First-time setup
First-time setup
Hello all, I am trying to install and use the NEURON environment in Windows 8. I would like to be able to use it in Python.
I tried reading here: http://www.neuron.yale.edu/neuron/node/47 but I could not figure most of it out. :( I am just not that skilled with installing anything more complicated than a download-and-double-click installation. Could someone list the exact, step-by-step procedures I need to take to get NEURON up and running, or link me to a page that does that?
I tried reading here: http://www.neuron.yale.edu/neuron/node/47 but I could not figure most of it out. :( I am just not that skilled with installing anything more complicated than a download-and-double-click installation. Could someone list the exact, step-by-step procedures I need to take to get NEURON up and running, or link me to a page that does that?
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Re: First-time setup
Just get the 64 bit cygwin installer from http://www.neuron.yale.edu/neuron/download.
After you install NEURON, look in the NEURON Program Group (in the start menu), or in the NEURON folder on your desktop, for an icon that will start NEURON with Python as the interpreter. If instead you want to use NEURON as a module under Python, follow the instructions under the heading
Compiling the standard distribution from source code
which you will find a bit farther down the page.
After you install NEURON, look in the NEURON Program Group (in the start menu), or in the NEURON folder on your desktop, for an icon that will start NEURON with Python as the interpreter. If instead you want to use NEURON as a module under Python, follow the instructions under the heading
Compiling the standard distribution from source code
which you will find a bit farther down the page.
Re: First-time setup
Alright. I am now able to bring this up:
Am I on the right track? If so, what documentation/beginner's guide should I read next? EDIT: Never mind, I see I need to get The NEURON Book or its corresponding paper.
Am I on the right track? If so, what documentation/beginner's guide should I read next? EDIT: Never mind, I see I need to get The NEURON Book or its corresponding paper.
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Re: First-time setup
You'll also want to read the papers about NEURON + Python -- see http://www.neuron.yale.edu/neuron/nrnpubs -- and spend some time perusing the Programmer's Reference, especially http://www.neuron.yale.edu/neuron/stati ... index.html. Or, if you can, sign up for the "NEURON Fundamentals" component of the NEURON Summer Course http://www.neuron.yale.edu/neuron/stati ... d2014.html and save yourself weeks to months of stubbing your toes.
Re: First-time setup
http://www.neuron.yale.edu/neuron/stati ... ython.html
These installation instructions are very confusing to me. I do not know where I am supposed to type this stuff, let alone what I am actually supposed to type.
These installation instructions are very confusing to me. I do not know where I am supposed to type this stuff, let alone what I am actually supposed to type.
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Re: First-time setup
If you have already installed NEURON and can use Python from it, why would you need to compile it from source code?
Re: First-time setup
I guess my question would be where I can go to edit and run scripts. Ideally I'd like to be able to run this on Spyder, which I have already installed.ted wrote:If you have already installed NEURON and can use Python from it, why would you need to compile it from source code?
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Re: First-time setup
Anywhere you like, as long as the result is a plain text file. Save it to disk. If it's a hoc file and you're using MSWin, double click on it and NEURON will start and read the file. If it's a .py file, you probably need to launch it from an rxvt terminal with a command line of the formtoll_booth wrote:I guess my question would be where I can go to edit and run scripts.
nrniv -python filename.py
or maybe
nrngui -python filename.py
Then you'll have to figure out how to make Spyder execute one of those command lines.Ideally I'd like to be able to run this on Spyder, which I have already installed.
