"

From 2013.igem.org

Modeling

01/07 We installed Matlab, took a look at some presentations about modeling. We are also investigating [http://www.mathworks.nl/products/simbiology/ SimBiology].

02/07 We watched some [http://www.mathworks.nl/products/simbiology/webinars.html webinars about SimBiology]. In the afternoon we had an appointment with prof. Bernaerts of the division of (bio)chemical procestechnology. 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. We could achieve this by expressing it during a short pulse, activated by the presence of a signal from other cells.

03/07 During the morning we brainstormed about some possible networks with oscillating behavior. We have to keep in mind that the colony has to be and stay synchronized. This could be achieved by a rapid (protein-protein interaction) feedback which is proportional to the phase difference. We had a meeting with the wetlab team and discussed our main focus for the upcoming weeks: figuring out an oscillating construct and simulating the behaviour of the methyl salicylate BioBrick.

04/07 Bert and Sander are working on simulating the Mortier Oscillator in SimBiology. Tina and Tomas are modeling the network to produce methyl salicylate. BSMT1 is the enzyme that catalyzes the reaction from salicylate to methyl salicylate. pchA and pchB catalyze the reactions from chorismate to isochorismate to salicylate. Tomas and Sander are looking on how to use the [http://opencobra.sourceforge.net/openCOBRA/Welcome.html COBRA toolbox] for our purpose. We would need to check the constraints on reaction rates and add our new reactions. Bert made contact with professors Suykens of the [http://www.esat.kuleuven.be/scd/ department of electrical engineering] and professor Degrève of the division of (bio)chemical procestechnology in order to have an idea of how to analyse the MO, we apparently need bifurcation analysis, which Bert started looking up about.

05/07 Knock-out/complementary RNA of genes responsible for chorismate mutase and chorismate lyase as a strategy to optimize methyl salicylate production? Tomas started the development of another oscillator, while Sander and Tina are looking deeper into metabolic network modeling.

07/07 We are in touch with professor Roose of the [http://wms.cs.kuleuven.be/groups/natw/index.html applied mathematics division], who suggested the use of [http://www.matcont.ugent.be/ MatCont] for the analysis of our oscillator.

08/07 We’re investigating the [http://pubs.acs.org/doi/abs/10.1021/sb300084h AutoBioCAD] software and looking for a better model to our quorum sensing system using PDEs.

09/07 We started investigation of literature of ecology. We chose our model species (aphid and crop). We’ll try to model aphid reproduction and the influence of bèta-farnesene and methylsalicylate on life cycle and movement. We’ll have to make an estimation of the damage/loss of crops due to a certain population of aphids. Bert added spatial heterogeneity in his Mortier Oscillator to see what happens on a population level.