Search found 36 matches

by ziemek
Fri Jul 03, 2020 9:47 am
Forum: NEURON + Python
Topic: Does the usage of the Shape may affect mV readouts?
Replies: 3
Views: 116

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: 3
Views: 116

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: 637

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: 637

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: 486

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: 568

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: 639

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: 639

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: 380

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: 380

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!
by ziemek
Thu Dec 19, 2019 12:43 pm
Forum: UNIX/Linux
Topic: Which environmental variables do I need to setup for NEURON to work after rpm installation without sudo with cpio
Replies: 1
Views: 619

Which environmental variables do I need to setup for NEURON to work after rpm installation without sudo with cpio

Since I have no sudo on CentOS I installed rpm package with: rpm2cpio nrn-7.7.x86_64-linux.rpm | cpio -id which installed neuron in $HOME/usr/local/nrn. I also added ~/usr/local/nrn/x86_64/bin to my $PATH. But when I execute nrnivmodl i have an error: cadif_rectangle.mod cadif_rectangle.mod make: /u...
by ziemek
Wed Dec 18, 2019 3:25 pm
Forum: Reaction-diffusion in NEURON
Topic: The best practice of Ca2+ pumps on the cell membrane implemented in RxD model
Replies: 3
Views: 531

Re: The best practice of Ca2+ pumps on the cell membrane implemented in RxD model

Yes, that was my assumption - if I have any *.mod file - it would be easier. But there are 3 things which worries me: 1. cad.mod computes cai for the inner shell (depth 0.1) defined in the mod. Since I created Ca2+ shells with RxD - they are defined as different objects - so i suppose their concentr...
by ziemek
Wed Dec 18, 2019 7:10 am
Forum: Reaction-diffusion in NEURON
Topic: The best practice of Ca2+ pumps on the cell membrane implemented in RxD model
Replies: 3
Views: 531

The best practice of Ca2+ pumps on the cell membrane implemented in RxD model

Hi! Ca2+ wave tutorial and Neymotin et al, 2015 model contain Cyt<->ER diffusion of Ca2+ through pumps implemented in RxD. So I wonder what is the best practice to implement Ca2+ pumps on the cell membrane in RxD? Should it be as well implemented in RxD, or it should based on ica current as it is in...
by ziemek
Tue Dec 17, 2019 11:54 am
Forum: UNIX/Linux
Topic: CentOS with RxD and NEURON build from source
Replies: 1
Views: 553

CentOS with RxD and NEURON build from source

Hi! I try to run NEURON on cluster for parallel computing with CentOS. I built the code from source, with iv (even though I can't use GUI through console). NEURON is working in general, but when I try to execute code with rxd - it crashes on the line: from neuron import rxd The error message looks l...
by ziemek
Thu Dec 12, 2019 5:25 am
Forum: Anatomically detailed models
Topic: Precise 3D morphology
Replies: 6
Views: 850

Re: Precise 3D morphology

Thanks for a very precise answer. I will go through references, but in the case of Neurolucida (which I'm actually not familiar with) - does it use as well truncated cones architecture? I'm asking because whenever I see its reconstructions with spines, it seems to be very precise.