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Notebook

Multiagent Modeling

Adrián Arellano

This is just the summer diary. During the academic course we all have spent much time working hard looking for money, organizing the team, giving talks in high-schools, writing in our synthetic biology blog, etc.

• Week 1

First week here in the dry lab! We are going to make our work in the physics lab, where we have some computers to work with. Moreover we plan to have weekly meetings to check the state of the project. This first week I have started a simple implementation of the spatial simulation of the bacterial biestable. I have spend much time searching for information about many parameters that we want to have present, as ribosome number in a bacterium or translation and transcription rates. The information is not always accurate and depends a lot on the source, but finally we have taken the decision of taking data mainly from CyberCell Database. After this, I have implemented a first version of the simulation and experimented several things with NetLogo.

• Week 2

I carry on programming day and night. NetLogo is a good tool because it is easy but there are many things that could be written in other way.

• Week 3

This week I have almost finished the final version of the simulation. I have spent a lot of time debugging thousand and thousand of little mistakes in the source code but it seems to be finished. I have just to implement the temperature effect and the IPTG effect and it will be finished, but now I am a bit more experienced with NetLogo it will not take me so long. (I think).

• Week 4

I have been trying to represent the RNA strings as real string which can bend like ropes, but it makes the simulation unnecessary complex. So soon I discarded this idea and finished the simulation. Now it is ready to run. Let’s see what can do!

• Week 5

With the simulation program finished, I have been the whole week making runs and changing conditions to see the effects in the biestable behavior. I have used some computers, including my personal laptop, but the effort to my computer is considerable and it sometimes turn off because of the heat. A run can last several hours, so I have to be patient. I have checked the behavior of the simulation in different conditions, changing promoter strength, changing repressors per promoter, etc, and finally I exported this data to .csv files. After this, I plotted this information to compare the results.

• Week 6

I have been this whole week still plotting the information I got from the simulation. Now the wiki freezing is close and I have to start also to write the text for the wiki.

• Week 7

Last week here! Eventually, I have spent many hours writing and documenting all the things I have worked in. Now the text is ready to upload to the wiki page. I have enjoyed a lot this year learning different things here in the dry lab.