Team:ITB Indonesia/Modeling

Learn, Criticize, Share!
“What am I going to do to start my team’s modelling?”
For us, getting the first step to learn biological system simulation is little tough. We must review the basic concept of biological system modelling, gather all information and mathematical expression from other team whom their project is analogous to us, and learn from scratch how to use Simbiology to simulate our system. Luckily, our job at modelling is to simulate some basic biological and physical phenomena on standard E. coli, which is used frequently by other team at iGEM competition. Then, we have an idea : “We love the idea of sharing and open source concept. How if we apply that to our modelling section?”

We design our modelling section to be more easy to learn by explaining basic concept of some frequently occuring phenomena and dividing it into bitesize chunk of information. This basic modelling information not only helped other team who need some basic guide to take their first step on modelling, but also educate everyone that modelling and simulation is not as hard as you think!
We hope that everyone can learn from our team, criticize our concept or model, and cut the learning process to achieve better modelling for your team with shorter time. That is the main goal of engineering, right? :)

If you have any question or suggestion, don’t hesitate to contact us : synbio.itb@gmail.com

Overview

“By simulating our cell, we saved a lot of money and resources to accelerate research progress!”

The main goal of this project is to create a working device that can be used easily by user in agricultural business or industrial quality control. However, achieving this goal means we need to construct standard protocol to use our device properly, such as how much sample do our device needs to start analyzing, how much cell do we need to make this device work effectively, etc. Answering this question through wetlab and direct experiment will waste a lot of time and material. By using software to conduct an in silico experiment, we saved a lot of resources while we still achieve the goal to construct a standard protocol for our device.

About our device
Our device will be designed to be easily used by user. So, we make a syringe-shaped device with a little amount of our dried cell inside of it. User then insert medium to prepare the cell for analyzing, and insert some amount of prepared sample (grinded sample dilluted with alcohol). After several minutes, user can see the change in fluorescent concentration as an effect of aflatoxin prescence.

General problem
To achieve a whole cell simulation, we must apply all physical and biological phenomena into our modelling software. In this project, we use Simbiology (computational biology toolbox from Matlab®) to handle the integration of all phenomena.

Hover and click to interact with above diagram.

As sample withdrawn into device, aflatoxin (B1 type) begin to diffuse into our biosensor cell. Then, aflatoxin inside our cell is going through enzymatic reaction with cytochrome P450 3A4 (common cytochrome in human for drug metabolism) and produce Aflatoxin-B1-Oxide. This oxidized form of aflatoxin B1 is very unstable and going through two possible reaction, the first one is become a harmless Aflatoxin-B1-diol, the other one is to react with DNA and causing damage to DNA. This damage then induced SOS response system to produce our reporter chromoprotein.