Graphs in Copasi

[Angelo Pisciotta]

Hello everyone, how can I depict in COPASI graphs two identical reactions with different concentrations? I want to illustrate the impact of concentration on degradation. Additionally, I need to show the same difference both in the presence of sunlight and in dark conditions.

[Frank Bergmann]

You'd be using the scan task for that. 

- create a scan for the initial concentration you want

- switch over to 'values' and enter the concentrations you want to run the time course for (in the example 1, 10 and 100). 

- select subtask to time course, ensure output-during subtask execution is on

when you run it, you will see the plot for the different concentrations. 

best

Frank

[Angelo Pisciotta]

Thank you so much! And in case I have 2 reactions and I want to show them both, what can I do? In my case the reaction is dark fenton and solar fenton

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[Frank Bergmann]

You can add as many scan items as needed. Also you can customise the plots to show only the traces you want to see. 

best

Frank

[Angelo Pisciotta]

I am facing difficulties because I am unable to combine the different values of Fe2+ and H2O2 according to my preferences. Additionally, do I always have to input two reactions in the parameter scan section?

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[Frank Bergmann]

Please attach the latest version of your model and describe precisely what you would like to see.

- inputs: what species initial concentrations should be used

- outputs: which reaction rates / transient concentrations 

best

Frank

[Angelo Pisciotta]

Here you are.
I want see the effect in one graph of this combination of concentration of [Fe2+] and [H2O2] on the degradation of MG.
the combination are: ("u" is for micro)
1. [Fe2+]:14.4 uM  [H2O2]: 4.9 mM
2. [Fe2+]:28.8 uM  [H2O2]: 4.9 mM
3. [Fe2+]:28.8 uM  [H2O2]: 0.98 mM

And this concentration is for dark and solar fenton (the solar fenton is also the reaction 19 and 20, signed by the name solar)

Thank you