Team:Manchester/Model
Welcome to our modelling section, we have used a novel ensemble modelling approach, to better aid the synergy between wetlab and dry lab teams. You will find on this page an overview of ensemble modelling and our model and what it achieve. Below there is a flowchart showing how the model worked and the different parts, click on them to find out about the theory and in these sections there are links to code analysis of why we did things these ways and how to do them. There is also a section on the story of what we did and how experiment and human practices fed into the model and vica versa.
Follow this github link to see the full code, feel free to use it. It’s meant to be easy to use. If you can make a simple model you can ensemble model. If you use please attribute us .
The short version……. Instead of running your model once with some specific parameters, you find all the possible parameters in literature and run your model for lots of combinations in a clever way. By doing this you take into account the uncertainty in your parameters and as such make meaningful conclusions. An example of this is what is your exact reaction scheme, you can run these simulations for different models and see which can be consistent with experimental data. Furthermore by testing your specific parameters set fit to data you can find out what values work and relationships between your parameters, better understanding them and providing physical insight.
We focused on modelling the cell free mechanism. See the experimental section for details, but essentially, Alcohol, alcohol oxidase, horseradish peroxidase and abts are mixed together making oxidised abts which is colourful, click here to see the potential reaction schemes. Click here to be taken to a detailed explanation in the experimental section. The process will work for any model however and this was chosen as a simpler example to demonstrate the technique.
Firstly we narrowed down the potential reaction schemes and increased our knowledge of our rate constants. Secondly we have created a blueprint for using ensemble modelling instead of simple ODE modelling in the hope that it can become standard practice for iGEM.
We found great inspiration from our human practices and guidance working both ways to the experiments. Click here to see the detail.
