How to use¶

1. Running a simulation¶

Once you've setup your project, you can now run your simulations.

To start, choose your parameters file in the parameters selector:

select_params

Next, choose the duration (hours) and the time step (hours) of the simulation.

Tip

It is recommened to use small time steps to capture the small changes in the system and have more accurate results.

Advanced options

Clicking on the Advanced options button will make them appear:

advanced_options

You can then change:

The fba threshold (h-1) : The threshold above which the optimal solution of FBA should be for the organism to be considered as growing. (default is 0.0001 h-1) (E.g. if the optimal solution of FBA is 0.00001 h-1 and the fba threshold is 0.0001 h-1, the organism will be considered as not growing)
The minimum biomass threshold (h-1) : The value to which the biomass concentration is rounded when it goes below the threshold. (default is 0.001 h-1) (E.g. if the biomass concentration is 0.0001 and the minimum biomass threshold is 0.001, the biomass concentration will be rounded to 0.001)

You can also check the simulate pH. (By default, this option is unchecked)

-> Checking this option will add the pH tab to the interface and will simulate the pH of the system during the simulation.

Analysis type

The Analysis type option allows to choose between dynpop_analysis, ko_analysis or batch_analysis:

analysis_type

dynpop_analysis : The default selected type representing the regular simulation.

ko_analysis : Used to run the simulation without any knockout (wild type) then run it with each gene knockout individually and compare the results.

batch_analysis : Used to run the simulation with multiple parameters files at once.
To use this option, you have to select the batch folder containing the parameters files you want to run the simulation with.
batch_folder
The folder needs to be inside the data/batch folder.

Now, you can start your simulation by clicking on the Start simulation button:

start_simulation_button

Info

If there are any problems with your files, the application should show useful messages to fix them.

2. Stopping a simulation¶

During the simulation, the Stop simulation button (previously grayed out) will become active (red):

stop_simulation_button

You can click on it at any point during the simulation to stop the simulation at the current time and display the results.

3. Continuing a simulation¶

Once the simulation is finished (or stopped), a continue simulation with same parameters button should appear with an Added duration (hours) input.

continue_simulation

You can now choose the desired added duration and click on the continue simulation with same parameters button.

4. Starting a new simulation¶

If you want to start a completely new simulation, you can click on the New simulation button new_simulation at the top tool bar then start fresh with step 1.

Warning

This will reset the interface including the input bar and the result figures so make sure to save the previous simulation results first.

5. Finding the limiting substrate(s)¶

Once you ran a simulation, you can find the limiting substrate(s) by clicking on the Find limiting substrate(s) button:

find_limiting_button

Info

If there are multiple organisms in the simulation, you will be prompted to choose the organism you want to find the limiting substrate(s) for.

choose_org

This feature will find the last time point where the chosen organism stopped growing and find the metabolite(s) that are limiting the growth of the organism starting from that time point.

Once the process is finished, the limiting substrate(s) will be displayed in a pop-up window where you can see the metabolite(s) with the corresponding new growth rate after one new time step, with the tested metabolite(s) concentration set to 1000 mM like this:

limiting_substrate_results

Once a limiting substrate combination is selected you can click on the OK button to set the concentrations of the chosen metabolite(s) to 1000 mM.

You can then either search for the next limiting substrate(s) again to try to increase the growth rate further or continue the simulation with the new concentrations.

6. Exploring results¶

Once the simulation is finished (or stopped), you can start exploring the results.

6.1. Biomass results¶

The biomass results should already be drawn on the corresponding canvas.

6.2. Volume results¶

The volume results should already be drawn on the corresponding canvas.

6.3. Metabolites results¶

For the metabolites, you have to choose the metabolites you want to display.

metabolites_selector

You can either click the down arrow to see the list or type in the search bar for fast access:

metabolites_selector_search

While you're selecting the metabolites they should appear on the bar above the selector like this:

selected_metabolites

You can unselect all of the selected metabolites at once just by clicking on the Clear metabolites button:

clear_metabolites_button

Once all the desired metabolites are selected you can display the metabolite results figure by clicking on the Display metabolites button:

display_metabolites_button

Info

If you continue the simulation with the same parameters, the metabolites results will be updated with the new results.

6.4. Fluxes results¶

For the fluxes, you have to first choose the organism you want to display the fluxes for.

Info

If you are using a single model for your simulation this is automatically selected.

