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Team:UPO-Sevilla/Project/Notebook/Mathematical Modeling
From 2011.igem.org
Notebook
Mathematical Modeling
Jesús Jiménez Sobrado
Week 1
Week 2
Week 3
Week 4
Week 5
Week 6
Week 7
Week 8
Week 9
The ‘dry lab’ has a first meeting where we begin to decide which work has to be done, and how are we going to achieve it. After that, I start collecting information about the equations of the basic toggle switch. My partners help me understanding how works the system and many other little things. Luis, offered us a lab where to work during the summer.
At the meeting, the group told me about using a specific software for modeling biological systems. I become to study how ‘Simbiology’ works and start doing small tests. I do the first basic bistable model, and run the simulations. The results have sense. Although the main working tool is simbiology, I also start doing some Matlab programs to confirm the results.
I continue making programs/simulations and thinking how to implement the controls of the basic bistable. Although I have a couple of equations, they don’t fit in my analysis.
On Wednesday we had a general meeting with the entire group. Each subgroup showed the work done and its perspectives. But before this, I met the ‘dry lab’ and showed the programs done. We tried to adapt the model to obtain some interesting simulations to show. Otherwise, to adapt the simulations to the real behavior, I need a lot of parameters values, so we decided to make an analysis with the simple model to adapt the real results, because it has fewer.
(The rest of the week I’m going to a blues festival, so I can’t do any work)
I found some interesting information about how to model the ‘IPTG induction’ reaction. Also, I decided to model the degradation of the thermosensitive protein with a mass action kinetics law. So I implemented these two new formulas. Results showed some problems because the system didn’t change the state.
On Wednesday I met Luis, Adri and Manuel to show them my advances. However, Manuel found some mistakes in my models, and we worked to fix them. We decided which work must be done before September.
On Friday I received a book which will help me to understand some reactions of the system.
Holidays!
In these two weeks I work at home. I made many implementations in Matlab, simulink and Simbiology. I tried to find the best tool for doing a stochastic integration. Matlab’s scripts seemed to be the best. I spend much time adjusting models.
Finally I start reading information about the following system, the modified toggle switch, however I don’t understand how the improvements works, so I decided to wait to September and meet Félix.
Almost the entire team is back from holidays and we start again the hard work. I met Luis and Adri to catch up. But almost the whole week I continued working on my models putting them ready for next week’s meeting. Also, modeling basic toggle switch must be done, because the deadline is two weeks later!
After the meeting with the entire group, I talk to Félix to be informed about how works the improved bistable. Also, I talk to Amalia, to have some parameters values, due to she had made many experiments with the basic bistable.
The rest of the week I spend my days trying to implement the modified model. I had lot of problems in this purpose.
I finished my work on Matlab and my programs seem to work without many problems, so I start making my working report.
Sponsors
