Wang, Buzsaki 1996's model running issue

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Wang, Buzsaki 1996's model running issue

Postby breakwave922 » Wed Aug 20, 2014 1:30 pm

Hi,
I downloaded the model file--Gamma oscillations in hippocampal interneuron networks (Wang, Buzsaki 1996), from modelDB. Then I compiled it and tried to run it on my local computer. When I click the jnsci16_6402F3.hoc file, it kept giving me error, saying intsall_vecst undefined function.
Do anyone have experience on running this model?
Here is the link for downloading the model http://senselab.med.yale.edu/ModelDB/Sh ... 6997&file=\wang1996

Any help would be appreciated.
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Re: Wang, Buzsaki 1996's model running issue

Postby tom_morse » Wed Aug 20, 2014 1:41 pm

Start with the mosinit.hoc file instead if that is OK.

I will help you get the model running if the mosinit.hoc doesn't have the part you would like. 1)Which platform (mswin, mac os x, unix/linux) and which 2) version of NEURON (7.3, alpha, hg) are you using?
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Re: Wang, Buzsaki 1996's model running issue

Postby breakwave922 » Wed Aug 20, 2014 3:03 pm

Thank you very much, Tom.
I started with the mosinit.hoc file. Yes, it works. It gave the GUI to ask for choosing Fig 1A or Fig 3A.
I use Windows 8 and Neuron version 7.3
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Re: Wang, Buzsaki 1996's model running issue

Postby breakwave922 » Wed Aug 20, 2014 8:30 pm

tom_morse wrote:Start with the mosinit.hoc file instead if that is OK.

I will help you get the model running if the mosinit.hoc doesn't have the part you would like. 1)Which platform (mswin, mac os x, unix/linux) and which 2) version of NEURON (7.3, alpha, hg) are you using?



Hi, Tom,
I just realized that I couldn't even compile it. When I compile it in NEURON7.3, it gave me error:"vecst.c : 162:23: fatal error: sys/time.h: No such file or directory".
Sorry for ignoring this important message before.
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Re: Wang, Buzsaki 1996's model running issue

Postby ted » Wed Aug 20, 2014 10:20 pm

Ah, the perils of assuming specific paths for key files. On whatever machine that Bill Lytton used, time.h lived in a particular location. Your task, if you want to reuse his code, is to locate where time.h lives on your own machine (if you're using MSWindows, you'll have to grope around in cygwin's directory structure, or maybe someone else knows where to point you). Then you'll want to identify the mod files that include time.h and revise those include statements to point to the correct location.
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Re: Wang, Buzsaki 1996's model running issue

Postby tom_morse » Thu Aug 21, 2014 11:10 am

Changing the include file from sys/time.h to just time.h got past this mknrndll error. However there were other errors with the
drand48 not being found.
I found another model in ModelDB that has some clues about how to convert this to windows from linux:
https://senselab.med.yale.edu/modeldb/S ... 9889&file=\lytton97\rand.mod
I will work on this and get back to you soon.
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Re: Wang, Buzsaki 1996's model running issue

Postby tom_morse » Thu Aug 21, 2014 7:35 pm

I updated the model in modeldb to run on mswin as well as unix/linux. Please download and try this new version:

http://senselab.med.yale.edu/modeldb/ShowModel.asp?model=26997
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Re: Wang, Buzsaki 1996's model running issue

Postby breakwave922 » Fri Aug 22, 2014 4:21 pm

Hi, Tom,
Yes. It works now. Thank you so much.
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Re: Wang, Buzsaki 1996's model running issue

Postby RBett » Wed Sep 13, 2017 3:58 am

Hi all,

I've come accross the same problem in the Pinsky-Rinzel reduced Traub model (1994)

https://senselab.med.yale.edu/modeldb/ShowModel.cshtml?model=35358#tabs-1

I used the fix that Tom suggested for sys/time.h to time.h but have got stuck with drand48. The relevant mod file is vecst. Any ideas?


(running version 7.4x86_64 on 64-bit windows 7 if you're curious)
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Re: Wang, Buzsaki 1996's model running issue

Postby RBett » Wed Sep 13, 2017 10:32 am

RBett wrote: but have got stuck with drand48.


...got past it. Followed directly the modifications that have been made to the Buzsaki Wang model and now Pinsky Rinzel seems to be running fine.

Is it worth updating the version on modelDB do you think?
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Re: Wang, Buzsaki 1996's model running issue

Postby tom_morse » Wed Sep 13, 2017 11:37 am

Yes it is worth putting in ModelDB. Please email me the code (will send separate email to you) and I will upload it!
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Re: Wang, Buzsaki 1996's model running issue

Postby tom_morse » Thu Sep 14, 2017 10:42 am

The model in modeldb has been updated with a vecst.mod file RBett sent. Thanks RBett!
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