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• How to use it

How to use it

To initiate the program with the selected variables you just have to click on the setup button. If you want to adjust all variables to the values by default just click on reset.

To initiate the simulation click on the go button. (aquí me falta añadir junto al texto las imágenes de los botones a los que me refiero con sus correspondientes pies)

The user can modify many variables and see which are the effects of modifying these variables in the simulation:

• He can change the number of starting molecules or select the number of repressors that can admit every promoter.

  

  Sliders to select the number of molecules

• The user can also control the life-span of RNA and repressors. The life-span of these molecules is distributed according to a normal distribution.

  

  Mean life and standard deviation of several species

• He can regulate the strength of the interaction with several molecules. The repressor strength is inversely proportional to the given number, because it gives the chances per second that an attached repressor to the DNA falls from it. Since the strength of the promoters gives the chances (in percentage) that a given RNAP which detects a promoter starts transcription.

  

  Interacition Strength of repressors and promoters

• The parameter called time-constant gives us the number of steps (or ticks) of simulation that the program performs by each second of evolution of the system and has a value of one hundred per default. The movement of the proteins in the cytoplasm and the speed of the RNAPs and ribosomes when they are “reading” has an optimal value if this number is 1000, but it also makes the program run slower. Taking as reference a medium-size protein (40 kDA) which moves with a speed of 5 nm per ms, the program only runs this thousand steps if the constant-time values 1000. If the number decrease, the simulation loss realism but it will run much faster, which could be interesting if we are interested in obtain just a more qualitative comprehension of the system.

  

• The slider cell-cycle-length gives us the length of a cell cycle, by default 30 minutes.The button divide-cells? allows us to eliminate half of the repressors and RNAs in a randomly way every cell-cycle.

  

  Controling the division cell process

• Under the title of Actions, the user can interact with the simulation in real time. This way, the user can toggle the bistable switch between the two possible states. For convenience, we have taken as “On” the state in which the protein LacI has a high concentration in the cell. To turn off the bistable we have to release a high concentration of IPTG and be patient. We have to give enough time to the simulation, because the RNA must be transcribed to produce after this the protein c1ts and the RNA, and free LacI proteins must disappear.

  

  Controls to turn off the bistable

  To turn on the bistable, we only have to increase the temperature. The temperature-effect gives us how many times faster grows old the protein c1ts. We can see that it is rather easier to turn the bistable on than to turn it off.

  

  Controls to turn on the bistable

• The show-view button allows us to turn-off the simulation window, although the plots and the monitor will carry on actualizing. To turn-off the view enables the simulation to run much faster, so it is strongly recommended.

  

• The program also allows to export data to a .csv file with the name Simulation data, and it is saved in the root folder where is saved the simulation. It is recommended that if you want to use the simulation to produce data the program must be open from the .nlogo file.

  

• The simulation represents the concentration of RNAs and repressors in the plot. Moreover, we can see in the monitors the amount of molecules of every kind, how many repressors can be found repressing, how many repressors with kind 1 are bound to IPTG and the temperature.

  

  General view of plots and monitors

The color legend is in the next table:

By default, the LacI promoter is 10 times stronger than the c1ts promoter and for this reason, if the user do not provide any input, LacI ends winning as the dominant repressor and blocks the transcription of c1ts.