Search found 43 matches
- Sat Jul 18, 2020 4:01 pm
- Forum: NetPyNE
- Topic: Reinforcement Learning with NetPyNE: a closed-loop with external stimulation
- Replies: 1
- Views: 492
Reinforcement Learning with NetPyNE: a closed-loop with external stimulation
Hi there, After a great tutorial of NetPyNE done by Salvador Dura I wanted to extend my question from the chat :) I would like to make a simulation where I will stimulate a network in a closed-loop with external stimulation similar to Reinforcement Learning paradigm. So let's say I have: The network...
- Sat Jul 18, 2020 3:34 pm
- Forum: NEURON + Python
- Topic: Does the usage of the Shape may affect mV readouts?
- Replies: 5
- Views: 796
Re: Does the usage of the Shape may affect mV readouts?
Sorry Ted, I tried to prepare the code for you and make sure that there is no interference from the core I wrote, but then I switched to a different task, and left it for later, but I will prepare the code next week and let you know.
- Tue Jul 14, 2020 1:00 pm
- Forum: Suggestions and Feedback
- Topic: Wrong behavior of h.parent_connection()
- Replies: 1
- Views: 633
Wrong behavior of h.parent_connection()
The function h.parent_connection() has wrong description and behavior: child.connect(parent(0.7), 0.0) h.parent_connection(child) # returns 0.0 child.parentseg().x # returns 0.7 Reference description of h.parent_connection() indeed points to the y value, however from the description you may expect t...
- Sat Jul 11, 2020 6:13 am
- Forum: NEURON + Python
- Topic: Best practice to run hundreds of simulations / remove all objects between runs
- Replies: 6
- Views: 889
Re: Best practice to run hundreds of simulations / remove all objects between runs
Thanks, that's an interesting comment. The problem arises with the Python object management and garbage collector. With simple objects, the removal is almost on demand, that's why you may see this scenario works well: class Experiment: def __init__(self): self.cell = Cell(name="cell") self...
- Fri Jul 10, 2020 4:23 am
- Forum: NEURON + Python
- Topic: Best practice to run hundreds of simulations / remove all objects between runs
- Replies: 6
- Views: 889
Re: Best practice to run hundreds of simulations / remove all objects between runs
Thanks, I will check the thread you mentioned. According to your own response from the last year (the first response to this thread): https://www.neuron.yale.edu/phpBB/viewtopic.php?f=2&t=1484&p=17633&hilit=delete_section#p17633 delete_section doesn't work in regular Python usage: You mu...
- Thu Jul 09, 2020 3:34 pm
- Forum: NEURON + Python
- Topic: Best practice to run hundreds of simulations / remove all objects between runs
- Replies: 6
- Views: 889
Re: Best practice to run hundreds of simulations / remove all objects between runs
It doesn't work for me. I created a custom object-oriented framework to manage NEURON's Python wrapper. So I have objects such as Cell, Simulation or Record. In a simplistic view, what I done looks like this: class Environment: def run(self): cell = Cell(name="cell") cell.add_sec(name=&quo...
- Thu Jul 09, 2020 9:16 am
- Forum: NEURON + Python
- Topic: Best practice to run hundreds of simulations / remove all objects between runs
- Replies: 6
- Views: 889
Best practice to run hundreds of simulations / remove all objects between runs
Hi there, I'm using Python wrapper. Before each run I would like to setup a fresh environment, so I want to remove all objects (sections, iclamps, netstims, point processes). Is there any way to do that? As indicated in the reference the function h.nrninit() is not helpful, so I see 3 ways: 1. Run e...
- Fri Jul 03, 2020 9:47 am
- Forum: NEURON + Python
- Topic: Does the usage of the Shape may affect mV readouts?
- Replies: 5
- Views: 796
Re: Does the usage of the Shape may affect mV readouts?
Dear Ted, I checked once more the code and I discovered that I use cvode(True), which means that there is a variable timestep. My current readouts for the same model but different compartment are: constant timestep with shape: ms: 50.00000000000341 mV: -8.280244904579009 no shape: ms: 50.00000000000...
