www.neuron.yale.edu

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...

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...

Hi.
Thank you very much.

Best regards
Stefano

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...

Hi.
Thank you.

Currently the easiest way to do this is with mod files describing pump mechanism.

I'll try this approach.

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...

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 ...

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...

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...

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

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_...

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

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...

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=...

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