simulate single cell with stimulate

Question

Dear devs,

I 'm trying to simulate single cells. Can I diversify the stimulation applied to the cells like in the example cd ${TUTORIALS}/02_EP_tissue/02_stimulation? Or can I use bench to define two types of stimuli simultaneously. Also, how can I observe changes in ion concentration and gating properties?

Any help or ideas would be appreciated, thank you!

Answer 1

Absolutely!

Those functions are documented in the openCARP user manual in the section on bench (chapter 8): https://opencarp.org/documentation/user-manual

The --validate flag will output the time courses for all state variables.

The --stim-file flag allows you to input arbitrary complex stimuli

Comments

Dear devs,
Can you please give me a little more detail about --stim-file  or give me an example?
Whether this instruction can produce the S1S2 stimulus which mentioned in 01_EP_single_cell/02B_APD_restitution?
Any help or ideas would be appreciated, thank you!

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The file format is described in section 4.1.5 of the openCARP manual: https://opencarp.org/documentation/user-manual

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Thank you for your reply. I have another question. The '--validate' command generates a lot of
variables, but I'm not sure what each one represents. Is there a way I can find out?
Any help or ideas would be appreciated, thank you!

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The last part of the filename indicates the name of the state variable as defined in the .model file: http://git.opencarp.org/openCARP/openCARP/-/tree/master/physics/limpet/models
More information on the data format is given in the *_header.txt file.

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Thank you for your reply.
In the example in the --stim-file tag, is 'val' a current stimulus? Can it be changed to a voltage stimulus?
Any help or ideas would be appreciated, thank you!

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A transmembrane voltage stimulus?
That can be applied using the Clamp functions, which can be used to predefined time courses for any state variable

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As shown in https://opencarp.org/documentation/user-manual section 9.6, ‘--stim-curr=FLOAT’ represents current stimulation, and ‘--stim-volt=FLOAT’ represents voltage stimulation. However, the trc file in ‘--stim-file=STRING’ does not specify the unit. Is it current or voltage stimulation?

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It's a current as specified in the help text for this parameter:

bench --help

--stim-file=STRING  use signal from a .trc file for current

                                  stimulus