Team:Waterloo/Modeling
Modeling
Mathematical modeling is a core part of Waterloo iGEM: we have nearly as many team members typing furiously away in our dry lab as we do wrangling transformations in our wet lab. This year, we created models in Python, MATLAB and NetLogo that examine the feasibility of our design and provide tools for assessing future designs. The code for each model is available on our GitHub and details on the formulation of each model may be found in the pages linked below.
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.
CRISPR Plant Defense
To model antiviral application, looked at the antiviral effects of CRISPR/Cas9 targeting on three scales: CaMV genomes, plant cells and plant leaves. A background primer on Cauliflower Mosaic Virus (CaMV) genetics, replication and spread can be found on the CaMV Biology page.
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 Intercellular 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.