Graphs in Copasi

87 views
Skip to first unread message

Angelo Pisciotta

unread,
Jan 25, 2024, 11:22:02 AMJan 25
to COPASI User Forum
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

unread,
Jan 26, 2024, 5:44:59 AMJan 26
to COPASI User Forum
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
scan.jpeg

Angelo Pisciotta

unread,
Jan 26, 2024, 8:31:59 AMJan 26
to copasi-u...@googlegroups.com
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

--
You received this message because you are subscribed to a topic in the Google Groups "COPASI User Forum" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/copasi-user-forum/VI8UAAaZYqk/unsubscribe.
To unsubscribe from this group and all its topics, send an email to copasi-user-fo...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/copasi-user-forum/a3fa5c18-90ff-438f-a42b-c7888ae80ac2n%40googlegroups.com.

Frank Bergmann

unread,
Jan 26, 2024, 8:44:02 AMJan 26
to COPASI User Forum
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

unread,
Jan 26, 2024, 10:24:36 AMJan 26
to copasi-u...@googlegroups.com
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?

You received this message because you are subscribed to the Google Groups "COPASI User Forum" group.
To unsubscribe from this group and stop receiving emails from it, send an email to copasi-user-fo...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/copasi-user-forum/7cf165c2-9582-422b-afa1-1015573a613cn%40googlegroups.com.

Frank Bergmann

unread,
Jan 26, 2024, 10:28:16 AMJan 26
to COPASI User Forum
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

unread,
Jan 29, 2024, 4:53:42 AMJan 29
to COPASI User Forum
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

fenton riusciuta.cps
Reply all
Reply to author
Forward
0 new messages