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
Instead of running your model once with some specific parameters (for example rate constants.), you find all the possible parameters in literature and run your model for lots of combinations sampled in a clever way. By doing this you take take into account the uncertainty in the parameters. You will create probabilistic outputs allowing you to make rigorous conclusions.
Following through our flow diagram blueprint should make this concept clear.
We focused on modelling the cell free mechanism, see the experimental section for details. The short version is the AlcoPatch relies on Alcohol, Alcohol Oxidase (AOx), Horseradish Peroxidase (HRP) and ABTS which are mixed together making oxidised ABTS which is colourful. The ensemble modellingprocess will work for any model however and this was chosen as a simpler example to demonstrate the technique, focusing on the process rather than the system itself.
All the modeling and experimental work for mechanism 1 was done using Glucose and GOx instead, this was due to laboratory limitations. This effects the modelling analysis in trying to predict things about alcohol which came from human practices. The equivalent analysis was done for glucose. Rerunning the analysis for alcohol would only require the change of some constants, so the analysis acts as a proof of concept and still shows the integration of human practices.
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. MATT THIS WAS A PLACE HOLDER YOU ARE TO WRITE THIS AFTER THE RESULTS SECTION AS YOU WILL BE ABLE TO LINK BETWEEN THE TOO.
What were we modelling?
We focused on modelling the cell free mechanism, see the experimental section for details. The short version is the AlcoPatch relies on Alcohol, AOx, HRP and ABTS are mixed together making oxidised ABTS which is colourful. The process will work for any model however and this was chosen as a simpler example to demonstrate the technique, focusing on the process rather than the system itself.
All the modelling and experimental work for mechanism 1 was done using Glucose and GOx instead, this was due to laboratory limitations. This effects the modelling analysis in trying to predict things about alcohol which came from human practices. From human practices we also noticed glucose would have the same mechanism scheme,[link to hp] The equivalent analysis was done for glucose. Rerunning the analysis for alcohol would only require the change of some constants, so the analysis acts as a proof of concept and still shows the integration of human practices.
A schematic diagram of the final scheme is given below. For more information about the steps click on the blue enzyme boxes.
(**********INSERT NETWORK DIAGRAM IMAGE HERE. CLICKABLE LINKS ON THE 2 ENZYME BOXES**********) (**********Box1 GOx**********) (*********Box2 HRP**********)
Alternatively you can click on the enzyme name below:
Glucose Oxidase Horseradish Peroxidase
What is Ensemble Modelling?
PLACEHOLDER
What did our model achieve?
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We found great inspiration from our human practices and guidance working both ways to the experiments. Click here to see the detail.
