[Re] Context-Dependent Encoding of Fear and Extinction Memories in a Large-Scale Network Model of the Basal Amygdala

[tawantayron]

Original article: Vlachos, I., Herry, C., Lüthi, A., Aertsen, A., & Kumar, A. "Context-dependent encoding of fear and extinction memories in a large-scale network model of the basal amygdala". PLoS Comput Biol, v. 7, n. 3, p. e1001104, 2011.

PDF URL: https://github.com/tawantayron/RE-Fear-and-extinction-in-a-BA-net-model/blob/master/article.pdf
Metadata URL: https://github.com/tawantayron/RE-Fear-and-extinction-in-a-BA-net-model/blob/master/metadata.yaml
Code URL: https://github.com/tawantayron/RE-Fear-and-extinction-in-a-BA-net-model

Scientific domain: Computational Neuroscience
Programming language: Python and Brian 2
Suggested editor: @benoit-girard
Suggested reviewer: @mstimberg @heplesser @rgutzen @TiinaManninen

[rougier]

@tawantayron Thanks for your submission, we'll assign an editor soon.

[rougier]

@benoit-girard @otizonaizit @oliviaguest @eroesch @gdetor Can one of you edit this submission?

[eroesch]

Yes, I can do it.

[rougier]

Thanks. I've just assigned you.

[tawantayron]

Dear editor,
We would like to kindly ask if there is any update on the progress of the review process of our submission.
We understand that we still are amidst difficult times and that the steps involving the revision of our manuscript can be longer than usual, but it would be great if this manuscript could be progressed in the not too distant future.
Cordially,

[eroesch]

Dear @tawantayron, I am working on it. It has been a bit difficult to find reviewers, but I remain optimistic. I will provide you with my own comments very soon.

[eroesch]

Hi @tawantayron, I am running into a runtime error, running runsim.py with protocol=1, =2 (I am still running 3 and above, some warnings but so far so good). See below. The code seems to carry on in a loop, and I assumed the code might still be running. After 24h+ of running though, it still does not complete. Can you let me know what you think?

ERROR Brian 2 encountered an unexpected error. If you think this is a bug in Brian 2, please report this issue either to the discourse forum at http://brian.discourse.group/, or to the issue tracker at https://github.com/brian-team/brian2/issues. Please include this file with debug information in your report: /var/folders/8f/5f00v5l94r91mtfll9t0x2sm0000gn/T/brian_debug_anijad72.log Additionally, you can also include a copy of the script that was run, available at: /var/folders/8f/5f00v5l94r91mtfll9t0x2sm0000gn/T/brian_script_54_70__1.py Thanks! [brian2]
Traceback ....

RuntimeError:
An attempt has been made to start a new process before the
current process has finished its bootstrapping phase.

    This probably means that you are not using fork to start your
    child processes and you have forgotten to use the proper idiom
    in the main module:

        if __name__ == '__main__':
            freeze_support()
            ...

    The "freeze_support()" line can be omitted if the program
    is not going to be frozen to produce an executable.

[eroesch]

Actually I spoke to soon, protocol=3 works, but not 4 or 5.

[tawantayron]

Dear editor,

We have double-checked the code on Linux systems and fix small issues encountered. We also noted a bug when running on MacOS that should be solved now, in case that is the system you are using let us know if you run into more issues while executing the code.

[eroesch]

@tawantayron, awesome. Thanks. Yes, MacOS. I will pull and try again.
What was the issue?