Re: First-time setup
But see, all of that is what I have NO CLUE how to do. None. Like, I don't even know where to begin. :( Are you saying I need to:ted wrote:Anywhere you like, as long as the result is a plain text file. Save it to disk. If it's a hoc file and you're using MSWin, double click on it and NEURON will start and read the file. If it's a .py file, you probably need to launch it from an rxvt terminal with a command line of the formtoll_booth wrote:I guess my question would be where I can go to edit and run scripts.
nrniv -python filename.py
or maybe
nrngui -python filename.py
1. Create some kind of file (in what language?) and save it as a .txt file, not a .c, .py, etc. file?
2. Somehow declare it as a hoc file?
3. If it's Python, go get an rxvt terminal?
4. Then run said file with certain command lines?
Then you'll have to figure out how to make Spyder execute one of those command lines.Ideally I'd like to be able to run this on Spyder, which I have already installed.
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Re: First-time setup
I can only provide advice based on what I know or can reasonably surmise, and I freely admit ignorance of how to use Spyder. Maybe someone who uses Spyder can help you with getting it to use NEURON to execute code.
pwd
cd
ls
for viewing paths, changing directories, and viewing directory contents. Information about those is all over the place, including introductory books on UNIX or Linux and dozens if not thousands of web sites. Ditto for answers to basic questions like "how to use a text editor to create a file" and "how to execute commands from the command line."
If you're using MSWindows, you'll find an "rxvt" item in the NEURON Program Group that will start an rxvt terminal. An rxvt terminal looks like a standard UNIX/Linux/BSD terminal, and offers typical commands such astoll_booth wrote:But see, all of that is what I have NO CLUE how to do.ted wrote:Anywhere you like, as long as the result is a plain text file. Save it to disk. If it's a hoc file and you're using MSWin, double click on it and NEURON will start and read the file. If it's a .py file, you probably need to launch it from an rxvt terminal with a command line of the formtoll_booth wrote:I guess my question would be where I can go to edit and run scripts.
nrniv -python filename.py
or maybe
nrngui -python filename.py
pwd
cd
ls
for viewing paths, changing directories, and viewing directory contents. Information about those is all over the place, including introductory books on UNIX or Linux and dozens if not thousands of web sites. Ditto for answers to basic questions like "how to use a text editor to create a file" and "how to execute commands from the command line."
Re: First-time setup
Okay. I got to here:
Now I presume I want to go http://www.neuron.yale.edu/neuron/stati ... stallation here to install this with Python. Question, what do I do with the "..."? The directory to install to or something? If so, how do I write it--can you give me an example?
Sorry, as I said, I'm a noob here :(
Now I presume I want to go http://www.neuron.yale.edu/neuron/stati ... stallation here to install this with Python. Question, what do I do with the "..."? The directory to install to or something? If so, how do I write it--can you give me an example?
Sorry, as I said, I'm a noob here :(
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Re: First-time setup
If you installed NEURON under MSWin, you already have a NEURON Program Group that contains a "NEURON + Python" item. Double click on that to start NEURON with Python as its interpreter. Read this article for whatever else you might glean:
Hines, M.L., Davison, A.P. and Muller, E. NEURON and Python. Frontiers in Neuroinformatics 3:10.3389/neuro.11.001.2009, 2009.
(available from a link at http://www.neuron.yale.edu/neuron/nrnpubs)
Hines, M.L., Davison, A.P. and Muller, E. NEURON and Python. Frontiers in Neuroinformatics 3:10.3389/neuro.11.001.2009, 2009.
(available from a link at http://www.neuron.yale.edu/neuron/nrnpubs)
Re: First-time setup
Grr, I tried this link: http://journal.frontiersin.org/Journal/ ... 9/abstractted wrote:If you installed NEURON under MSWin, you already have a NEURON Program Group that contains a "NEURON + Python" item. Double click on that to start NEURON with Python as its interpreter. Read this article for whatever else you might glean:
Hines, M.L., Davison, A.P. and Muller, E. NEURON and Python. Frontiers in Neuroinformatics 3:10.3389/neuro.11.001.2009, 2009.
(available from a link at http://www.neuron.yale.edu/neuron/nrnpubs)
But it doesn't work. And BTW I just found the FAQ, and hopefully it might be able to answer some of the questions that I've had...maybe!