Search found 41 matches

by ziemek
Tue Jul 14, 2020 1:00 pm
Forum: Suggestions and Feedback
Topic: Wrong behavior of h.parent_connection()
Replies: 1
Views: 26

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...
by ziemek
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: 169

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.cell.sec ...
by ziemek
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: 169

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 must have seen...
by ziemek
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: 169

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="soma", diam=1...
by ziemek
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: 169

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...
by ziemek
Fri Jul 03, 2020 9:47 am
Forum: NEURON + Python
Topic: Does the usage of the Shape may affect mV readouts?
Replies: 4
Views: 149

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...
by ziemek
Mon Jun 29, 2020 6:29 am
Forum: NEURON + Python
Topic: Does the usage of the Shape may affect mV readouts?
Replies: 4
Views: 149

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&file=/...
by ziemek
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: 651

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","gIhbar_Ih",...
by ziemek
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: 651

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...
by ziemek
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: 498

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...
by ziemek
Wed Jan 08, 2020 7:26 pm
Forum: Modeling networks
Topic: Simulation with external feedback
Replies: 1
Views: 576

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...
by ziemek
Fri Jan 03, 2020 1:15 pm
Forum: Reaction-diffusion in NEURON
Topic: Cell membrane with PMCA pump
Replies: 3
Views: 650

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...
by ziemek
Fri Jan 03, 2020 10:56 am
Forum: Reaction-diffusion in NEURON
Topic: Cell membrane with PMCA pump
Replies: 3
Views: 650

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...
by ziemek
Fri Jan 03, 2020 10:53 am
Forum: Reaction-diffusion in NEURON
Topic: Checking the units
Replies: 2
Views: 389

Re: Checking the units

Thanks for the help! :)
by ziemek
Fri Jan 03, 2020 9:11 am
Forum: Reaction-diffusion in NEURON
Topic: Checking the units
Replies: 2
Views: 389

Checking the units

Hi!

I would like to control explicitly unites in RxD and I have 2 questions:
  • Is there any way to check units of parameters of RxD object?
  • What is the unit of Species d param (diffusion coefficient) ? I guess it's um^2/ms
Thanks for your help!