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Team:KU Leuven/Journal/Modelling
From 2013.igem.org
Secret garden
Congratulations! You've found our secret garden! Follow the instructions below and win a great prize at the World jamboree!
- A video shows that two of our team members are having great fun at our favourite company. Do you know the name of the second member that appears in the video?
- For one of our models we had to do very extensive computations. To prevent our own computers from overheating and to keep the temperature in our iGEM room at a normal level, we used a supercomputer. Which centre maintains this supercomputer? (Dutch abbreviation)
- We organised a symposium with a debate, some seminars and 2 iGEM project presentations. An iGEM team came all the way from the Netherlands to present their project. What is the name of their city?
Now put all of these in this URL:https://2013.igem.org/Team:KU_Leuven/(firstname)(abbreviation)(city), (loose the brackets and put everything in lowercase) and follow the very last instruction to get your special jamboree prize!
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Week 1
The modelling team is ready to rock Matlab after watching some tutorials and webinars about modelling and Symbiology.
We are excited to get our modelling team going and therefore we had an appointment with professor Bernaerts. It was very useful, as she gave some good ideas on how to get started. We will have to design a way of expressing the enzyme(s) in a cyclic manner and a possible way to achieve this would be by expressing it during a short pulse, stimulated by the presence of a signal from other cells.
And to tackle this problem we also started brainstorming about some possible networks with oscillating behavior. Here we have to keep in mind that the bacterial colonies have to get and stay synchronized and this might be achieved by a rapid (protein-protein interaction) feedback which is proportional to the phase difference. In an attempt to collaborate with the wetlab team we discussed our main focus for the upcoming weeks: figuring out an oscillating construct and simulating the behaviour of the methyl salicylate BioBrick.
And since organization comes after thought Bert and Sander started working on simulating the Mortier Oscillator (as Bert likes to call it) in SimBiology, while Tina and Tomas started modelling the network to produce methyl salicylate by looking at BSMT1(the enzyme that catalyzes the reaction from salicylate to methyl salicylate) and at pchA and pchB which catalyze the reactions from chorismate to isochorismate to salicylate.
Later this week Tina had a look on how to use the COBRA toolbox for our purpose and we would have to check the constraints on reaction rates and add our new reactions.
Bert contacted professor Suykens and professor Degrève to get an idea of how to analyse the MO. He gave the advice towards a bifurcation analysis, on which Bert will have a closer look.
Tomas on the other hand started on the development of another oscillator and contacted professor Roose of mathematical engineering, who suggested the use of MatCont.Furthermore we are also considering a strategy of a knock-out/knock-down of genes responsible for chorismate mutase and chorismate lyase to optimize methyl salicylate production.
