Fixed. Thanks.
For what it's worth, the tutorials at https://nrn.readthedocs.io are generally more up-to-date than the ones on the NEURON yale site (but we haven't moved all of them over yet).
Search found 267 matches
- Mon Jun 13, 2022 3:56 pm
- Forum: NEURON + Python
- Topic: Minor typo in tutorial
- Replies: 1
- Views: 8662
- Thu Apr 14, 2022 1:09 pm
- Forum: NetPyNE
- Topic: Save rxd concentration
- Replies: 3
- Views: 12668
Re: Save rxd concentration
If you're using NEURON 8.1+, the pure-NEURON solution is to either use h.SaveState (which saves ~everything) or rxd.save_state() and rxd.restore_state(), where the rxd-specific solutions represent state using byte-strings. See the (admittedly brief) discussion at https://nrn.readthedocs.io/en/latest...
- Sat Apr 02, 2022 5:35 pm
- Forum: Reaction-diffusion in NEURON
- Topic: Assignments in time and time-dependent functions
- Replies: 2
- Views: 8712
Re: Assignments in time and time-dependent functions
Unfortunately rxd doesn't directly support expressions that depend on time.
Algebraic expressions should just work. (There's an example of this in the documentation linked below.)
For math functions, you'll want to use rxdmath see the rxdmath discussion in the documentation
Algebraic expressions should just work. (There's an example of this in the documentation linked below.)
For math functions, you'll want to use rxdmath see the rxdmath discussion in the documentation
- Sat Apr 02, 2022 5:23 pm
- Forum: Anatomically detailed models
- Topic: Uploading .swc file through .hoc
- Replies: 3
- Views: 7677
Re: Uploading .swc file through .hoc
Roughly speaking the HOC code would look exactly like the Python, but drop the h. part. That said, HOC and Python are just two different interfaces to the same simulator. You can mix and match. e.g. from Python, you can run a HOC script called my_script.hoc via: h.load_file("my_script.hoc"...
- Fri Mar 25, 2022 11:07 am
- Forum: NetPyNE
- Topic: After updating to MacOS 12.3 Monterey
- Replies: 5
- Views: 13028
Re: After updating to MacOS 12.3 Monterey
This looks like an install from the PKG installer?
In particular, you'll find you have a NEURON folder in Applications. Remove that, and then enter the following into the terminal:
In particular, you'll find you have a NEURON folder in Applications. Remove that, and then enter the following into the terminal:
Code: Select all
pip3 install neuron
- Mon Mar 07, 2022 11:40 am
- Forum: Reaction-diffusion in NEURON
- Topic: Using setpointer() and RXD concentrations
- Replies: 3
- Views: 10193
Re: Using setpointer() and RXD concentrations
Glu.nodes is a list of all Glu nodes. If there is only one, then it is unambiguously safe to use Glu.nodes[0] . Otherwise, you'll want to filter down to a specific node by specifying e.g. segment, possibly region if there are multiple by using () for the filtering... So something like Glu.nodes(som...
- Tue Nov 16, 2021 6:42 pm
- Forum: NetPyNE
- Topic: elaborate visualization of neuron morphologies and synapses
- Replies: 8
- Views: 15443
Re: elaborate visualization of neuron morphologies and synapses
I don't understand the distinction that you're making. Synapses are at some specific location, and using the mark method of a matplotlib/plotly h.PlotShape (or the point_mark method of a h.Shape), you can put points at specific locations in whatever style... e.g. with a matplotlib PlotShape, you can...
- Tue Nov 16, 2021 2:18 pm
- Forum: NetPyNE
- Topic: elaborate visualization of neuron morphologies and synapses
- Replies: 8
- Views: 15443
Re: elaborate visualization of neuron morphologies and synapses
Why not something like:
You can pass regular matplotlib arguments to mark to specify color, marker type, etc.
Code: Select all
ps = h.PlotShape(False)
ps.plot(pyplot).mark(h.soma[0](0.5)).mark(h.apical_dendrite[68](1))
plt.show()
- Wed Jul 28, 2021 6:11 am
- Forum: The GUI
- Topic: Preproducing updating PlotShape() figures in
- Replies: 1
- Views: 8407
Re: Preproducing updating PlotShape() figures in
You don't have to use pyplot or plotly (I prefer the interactivity of plotly) for visualizing PlotShapes. If you have an existing process that worked with interviews windows, you can still use that. If you do use the pyplot version though, you can save to a png in the usual pyplot way, and use that ...
- Mon Jul 19, 2021 5:10 am
- Forum: Reaction-diffusion in NEURON
- Topic: Pass ._ref_concentration to pc.source_var()?
- Replies: 6
- Views: 12397
Re: Pass ._ref_concentration to pc.source_var()?
If you got an error or unexpected result with source_var, can you please post it here?
That should just work.
That should just work.
- Tue Jul 13, 2021 3:28 pm
- Forum: NEURON Announcements
- Topic: 2021 NEURON Online Course
- Replies: 4
- Views: 15619
Re: 2021 NEURON Online Course
You can always check out the YouTube playlist to see what's new and jump directly to videos of interest: https://www.youtube.com/playlist?list=P ... cdRSFwRLOU.
- Tue Jun 29, 2021 10:49 am
- Forum: Reaction-diffusion in NEURON
- Topic: RxD with ParallelContext
- Replies: 3
- Views: 7507
Re: RxD with ParallelContext
Yes. Intracellular reaction-diffusion (both 1D and 3D) parallelizes trivially as all cell-to-cell communication is through the regular spike exchange or gap junction mechanisms. (You still need ParallelContext for those, but you get the full speedup from splitting the cells onto different processors...
- Wed Jun 09, 2021 11:59 am
- Forum: NEURON + Python
- Topic: hh.mod + Python + membrane potential at several points of the soma
- Replies: 5
- Views: 10205
Re: hh.mod + Python + membrane potential at several points of the soma
I suggest in Python using the object-oriented form ( h.hh ) rather than the string ( "hh" ) because it gives you an object whose properties you can explore (although your exploration options depend on whether or not you have the nmodl Python module installed...); i.e. soma.insert(h.hh) You...
- Thu Apr 15, 2021 12:33 am
- Forum: NEURON + Python
- Topic: Simulation Setup when using a List of NetCons, VecStims and Exp2Syn for multiple spike train stimulation
- Replies: 3
- Views: 4815
Re: Simulation Setup when using a List of NetCons, VecStims and Exp2Syn for multiple spike train stimulation
I haven't wrapped my head around all of this, but here's a few points to help: I'm not sure I understand your placement array, but there's a comment "L = Length of each segment = 1/nseg"... the length of a segment is the length of the section (which presumably isn't 1 micron) divided by th...
- Wed Mar 24, 2021 8:34 pm
- Forum: NEURON Announcements
- Topic: 8.0 release plan?
- Replies: 3
- Views: 13059
Re: 8.0 release plan?
We don't have a timeline for an official 8.0 release yet, but:
There was an alpha release in January: https://github.com/neuronsimulator/nrn/ ... s/tag/8.0a
On mac and linux, you can get the nightly development build via: pip install neuron-nightly
There was an alpha release in January: https://github.com/neuronsimulator/nrn/ ... s/tag/8.0a
On mac and linux, you can get the nightly development build via: pip install neuron-nightly