- Mon Jun 29, 2020 6:29 am
- Forum: NEURON + Python
- Topic: Does the usage of the Shape may affect mV readouts?
- Replies: 5
- Views: 796
Does the usage of the Shape may affect mV readouts?
Hi there! I use a model of Combe et al. 2018: https://doi.org/10.1523/JNEUROSCI.0449-18.2018 https://senselab.med.yale.edu/modeldb/ShowModel?model=244416 When I removed all tmpo2 variable usage from cell_setup.hoc: link to the file: https://senselab.med.yale.edu/modeldb/ShowModel?model=244416&fi...
- Fri Jan 31, 2020 6:15 am
- Forum: NEURON + Python
- Topic: For loop over section's segments in Python and HOC returns different values
- Replies: 4
- Views: 1188
Re: For loop over section's segments in Python and HOC returns different values
Thanks for the fast and detailed answer! However I work with Hay et al. 2011 model. In one file, they call distribute_channels() function: https://senselab.med.yale.edu/modeldb/showModel.cshtml?model=180373&file=/ShaiEtAl2015/models/L5PCbiophys5.hoc#tabs-2 $o1.distribute_channels("apic"...
- Fri Jan 31, 2020 5:14 am
- Forum: NEURON + Python
- Topic: For loop over section's segments in Python and HOC returns different values
- Replies: 4
- Views: 1188
For loop over section's segments in Python and HOC returns different values
Hi! When I iterate over segments in a section using Python: [x for x in sec] I got the following values: [0.166667, 0.5, 0.833333] However if I iterate over the same section in HOC: for(x) {print x} I got: [0, 0.166667, 0.5, 0.833333, 1] So as you can see - the beginning and the end (0 and 1) are al...
- Fri Jan 24, 2020 5:37 am
- Forum: Parallel NEURON
- Topic: multiple signals to a single POINT_PROCESS and thread safety of a POINTER.
- Replies: 1
- Views: 769
multiple signals to a single POINT_PROCESS and thread safety of a POINTER.
Hi! I have a STDP-like POINT_PROCESS which I want to modulate with additional Dopamine stimulation (another POINT_PROCESS). I created a dummy da.mod POINT_PROCESS which only receives weight which is read by the STDP-like POINT_PROCESS (through POINTER). Then the weight on the dummy da.mod is zero-ou...
- Wed Jan 08, 2020 7:26 pm
- Forum: Modeling networks
- Topic: Simulation with external feedback
- Replies: 1
- Views: 851
Simulation with external feedback
I want to perform multiple runs for the same simulation. Between runs I want to give new stimulations to my neurons, but do not reset the simulation - the network (and its state) must remain the same. The motivation for this comes from the artificial neural network field (ANN). Just like for ANN you...
- Fri Jan 03, 2020 1:15 pm
- Forum: Reaction-diffusion in NEURON
- Topic: Cell membrane with PMCA pump
- Replies: 3
- Views: 1077
Re: Cell membrane with PMCA pump
Thank you for the fast and very detailed response! :) Currently I don't care so much about extracellular space so I wonder if there is any other way to pump out Ca2+? Because I assume that the extracellular computation maybe much more expensive. Also I would like to specify explicitly 2 reactions: c...
- Fri Jan 03, 2020 10:56 am
- Forum: Reaction-diffusion in NEURON
- Topic: Cell membrane with PMCA pump
- Replies: 3
- Views: 1077
Cell membrane with PMCA pump
Hi! I would like to model PMCA pump on the cell membrane. In the Calcium wave example there is a serca pump model: cyt_er_membrane = rxd.Region(h.allsec(), geometry=rxd.DistributedBoundary(1)) serca = rxd.MultiCompartmentReaction(ca[cyt], ca[er], gserca / ((kserca / (1000. * ca[cyt])) ** 2 + 1), mem...