Difference between revisions of "Team:Waterloo/Modeling"

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     <section id="cas9" title="Antiviral Application">
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         <p> Some visual representation of the model and ~100 words about what it contributed to our project, with a link to the <a href="https://2015.igem.org/Team:Waterloo/Modeling/Antiviral_Application">Antiviral Application</a>. </p>
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         <p> To model antiviral application, looked at the antiviral effects of CRISPR/Cas9 targeting on three scales, the details of which are described on their own pages. On the <strong>scale of individual genomes</strong>, we used our  <a href="https://2015.igem.org/Team:Waterloo/Modeling/Cas9_Dyanmics">dynamics model of CRISPR/Cas9</a> to model viral genomes becoming non-functional over time as frameshift mutations were introduced. The results of <em>insert details of running the simulation for our chosen sgRNA targets, we probably don't need a whole page for it</em> provide the following graph of P6 functionality over time.
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<p><strong>Insert graph of functional P6/time</strong></p>
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<p>On the <strong>intracellular scale</strong>, we modelled <a href="https://2015.igem.org/Team:Waterloo/Modeling/CaMV_Replication">CaMV Replication</a> in a single infected cell and the effect it would have on virion production. <em>insert another ~= 100 words about the model</em></p>
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<p><strong>Insert graph of virons/time under different conditions</strong></p>
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<p>We also modelled <strong>intercellular infection spread</strong> using an agent-based framework, which is described in detail on the <a href="https://2015.igem.org/Team:Waterloo/Modeling/Intracellular_Spread">Intracellular Viral Spread</a> page.</em></p>
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<p><strong>Insert gif of agent-based model with and without P6</strong></p>
 
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Revision as of 19:10, 13 September 2015

Modeling

We should have a nice paragraph about what role modelling has played in our project.

Cas9 Frameshift Dynamics

Some visual representation of the model and ~100 words about what it contributed to our project, with a link to the CRISPR/Cas9 Frameshift Dynamics page.

PAM Structural Bioinformatics

Some visual representation of the model and ~100 words about what it contributed to our project, with a link to the PAM Structural Bioinformatics page.

Antiviral Application

To model antiviral application, looked at the antiviral effects of CRISPR/Cas9 targeting on three scales, the details of which are described on their own pages. On the scale of individual genomes, we used our dynamics model of CRISPR/Cas9 to model viral genomes becoming non-functional over time as frameshift mutations were introduced. The results of insert details of running the simulation for our chosen sgRNA targets, we probably don't need a whole page for it provide the following graph of P6 functionality over time.

Insert graph of functional P6/time

On the intracellular scale, we modelled CaMV Replication in a single infected cell and the effect it would have on virion production. insert another ~= 100 words about the model

Insert graph of virons/time under different conditions

We also modelled intercellular infection spread using an agent-based framework, which is described in detail on the Intracellular Viral Spread page.

Insert gif of agent-based model with and without P6

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.

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