Team:Manchester/Model
Welcome to our modelling section. We have used a novel ensemble modeling approach, to better aid the synergy between wetalb and dry lab teams. On this page you will find short answers to the questions; What is ensemble modelling? What did we model? what did our model achieve?
For navigating the wiki you need to know that the sections on results and human practice/lab integration can be accessed in the menu bar.
Part of what we hope to achieve with this ensemble methodology is a blueprint for other igem teams. As such each step in creating and using our model is laid out in the below diagram. Clicking on a specific step will take you to a page explaining the theory. Going deeper you can access a discussion of the code. There will be a link to the relevant parts of our github (a website storing our code) Use these codes as you wish.
Link to github homepage
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.
