COMETS E.coli simulation example

The first three steps are Windows specific. The detailed instructions for all three systems (Windows, Linux and Mac) are in the RUNNING_COMETS file distributed with COMETS.

Make sure that:

>echo %COMETS_HOME%

returns the right directory. Search for %COMETS_HOME% at the start menu. This should take you to the directory where you installed comets.

1. First create a working directory.

2. Copy the following files in the working directory:

%COMETS_HOME%\comets_wXX_params
%COMETS_HOME%\global_params.txt
%COMETS_HOME%\package_params.txt
%COMETS_HOME%\layouts_and_models\Ecoli_colony_layout.txt
%COMETS_HOME%\layouts_and_models\EC_ijo1366_model.txt

3. Run comets by double-clicking on comets_wXX_params.

This should start the GUI:

COMETS_at_start

and open a ‘Welcome to Comets!’ window:

COMETS_Welcome_to_COMETS

 

4. Load the layout file.

On the ‘Welcome to Comets!’ window, click on the ‘Load layout file’ button. When the file chooser shows up, choose and open the ‘Ecoli_colony_layout.txt’ file:

COMETS_Layout_file_choose

This should open the layout, load the model and test it. The graphical panel should contain an image
of the starting colony (a single dot):

COMETS_after_load

 

5. Once the layout (and the model) is loaded, you can set and customize the parameters
by going to the ‘Edit’ then ‘Edit Parameters’ menu. The ‘Edit Parameters’ menu has several sub menus.

The first one is ‘Diffusion.’ Here you can set the type of diffusion algorithm and the diffusion parameter for the metabolites. You can also set the number of diffusion steps to be executed per single FBA calculation.

COMETS_Params_diffusion

 

Next you can customize the display by setting the background color, size of the image etc.

COMETS_Params_Display

 

Here you can set the exchange style and the exchange model parameters:

COMETS_Params_Exchange

 

If you run on a multi-processor/core machine you can set the number of thread higher than one to speed up the simulation:

COMETS_Params_Threads

 

Here you can specify what results you want to save:

COMETS_Params_outputlog

 

The following one is one of the most important collection of parameters. Here you can set the lowest biomass concentration that will be considered different than zero, the highest biomass concentration that can be generated in a unit of the space grid. You can specify the time step and space width size. If you set death rate other than zero a portion of the biomass will die in each time step at the given rate. You can run the simulation indefinitely or specify the total of time steps for the run. Finally, if you check the activation box and specify the activation rate, the model(s) will be dormant at the start of the simulation and be activated at the given rate.

COMETS_Params_Simulation

 

You can save the images of the colony. Here you can specify the details of where and at what rate to save them:

COMETS_Params_slideshow

 

6. Run the simulation.

To run the simulation, click on the ‘Simulation’ menu, then click on ‘Start Simulation’. The simulation panel will show up next to the image of the colony. Click on the ‘Run/Pause Simulation’ button. This will propagate the simulation by a single cycle. To run uninterrupted simulation (in this case 200 cycles) check off the ‘Pause after cycle’ box. The image of the colony will be updated with each cycle.

COMETS_Simulation_start

After several cycles the colony will show visible growth:

COMETS_Simulation_middle

You can also visualize the nutrients by choosing one of them on the right of the image. Here the depletion of glucose is evident after the colony has started growing:

COMETS_Simulation_glcD

This is the colony at the end of the simulation:

COMETS_Simulation_end

 

7. This is what you will get for the total biomass if you chose to save it in a file. This is a two column file plotted below using Grace.

COMETS_Biomass_plot