Next, you have to choose the desired fluxes to display of the chosen organism:

fluxes_selector

You can either click the down arrow to see the list or type in the search bar for fast access:

fluxes_selector_search

While you're selecting the fluxes they should appear on the bar above the selector like this:

selected_fluxes

You can unselect all of the selected fluxes at once just by clicking on the Clear fluxes button:

clear_fluxes_button

Once all the desired fluxes are selected you can display the fluxes results figure by clicking on the Display fluxes button:

display_fluxes_button

Info

If you continue the simulation with the same parameters, the fluxes results will be updated with the new results.

6.5. Display exact values on hover¶

You can see the exact values of the curves by hovering over the time points on the canvas to have a quick look at the values.

The values should appear in a pop-up like this:

hover_values

6.6. Showing/hiding curves¶

You can show/hide the curves by clicking on the legend of the curves on the canvas.

The curves should disappear/appear when you click on the legend.

The axis limits will be automatically adjusted to the new curves displayed.

show_hide_curves

6.7. Customizing figures¶

Each canvas has a toolbar that allows you to customize the figure: canvas_toolbar

6.7.1. Zooming¶

By selecting the Zoom button zoom_button you can zoom in by clicking and drawing a rectangle on the canvas.

6.7.2. Dragging¶

By selecting the Drag button drag_button you can move the figure around by clicking and dragging on the canvas.

6.7.3. Customizing dimensions, shapes, colors and labels¶

By selecting the Customize button customize_button you can customize the shapes and colors of the figure as well as the title and the axis labels.

The following window should appear with the Axes tab selected by default:

customize_window

Here you can change the title and the axis labels as well as the dimensions of the figure and the scale of the axes.

Or you can go to the Curves tab to change the shapes, colors and labels of the curves:

customize_window

6.7.4. Changing layout¶

By selecting the Layout button layout_button you can change the layout of the figure.

The following window should appear:

layout_window

You can choose the tight layout option to make the figure fit the canvas and become more readable or reset the layout to the default layout.

6.7.5. Resetting¶

By selecting the Reset button reset_button you can reset the figure to its original state.

6.7.6. Saving¶

By selecting the Save button save_button you can save the figure as a png image.

You will be prompted to choose the folder where you want to save the figure and the name of the figure file.

6.7.7. Open graph data in table format¶

By selecting the Open graph data button open_graph_data_button you can open the data of the figure in a table format.

The following window should appear:

graph_data_table

You can then see the raw data of the figure and copy, paste values.

6.7.8. Dragging the legend¶

You can also drag the legend of the figure by clicking and dragging it around the canvas.

This is useful when you have multiple curves and the legend is blocking the view of the curves.

before_drag_legend

drag_legend

7. Saving results¶

Once you're done exploring the results, you can save them by clicking on the Save results button:

save_results_button

You will be prompted to choose the folder where you want to save the results and the name of the results file. Once you're done, click on Save and the results will be saved in the chosen folder.

8. Uploading results¶

You can upload one or more results files by going to:

Upload -> results file(s)

upload_results

Then you can choose the results file(s) you want to upload and click on Open.

9. Visualizing and comparing results from uploaded files¶

Once the results file(s) are uploaded, you can visualize the results by going to:

Visualize -> results file(s)

visualize_results_menu_option

Then you can choose the results file(s) you want to visualize and click on Visualize.

visualize_results_side_menu

The results will be displayed just like the end of a simulation.

Choosing multiple results files will allow you to compare the results of the different simulations.

10. Generating parameters file from results¶

You can also generate a new parameters file from the results by clicking on the Save parameters file button:

generate_params_button

What this will do, is generate a new parameters file by copying the initial parameters file used for the simulation. Then it will replace the initial concentrations of biomass and metabolites with the latest concentrations from the results for the next simulation you want to run.

11. Modifying uploaded files¶

If you want to modify the parameters file or any other uploaded file, you can open the data folder by going to:

Open -> data folder

open_data_folder

Warning

Please do not modify the folder structure in any way as it may cause problems with the application.

12. Exporting simulation files¶

This feature is useful when you want to share the simulation files with someone else or if you want to run the simulation on another computer.

If you want to export the simulation files, you can go to Export -> Export ssimulation files:

export_simulation_files

Then you can choose the parameters file related to the simulation you want to export and click on Open.

Now choose the folder where you want to save the simulation files and click on Save.

13. Toggle notification sound¶

You can toggle the notification sound for simulation end/error by clicking on the Toggle notification sound button: toggle_notification_sound