How to specify the reaction rates in batch simulations with rule based model

[Kun]

Hello, I learnt that is I want to run batch simulation, I have to prepare a .dat file containing the configurations, and I have successfully run experiments with different substance initializations. Now I would like to specify the reaction rates as well, I understand that something like ' Kr_Transport_DirectHalf_0=55, Kf_C_p1_InverseHalf_0=12  ' is allowed, but what I'm confused is what does DirectHalf and InverseHalf mean? I tried to replace  Kf_C_p1_InverseHalf_0 with  Kf_C_p1_DirectHalf_0, but it seems that the owritten parameter was always the Kf of the same reaction.

Thanks

[Blinov,Michael]

Hello,

In my previous email I explained the meaning of DirectHalf and InverseHalf. Batch file modifies a generated math by simply replacing the values in a MathModel: Simulations -> Generated Math -> Math Description Language.

The complicated part is that some rates are defined as constants (those that are not adjusted by symmetries), and some rates are defined as functions (those adjusted by symmetries, see my previous email). Adjusting functions in a batch file is not possible - they are computed based on proper thermodynamic and mass-conservation constraints and can not be changed. So, if you want to change these values, you need to find a way around, may be defining a rule that deals with some specific cases.

Feel free to ask more questions, it's a really complicated part of VCell.

Best,

Michael

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From: vcell-...@googlegroups.com <vcell-...@googlegroups.com> on behalf of Kun <b22...@gmail.com>
Sent: Thursday, October 5, 2023 7:19 PM
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Subject: [VCell] How to specify the reaction rates in batch simulations with rule based model

 

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Hello, I learnt that is I want to run batch simulation, I have to prepare a .dat file containing the configurations, and I have successfully run experiments with different substance initializations. Now I would like to specify the reaction rates as well, I understand that something like ' Kr_Transport_DirectHalf_0=55, Kf_C_p1_InverseHalf_0=12  ' is allowed, but what I'm confused is what does DirectHalf and InverseHalf mean? I tried to replace  Kf_C_p1_InverseHalf_0 with  Kf_C_p1_DirectHalf_0, but it seems that the owritten parameter was always the Kf of the same reaction.

Thanks

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