Search found 14 matches

by alexandrapierri
Tue Jun 04, 2019 2:46 pm
Forum: NEURON + Python
Topic: 'hoc.HocObject' object has no attribute 'instantiate'
Replies: 4
Views: 361

Re: 'hoc.HocObject' object has no attribute 'instantiate'

Bloody true. The code is too big and depends on the bluepyopt package hence by descriptive approach.
I will send a zip file to you soon.
by alexandrapierri
Mon Jun 03, 2019 9:23 pm
Forum: NEURON + Python
Topic: 'hoc.HocObject' object has no attribute 'instantiate'
Replies: 4
Views: 361

Re: 'hoc.HocObject' object has no attribute 'instantiate'

Thank you Ted I have done some further digging into the problem and I realize the the issue is with the instantiation of my cell model in python. I changed the title to reflect the issue more accurately. So I want to instantiate my cell model whose morphology is given in a cell template. I get the e...
by alexandrapierri
Fri May 31, 2019 4:56 pm
Forum: NEURON + Python
Topic: 'hoc.HocObject' object has no attribute 'instantiate'
Replies: 4
Views: 361

'hoc.HocObject' object has no attribute 'instantiate'

Hello

What is the general meaning behind the error: "a template cannot be redefined"?
In my case I am trying to stimulate a neuron written in a hoc template using a python script.
Is it because stimulating my cell modifies the template and modifying a template is not allowed?

thank you,
Alexandra
by alexandrapierri
Thu Jan 10, 2019 3:27 pm
Forum: NEURON + Python
Topic: How can python read from a hoc file templates and procs?
Replies: 7
Views: 1573

Re: How can python read from a hoc file templates and procs?

Thank you Ted. I now understand that "newpyr = h.Pyr()" creates a new instance of "Pyr" and this explains the zero values I was getting in the first example I posted. However if we go back to my first example listed again below, how can I have python print h.NumApical? "print h.axoaxoniccell_temp.Nu...
by alexandrapierri
Fri Jan 04, 2019 3:02 pm
Forum: NEURON + Python
Topic: How can python read from a hoc file templates and procs?
Replies: 7
Views: 1573

Re: How can python read from a hoc file templates and procs?

Thank you Ted. As a matter of fact, the code I posted is a toy code I use to experiment/understand how Python reads variables, parameters and their values from NEURON. From your response I realize that the idea is that Python reads the type of variables and parameters defined in hoc but expects that...
by alexandrapierri
Fri Dec 21, 2018 6:01 pm
Forum: NEURON + Python
Topic: How can python read from a hoc file templates and procs?
Replies: 7
Views: 1573

How can python read from a hoc file templates and procs?

Hello developers I want my python script to read from a NEURON hoc script and and I am facing difficulties having python read variables if they are defined within a template or a proc and not on top level. How can python read parameters right (and in general any variable in hoc) if defined within a ...
by alexandrapierri
Wed Dec 19, 2018 8:34 pm
Forum: SimTracker
Topic: fscan confused with comment lines
Replies: 1
Views: 2701

fscan confused with comment lines

Hello

Is it true that fscan is confused with comment lines and is there a way to add comments in a text file that needs to be read by fscan?
by alexandrapierri
Sat Jun 23, 2018 8:54 pm
Forum: UNIX/Linux
Topic: libreadline.so.0: cannot open shared object file: No such file or directory
Replies: 1
Views: 1372

libreadline.so.0: cannot open shared object file: No such file or directory

hello after installation of NEURON 7.5 in linux, trying to execute a previous hoc script by running nrniv produces the following errors: NEURON: Couldn't find: stdlib.hoc NEURON: Couldn't find: import3d.hoc libreadline.so.0: cannot open shared object file: No such file or directory I searched for th...
by alexandrapierri
Mon Jan 01, 2018 11:41 pm
Forum: MSWin
Topic: neuron 7.5 crashes on cygwin 2.9.0
Replies: 6
Views: 4437

Re: neuron 7.5 crashes on cygwin 2.9.0

I will keep that in mind about finding a workaround with Python ( I do have Python installed) but will switch to linux for now.

thanks a lot for all help Ted!
by alexandrapierri
Sat Dec 30, 2017 11:35 am
Forum: MSWin
Topic: neuron 7.5 crashes on cygwin 2.9.0
Replies: 6
Views: 4437

Re: neuron 7.5 crashes on cygwin 2.9.0

Thanks again Ted Based on SimTracker instructions Cygwin is required on Windows operating systems to enable certain Linux commands used by the SimTracker. http://mariannebezaire.com/simtracker/ For instance based on the instructions the packages below are required: • openssh • procps • rsync Unfortu...
by alexandrapierri
Thu Dec 21, 2017 1:26 pm
Forum: MSWin
Topic: neuron 7.5 crashes on cygwin 2.9.0
Replies: 6
Views: 4437

Re: neuron 7.5 crashes on cygwin 2.9.0

Hi Ted thanks so much for your prompt response. I need cygwin for SimTracker (by Marianne Bezaire) and I assumed that the latest version of NEURON is what I should install. Would you suggest that I install a previous version of NEURON to use with cygwin on Sim Tracker? thank you again, Alexandra
by alexandrapierri
Wed Dec 20, 2017 10:15 pm
Forum: MSWin
Topic: neuron 7.5 crashes on cygwin 2.9.0
Replies: 6
Views: 4437

neuron 7.5 crashes on cygwin 2.9.0

Hello NEURON team, 1. On my Windows 10 machine NEURON 7.5 crashes on cygwin 2.9.0 after successful installation of cygwin. I have tried to install first NEURON and then cygwin or reverse the order of installation and the problem persists. The extra packages I have installed with cygwin are: 1. procp...
by alexandrapierri
Tue Nov 21, 2017 10:22 pm
Forum: SimTracker
Topic: Welcome to the SimTracker Forum!
Replies: 1
Views: 20249

Re: Welcome to the SimTracker Forum!

Hello! After installing Sim Tracker I encounter the following issue when trying to run NetClamp. As per the installation instructions I run Netclamp from the CA1 repository while importing the ca1_centerlfp_long_exc_065_01 from Open Science Framework. Any help with this matlab error would be greatly...