Search found 35 matches

by bremen
Mon Oct 07, 2019 2:52 pm
Forum: Reaction-diffusion in NEURON
Topic: NEURON 7.7.1 RxD issue
Replies: 2
Views: 120

Re: NEURON 7.7.1 RxD issue

Hi.

The fix solved the issue.
Thank you.

Best
Stefano
by bremen
Thu Oct 03, 2019 8:45 am
Forum: Reaction-diffusion in NEURON
Topic: NEURON 7.7.1 RxD issue
Replies: 2
Views: 120

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...
by bremen
Sat Mar 16, 2019 12:06 pm
Forum: Reaction-diffusion in NEURON
Topic: Reactions only when concentration above a certain limit?
Replies: 1
Views: 938

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...
by bremen
Sun Mar 03, 2019 8:17 am
Forum: Reaction-diffusion in NEURON
Topic: diffusion intracellular->extracellular->intracellular
Replies: 7
Views: 1340

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...
by bremen
Sat Feb 23, 2019 6:43 am
Forum: Reaction-diffusion in NEURON
Topic: diffusion intracellular->extracellular->intracellular
Replies: 7
Views: 1340

Re: diffusion intracellular->extracellular->intracellular

Hi.
Thank you very much.

Best regards
Stefano
by bremen
Sat Feb 16, 2019 5:01 pm
Forum: Reaction-diffusion in NEURON
Topic: diffusion intracellular->extracellular->intracellular
Replies: 7
Views: 1340

Re: diffusion intracellular->extracellular->intracellular

Hi. After some more testing i have some questions: 1) I have recorded a vector, pointed to the outside name of the substance "self.soma(0.5)._ref_xo", to record the concentration in the ecs. The resulting graph is congruent with my expectation since it records only a part of the entire diffusion. ht...
by bremen
Tue Feb 12, 2019 8:22 am
Forum: Reaction-diffusion in NEURON
Topic: diffusion intracellular->extracellular->intracellular
Replies: 7
Views: 1340

Re: diffusion intracellular->extracellular->intracellular

Hi.
Thank you.
Currently the easiest way to do this is with mod files describing pump mechanism.
I'll try this approach.
by bremen
Sun Feb 10, 2019 10:32 am
Forum: Reaction-diffusion in NEURON
Topic: diffusion intracellular->extracellular->intracellular
Replies: 7
Views: 1340

Re: diffusion intracellular->extracellular->intracellular

Hi. I was able to solve most of the workflow but I'm missing something in the "MultiCompartmentReaction". I'm trying to release the substance X, correctly generated in the internal region of cell_1, to the ecs. With the MultiCompartmentReaction wrote in this way: rxd.MultiCompartmentReaction(sub_x[i...
by bremen
Thu Feb 07, 2019 11:25 am
Forum: Reaction-diffusion in NEURON
Topic: diffusion intracellular->extracellular->intracellular
Replies: 7
Views: 1340

diffusion intracellular->extracellular->intracellular

Hi. After reading the 2018 paper, i was wondering if is feasible, with rxd.extracellular, to reproduce the following situation: A substance X is internally produced by cell_1. It is pumped outside the membrane into the extracellular space. Here it diffuses until it reaches cell_2. It is then uptake ...
by bremen
Sat Jun 23, 2018 5:09 am
Forum: UNIX/Linux
Topic: Make error on Piz Daint cluster
Replies: 0
Views: 1851

Make error on Piz Daint cluster

Hi. I'm trying to compile NEURON on Piz Daint (Cray) but i have encountered an error during the make. export MPICC=cc ./configure --prefix=`pwd` --without-x --with-paranrn --without-nmodl --without-memacs CC=cc CXX=CC With this configure i obtain and "undefined reference to symbol '__tls_get_addr@@G...
by bremen
Sat May 12, 2018 12:07 pm
Forum: NetPyNE
Topic: Spike source and target sections
Replies: 17
Views: 9772

Re: Spike source and target sections

Hi. I have changed the previous code with something simpler but there is still something odd. Let assume to connect 10 B_cell to 1 C_cell on the same section ['soma'] with 10 synPerConn. netParams.connParams['B_pop_2_C_pop] = {'preConds': {'pop': 'B_pop'}, 'postConds': {'pop': 'C_pop'}, 'sec': ['som...
by bremen
Sat Apr 28, 2018 4:05 pm
Forum: NetPyNE
Topic: VERSION RELEASES
Replies: 16
Views: 11368

Re: VERSION RELEASES

Hi Salva.

I think there is an issue with pip --upgrade to 0.7.8. It says that the latest available is the 0.7.7

Cheers
Stefano
by bremen
Sat Apr 28, 2018 3:51 pm
Forum: NetPyNE
Topic: Spike source and target sections
Replies: 17
Views: 9772

Re: Spike source and target sections

Hi Salva. I have a doubt about this for cycle. pop_C = 10 for p in range(0,len(pop_C)): netParams.connParams['Pop_B->Pop_C'+str(p)] = {'preConds': {'pop': 'Pop_B'}, 'postConds': {'pop': 'Pop_C'}, 'weight': 1, 'sec': location[p], 'delay': 0.1, 'loc': 0.5, 'synsPerConn' : 30, 'connList': [Pop_B_2_Pop_...
by bremen
Sat Apr 28, 2018 3:15 pm
Forum: NetPyNE
Topic: Slow speed to save sim results
Replies: 2
Views: 1710

Re: Slow speed to save sim results

Hi Salva.
- if you only need the traces, you can reduce the save time by setting cfg.saveDataInclude = ['simData']
With this option and saveMat, the saving time was reduced over 100 times. From minutes/hours to a few seconds.
It is great.

Thank you

Best
Stefano
by bremen
Sat Apr 21, 2018 10:32 am
Forum: NetPyNE
Topic: Slow speed to save sim results
Replies: 2
Views: 1710

Slow speed to save sim results

Hi Salvador. I'm saving the voltage traces of about 200 neurons, into a mat file, and the time to save them can be up to 3 time the total run time of the simulation. The file is saved at the same rate (about 2-3MB/s) on clusters and on workstations with SSD drives, and it is independent on the numbe...