 2017 Medals Page</a> for more information.
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<p>This time, we decided to adapt the model from Smeal <i>et al.</i> of a "wild-type" M13's biology to fit our own engineered version of M13 and better inform wetlab experiments, as well as explain some of their preliminary findings!<br/>
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Model validation: compare particle profile to that obtained in wetlab<br/>
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--> Insufficient p3 could cause the packing of several DNA molecules per phage.<br/>
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What is the ideal number of plasmid copies if we produce p3 on a different plasmid?<br/>
 
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<h5>Bibliography:</h5>
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<h3>Best Model Special Prize</h3>
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<p>Smeal <i>et al</i>, Simulation of the M13 life cycle I: Assembly of a genetically-structured deterministic chemical kinetic simulation, Virology, 500, January 2017, Pages 259-274<br/>
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Smeal <i>et al</i>, Simulation of the M13 life cycle II: Investigation of the control mechanisms of M13 infection and establishment of the carrier state, Virology, 500, January 2017, Pages 275-284</p>
  
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To compete for the <a href="https://2017.igem.org/Judging/Awards">Best Model prize</a>, please describe your work on this page  and also fill out the description on the <a href="https://2017.igem.org/Judging/Judging_Form">judging form</a>. Please note you can compete for both the gold medal criterion #3 and the best model prize with this page.
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You must also delete the message box on the top of this page to be eligible for the Best Model Prize.
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<h5> Inspiration </h5>
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Here are a few examples from previous teams:
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<li><a href="https://2016.igem.org/Team:Manchester/Model">Manchester 2016</a></li>
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<li><a href="https://2016.igem.org/Team:TU_Delft/Model">TU Delft 2016  </li>
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<li><a href="https://2014.igem.org/Team:ETH_Zurich/modeling/overview">ETH Zurich 2014</a></li>
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<li><a href="https://2014.igem.org/Team:Waterloo/Math_Book">Waterloo 2014</a></li>
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Revision as of 01:27, 23 October 2017

{{{title}}}

{{{toc}}} Engineered M13 modelling
Wet- and dry-lab back and forth:

Reste à rédiger, et ça je ne peux pas le faire seul


What are we modeling?

Reste à rédiger: décrire succintement le cycle de M13, idéalement avec un schéma (je peux m'en occuper. Du schéma aussi s'il n'y a pas de graphiste dispo)


First iteration of the model:

We started with an excessively simple model to see wether our understanding of our system was profound enough to allow room for such simplifications. We made the following assumptions in this spirit:

Table 1: assumptions of our "simplistic" model
Assumption Reasonning
Neglecting cooperative effects
Constant rate of p5 transcription/traduction
One M13KO7 per factory cell
Phage assembly isn't a limiting factor
Neglecting stochasticity

Which led to the following model:
insérer image que j'ai dans la présentation que j'ai faite, mais en mieux dessinée / plus travaillée / classe / raccord avec le reste du thème graphique + comment je mets les images sur le site pour qu'elle s'intègrent dans le wiki? Est-ce que je les met sur internet sinon?
Simplistic model
Which yielded the following results:
là aussi mon graphique n'est pas adapté esthétiquement

Second iteration:

This time, we decided to adapt the model from Smeal et al. of a "wild-type" M13's biology to fit our own engineered version of M13 and better inform wetlab experiments, as well as explain some of their preliminary findings!
Model validation: compare particle profile to that obtained in wetlab
--> Insufficient p3 could cause the packing of several DNA molecules per phage.
What is the ideal number of plasmid copies if we produce p3 on a different plasmid?


Bibliography:

Smeal et al, Simulation of the M13 life cycle I: Assembly of a genetically-structured deterministic chemical kinetic simulation, Virology, 500, January 2017, Pages 259-274
Smeal et al, Simulation of the M13 life cycle II: Investigation of the control mechanisms of M13 infection and establishment of the carrier state, Virology, 500, January 2017, Pages 275-284