Search found 33 matches

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: 882

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: 1212

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: 1212

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: 1212

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: 1212

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: 1212

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: 1212

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: 1773

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: 9468

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: 11093

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: 9468

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: 1626

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: 1626

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...
by bremen
Sun Mar 25, 2018 7:34 am
Forum: NetPyNE
Topic: Spike source and target sections
Replies: 17
Views: 9468

Re: Spike source and target sections

Hi Salvador. I'm checking that everything, so far, is correct but, looking at the complete output, i saw something strange: Created connection preGid=0, postGid=1, sec= dend_0 , loc=0.7421, synMech=CF_AMPA, weight=1, delay=1.00, threshold=10 Created connection preGid=0, postGid=1, sec= dend_0 , loc=...
by bremen
Sun Mar 25, 2018 6:21 am
Forum: NetPyNE
Topic: Field names are restricted to 31 characters
Replies: 2
Views: 1711

Re: Field names are restricted to 31 characters

Hi Salvador.
Yes that was the cause.
I have reduces the length of the names, involved in the connection description, and the mat file was saved without problems.

Cheers
Stefano