www.neuron.yale.edu

emuller wrote: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

would an nrn.load_dll(path_to_so) be provided so external mechanisms can be loaded?

eacheon wrote:Nice job, Micheal! You did it so fast!

May I ask why you are reluctant to numpy dependency? My guess is every one is going to use numpy with NEURON so there should not be a dependency issue.

I am sorry, Micheal. I realized you meant the "build dependency"...

Seems r1729 of NEURON fixed this. I had difficulty building r17: gcc version 4.1.2 20061115 (prerelease) (Debian 4.1.1-21) /bin/bash ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I...

I had difficulty building r17: gcc version 4.1.2 20061115 (prerelease) (Debian 4.1.1-21) /bin/bash ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I. -I../../src...

As Micheal pointed out, doNotify() need to be called periodically in a separate thread to make mainmenu reacting to GUI operations. IPython is doing similar things to GTK, Qt GUIs, but it is said to do it via python binding of those toolkits. Does anyone know of existence of an Interview python bind...

Nice job, Micheal! You did it so fast! May I ask why you are reluctant to numpy dependency? My guess is every one is going to use numpy with NEURON so there should not be a dependency issue. At the same time I am not aware python has a way (with standard library) to represent a double vector. Numpy ...

If I can get the Vectors into python efficiently, I'll switch to python. Do you have a good way to manage to getting hoc's Vectors into python?

An idiom for exploring parameter space is proc explore_params() { local working working = 1 while (working==1) { working = new_params(args2) adjust_params() custom_init() continuerun(tstop) postprocess() savetofiles() } } explore_params(args1) where --new_params() is a function that generates a new...

Good question. Your code executes nc.event when the file is first parsed. However, when you initialize, the event is discarded. To quote from 8.2 Basic initialization in NEURON: finitialize() on page 185 of The NEURON Book: Basic initialization in NEURON . . . carries out several actions: 1. t is s...

Hello, NetCon.event doesn't work for me, could you run the following little script and tell me what's wrong with it? When I hit the "init and run" button, there's no synaptic events at 2.5 ms as I expected ... loaderr = load_file("nrngui.hoc") proc morpho_passive_init () { nseg =...

Hi, I am wondering are more methods planned to be added into SectionList? Say, supporting intersect operation of 2 sectionLists etc... Right now I find myself always doing something like: objref intersec_seclist intersec_seclist = new SectionList() forsec seclist1 { ifsec seclist2 intersec_seclist.a...

I want to include metadata about the vectors I'm writing to a binary file. Can I include information like descriptions of the experiment, type of data(voltage, conductance, current), location of the recording, etc. for each vector? The corollary of this is would be can I use fread in matlab to read...

Hello, I am getting this error message: Assertion failed: file exp2synT.c, line 249 /home/me/nrn59/nrn/i686/bin/nrniv: _tsav <= t near line 0 during running of my model. The mechanism exp2synT.mod used has the following in its NET_RECEIVE block: NET_RECEIVE(weight (uS)) { VERBATIM fprintf(stderr, &...

Hello, I am getting this error message: Assertion failed: file exp2synT.c, line 249 /home/me/nrn59/nrn/i686/bin/nrniv: _tsav <= t near line 0 during running of my model. The mechanism exp2synT.mod used has the following in its NET_RECEIVE block: NET_RECEIVE(weight (uS)) { VERBATIM fprintf(stderr, &q...

I am also interested in parallelized fitting even with only one generator. I have one Multiple Run Fitter as my generator. It tooks minutes to finish one run of the model, I hope this can somehow be improved by rewriting some of my code so when I click on "|| Optimize", NEURON could distri...