Variables in the CNAregMCSEnumerator function are not commented, and the meaning is not understood

[Mike]

I'm hoping to use parts of the CNAregMCSEnumerator function to solve a problem I'm working on, but there are too many variables and some of them are missing comments, where should I find out what they mean, looking forward to your reply!

[Steffen]

Hello Mike,

for which variables do you need more information?

Best regards,
Steffen.

[Mike]

In the source code of the function CNAregMCSEnumerator, there is a function called add_flux_bound_interventions, I know that its function is to add pseudo-metabolites and pseudo-reactions, and I basically understand the meaning of the variables in it.
However, I did not find out where, after adding the pseudo-metabolite and pseudo-reaction, the pseudo-metabolite is deleted in order to up- and down-regulate the reaction, a step that is very important for me to carry out my experiments. I found a potentially relevant code snippet somewhere on my own (below), but I don't see an explicit deletion for modulation operation here either.
I hope to be able to communicate with you more, it's a great help for a newbie just getting started!
Thanks for your reply.

Steffen 在 2024年7月9日 星期二下午3:52:14 [UTC+8] 的信中寫道：

[axel]

Hello Mike,

the calculation of (regulatory) MCS in this implementation is set up as a MILP (mixed-integer linear program). This is then (repeatedly) solved with the CPLEX solver and the solution(s) indicate which reactions are being knocked out. The result is returned as 'mcs' by the CNAregMCSEnumerator function and there you can see which reactions are knocked out and which regulations are active (cf. the description of 'mcs' in the help section of the function).
Also, the regulations are activated by knocking out slack reactions (cf. Fig 1 of "Genome-scale strain designs based on regulatory minimal cut sets"), the pseudo-metabolites always remain in the system.

I am not entirely sure if this answers your question so please let me know if you require further assistance.

Best regards,

Axel

[Mike]

How are you?
It's nice to hear from you, I'll try to describe my problem in more detail below to understand it.
Attached is the source code I am running, it is an open source MCS article code, my goal right now is that he for the preprocessing done during the MCS calculations not to delete it, but just to change the final MCS calculations to FBA calculations. That is, none of the constraints between the added pseudo-reactions, which the author is preparing for the MCS calculation, need to be deleted, I would like to keep the process, just change the final calculation to an FBA calculation.
If you don't have time to watch the whole code for a while, my question is probably as follows: the source code of the CNAregMCSEnumerator function sets constraints for the relaxation reaction and the demand reaction not to coexist, but how does he adjust the reaction rate up and down after removing the relaxation reaction, and I would very much like to find out where the code for this step is located so I can figure out how to do my own FBA calculations.
Yours sincerely
Mike

axel 在 2024年7月15日 星期一下午3:48:40 [UTC+8] 的信中寫道：