Team:ITB Indonesia/Notebook/Modelling


Modelling Notebook

June 2013

We tried to tackle down our model into smaller pieces based on their phenomena.

  1. Diffusion model
  2. Gene transcription and translation
  3. Enzymatic reaction
  4. DNA damage
  5. SOS response kinetic
  6. Final integration of our whole cell biosensor model

We also divided our workflow into two main phase : translating phenomena into mathematical model and translating phenomena into mathematical model must be based on scientific journal and research, and with a lot of parameter in this model, it's a tough phase.

August 2013

August, 1, 2013
After a long time searching for the best tools to help our modelling team, we decide to choose Simbiology (Matlab toolbox for biological system) as our main tools. Now is the hardest part : learn how to use it.

August, 19, 2013
Yeay! We finished our first phase! Next phase is to integrate our small model into whole cell simulation.

August, 31, 2013
Another challenge for modelling team : we must recalculate our model to predict aflatoxin concentration in each of our cell more accurately. Ouch!

September 2013

September, 7, 2013
Thank God we can find the solution for our current problem. The solution is easier than we ever thought before :P. See how we tackle this challenge in modelling section. And also our third presentation for modelling team with our advisor. He gives us a lot of advise and things to do to keep it stay on schedule. Thank you very much!

September, 8, 2013
We validate our theory on enzymatic reaction of AFB1 to AFB1 oxide. Is it fit to Hill kinetic or Michaelis-Menten?

September, 10, 2013
Uh oh, our simulation result show something illogical, because the amount of single stranded DNA in our cell is way more higher than AFBdiol. Better check all of our parameters.