Never mind.
I have just resolved my issues directly with the seclamp MOD file.
Search found 45 matches
- Sat Jun 24, 2023 12:38 pm
- Forum: NEURON + Python
- Topic: Two voltage clamp with a delay
- Replies: 1
- Views: 13593
- Fri Jun 09, 2023 4:48 am
- Forum: NEURON + Python
- Topic: Two voltage clamp with a delay
- Replies: 1
- Views: 13593
Two voltage clamp with a delay
Hi. I need to write a protocol containing: a voltage clamp for x second, followed by a current clamp for y seconds and again a voltage clamp for x second. The functions Vclamp and Seclamp do no have a delay option and, as for the documentation, "Do not insert several instances of this model at ...
- Mon Feb 01, 2021 7:28 am
- Forum: Adding new mechanisms and functions to NEURON
- Topic: A pump MOD file and no concentration inside
- Replies: 3
- Views: 9555
Re: A pump MOD file and no concentration inside
Hello Ted.
Thank you very much.
I was missing the "mass balance equation".
I have added it to the MOD file and everything is working fine.
Best
Stefano
Thank you very much.
I was missing the "mass balance equation".
I have added it to the MOD file and everything is working fine.
Best
Stefano
- Sat Jan 30, 2021 3:00 am
- Forum: Adding new mechanisms and functions to NEURON
- Topic: A pump MOD file and no concentration inside
- Replies: 3
- Views: 9555
A pump MOD file and no concentration inside
Hi. My workflow contains the following steps: a substance is generated into a section (MOD file), is pumped out (MOD file) in a cubic ECS (RxD). Than from the ECS it is pumped (MOD file) into another section where there are a series of reactions (RxD). This works fine. Now I'm trying to substitute t...
- Fri Mar 27, 2020 3:37 pm
- Forum: Adding new mechanisms and functions to NEURON
- Topic: Syncronized concentrations in and out the membrane
- Replies: 1
- Views: 9603
Re: Syncronized concentrations in and out the membrane
Never mind. I have found the underlying issue.
- Thu Mar 26, 2020 11:11 am
- Forum: Adding new mechanisms and functions to NEURON
- Topic: Syncronized concentrations in and out the membrane
- Replies: 1
- Views: 9603
Syncronized concentrations in and out the membrane
Hi. I'm trying to define a MOD file capable of reading the internal concentration of a substance and, with a slim to none delay, "transpose" the same concentration in a ecs. The ecs is defined with rxd.Extracellular(). The substance is generated by a MOD file in the inside and as an rxd.sp...
- Fri Feb 28, 2020 9:13 am
- Forum: Reaction-diffusion in NEURON
- Topic: Multicomp model, ECS, pumps and strange concentrations
- Replies: 3
- Views: 10162
Re: Multicomp model, ECS, pumps and strange concentrations
Thank you. I have modified your code and i can reproduce the strangeness. from neuron import h, rxd from neuron.units import mV, ms h.load_file('stdrun.hoc') soma = h.Section(name='soma') dend0 = h.Section(name='dend0') dend00 = h.Section(name='dend00') dend00.insert('pump') dend1 = h.Section(name='...
- Thu Feb 27, 2020 10:17 am
- Forum: Reaction-diffusion in NEURON
- Topic: Multicomp model, ECS, pumps and strange concentrations
- Replies: 3
- Views: 10162
Multicomp model, ECS, pumps and strange concentrations
Hi. I was checking my RxD code, after implementing it into a multi compartmental model and something very odd came up. I have a substance, produced by a few dendrites and, trough pumps (the same used in the RxD examples) diffused into the ECS. If I cancel the code responsible for the generation of t...
- Thu Jan 16, 2020 4:10 pm
- Forum: NEURON + Python
- Topic: different section names, morphology - h.Section
- Replies: 2
- Views: 2250
Re: different section names, morphology - h.Section
Hi.
Thank you very much, it solved my Netcon issue.
Best
Stefano
Thank you very much, it solved my Netcon issue.
Best
Stefano
- Fri Jan 10, 2020 4:53 pm
- Forum: NEURON + Python
- Topic: different section names, morphology - h.Section
- Replies: 2
- Views: 2250
different section names, morphology - h.Section
Hi. I was looking at a h.topology() of one of my Python/NEURON models and sow something "odd" in the names of the sections. Part of the cell uses a neurolucida morphology, which i load with: cell = h.Import3d_Neurolucida3() cell.input('morphology.asc') In this case the sections are called ...
- Mon Oct 07, 2019 2:52 pm
- Forum: Reaction-diffusion in NEURON
- Topic: NEURON 7.7.1 RxD issue
- Replies: 2
- Views: 10854
Re: NEURON 7.7.1 RxD issue
Hi.
The fix solved the issue.
Thank you.
Best
Stefano
The fix solved the issue.
Thank you.
Best
Stefano
- Thu Oct 03, 2019 8:45 am
- Forum: Reaction-diffusion in NEURON
- Topic: NEURON 7.7.1 RxD issue
- Replies: 2
- Views: 10854
NEURON 7.7.1 RxD issue
Hello. I haven't worked on my RxD model for months and now, after installing the latest NEURON version from git (3 october 2019) to be up to date, my code give rise to an error. The issue is generated by reactions with species placed across different locations, in this case, the soma of two distinct...
- Sat Mar 16, 2019 12:06 pm
- Forum: Reaction-diffusion in NEURON
- Topic: Reactions only when concentration above a certain limit?
- Replies: 1
- Views: 11275
Reactions only when concentration above a certain limit?
Hi. Is there a way to know the concentration of a species, during the simulation, so that it can be used to automatically start specific reactions? I have found this command in the help: https://www.neuron.yale.edu/neuron/static/py_doc/modelspec/programmatic/rxd.html#neuron.rxd.species.SpeciesOnRegi...
- Sun Mar 03, 2019 8:17 am
- Forum: Reaction-diffusion in NEURON
- Topic: diffusion intracellular->extracellular->intracellular
- Replies: 7
- Views: 13706
Re: diffusion intracellular->extracellular->intracellular
Hi. I will soon start working on a particular reaction and, before doing it with a mod file, i tried MultiCompartmentReaction with the lastest code (compiled today). ecs_cell2_membrane = rxd.Region([cell2.soma], name='mem', geometry = rxd.ScalableBorder(1, on_cell_surface=False)) pump_ecs_cell2 = rx...
- Sat Feb 23, 2019 6:43 am
- Forum: Reaction-diffusion in NEURON
- Topic: diffusion intracellular->extracellular->intracellular
- Replies: 7
- Views: 13706
Re: diffusion intracellular->extracellular->intracellular
Hi.
Thank you very much.
Best regards
Stefano
Thank you very much.
Best regards
Stefano