www.neuron.yale.edu

The most recent OS X installers available from http://www.neuron.yale.edu/neuron/install/install.html should now work with newer versions of EPD. Please give it a try and let me know.

Generally, at least since NEURON 7.0, one can do the following:

$ python
>>> from neuron import gui

And the GUI will appear.

See:
https://www.neuron.yale.edu/phpBB2/view ... 1405#p5213

Running the Interviews GUI in ipython is possible with the 7.0 alpha development code, by doing the following: $ ipython ... In [1]: from neuron import h NEURON -- VERSION 7.0 (228: fbb244f333a9 ) 2008 -11 -25 Duke , Yale , and the BlueBrain Project -- Copyright 1984 -2007 See http :// www . neuron ...

You might also try the interactive distributed features of Ipython (formerly Ipython1, http://ipython.scipy.org/moin/) I have looked at ParallelPython before, but I find ipython1 more powerful. Also, it might be interesting to know that ipython supports mpiexec to execute python on each slave node, ...

Is there a better way to play a specified conductance input than what I'm doing below? # create an SEClamp object which is accessible in both python and NEURON soma.push() h('objref estim') h('estim = new SEClamp(0.5)') h.pop_section() estim = h.estim # Create a stimulus Vector rs_exc = neuron.Vecto...

Modules in python are singleton. Therefore, all references made in a running program are to the same module.

As a result, neuron.h is one and the same object each time you import it in the constructor.

Making all in e_editor make[3]: Entering directory `/home/gartland/neuron/nrnpy/src/e_editor' if gcc -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../.. -I../../src/oc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpytho...

The nrnpy trunk (http://neuralensemble.org/trac/nrnpy) now contains code for optimized conversion of Hoc Vectors to numpy arrays. In [10]: a = numpy.arange(0,10.0,0.00001) In [11]: v = neuron.Vector(a) In [12]: t1 = time.time(); a = numpy.array(v); t2 = time.time();print t2-t1 0.0429871082306 These ...

After looking into the numpy.array function, I've changed my mind regarding the creation of toarray, fromarray functions. In [17]: a = numpy.array() In [18]: ? a.__array__ Type: builtin_function_or_method Base Class: <type 'builtin_function_or_method'> String Form: <built-in method __array__ of nump...

I would like to point out that the class neuron.Vector already has a complete interface to play with numpy: In [1]: import neuron NEURON -- VERSION 6.2.11 (40) 2008-02-04 (40M) Duke, Yale, and the BlueBrain Project -- Copyright 1984-2007 See http://www.neuron.yale.edu/credits.html In [2]: l = [1,2,3...

I have just attempted a build from a recent SVN revision, and confirm that numpy support is currently broken. I will fix it and submit a patch shortly. However, presently the following should work: import numpy import neuron v = neuron.Vector(10) a = numpy.array(v) print repr(a) # out: array([ 0., 0...

after make install I switched to the src/nrnpython dir and typed python setup.py install in super user mode: ... Python 2.5.1 (r251:54863, May 2 2007, 16:56:35) [GCC 4.1.2 (Ubuntu 4.1.2-0ubuntu4)] on linux2 Type "help", "copyright", "credits" or "license" for...

The big question in my mind is: how can I get python to load a dll which wasn't built for python ... I guess something from ctypes would help here. in neuron.py we could define something like: def load_mechanism(dll_file): import ctypes dll = ctypes.CDLL(dll_file) hoc.register_py_dll(dll) then regis...

would an nrn.load_dll(path_to_so) be provided so external mechanisms can be loaded? This sounds like a good idea to me, however I must admit I don't know the specifics of NEURON's mechanism loader. We did have some problems getting pynest to dynamically load external mechanisms, but we were trying ...

Are plans to eventually provide neuron as a python module?

i.e:

ipython -pylab

>>> import nrn
>>> ...

What would be the limitations, if any, in taking this route?

cheers,

Eilif