regarding netpyni gui upload mod files

[Arpit Shrimankar]

Respected sir,

as i am going through tutorial4 of netpyne

http://www.netpyne.org/tutorial.html#tutorial-4-using-a-simplified-cell-model-izhikevich

i want to use gui for this.to do that i had copy the tut4.py code and paste in the gui python console .

here to run this code i wanted to upload izhi2007b.mod and compile it .so how can i do and upload through gui and run the tut4 ?




in gui ihave uploaded the file through 

but i was unable to locate the file...

so my question is how can i do that ?

awaiting for reply...

thanks ,

arpit

[Salvador Dura]

Hi Arpit, you can upload a .zip with multiple files and folders. It will be available in the /uploads folder. You can then use the "Import" -> "From Python" to select netParams, simConfig and compile mod files. 

[arpitsh...@gmail.com]

i had try as u mentioned and now i can run tut4 .

thank you ...

arpit

[Reza]

Hello guys!

I am trying to have the outputs in tutorial 4 as we have (tut4.py) by adding Izhikevich mechanism besides HH as below;
[PYR_Izhi = {'secs': {}}PYR_Izhi['secs']['soma'] = {'geom': {}, 'pointps': {}} # soma params dict PYR_Izhi['secs']['soma']['geom'] = {'diam': 10.0, 'L': 10.0, 'cm': 31.831} # soma geometry PYR_Izhi['secs']['soma']['pointps']['Izhi'] = { # soma Izhikevich properties 'mod':'Izhi2007b', 'C':1, 'k':0.7, 'vr':-60, 'vt':-40, 'vpeak':35, 'a':0.03, 'b':-2, 'c':-50, 'd':100, 'celltype':1} netParams.cellParams['PYR_Izhi'] = PYR_Izhi # add dict to list of cell parameters]


but, even with making sure the directory for the "izhi2007b.mod" is correct, it seems I cannot use the this mechanism and I get the following error:

[

netParams.cellParams.keys(): odict_keys(['PYR_HH', 'PYR_Izhi']) Start time: 2024-05-20 12:01:33.570876 Creating network of 3 cell populations on 1 hosts...

--------------------------------------------------------------------------- AttributeError Traceback (most recent call last) <ipython-input-65-408b010db006> in <cell line: 115>() 113 114 # Create network and run simulation --> 115 sim.createSimulateAnalyze(netParams = netParams, simConfig = simConfig) 116 sim.analysis.plotRaster()

---

8 frames

---

/usr/local/lib/python3.10/dist-packages/netpyne/cell/compartCell.py in _addPointProcesses(self, sectName, sectParams, cellType, cellVars) 501 sec['pointps'][pointpName] = Dict() 502 loc = pointpParams['loc'] if 'loc' in pointpParams else 0.5 # set location --> 503 Pointp = getattr(h, pointpParams['mod']) 504 pointpObj = Pointp(loc, sec=sec['hObj']) # create h Pointp object (eg. h.Izhi2007b) 505  

AttributeError: 'hoc.HocObject' object has no attribute 'Izhi2007b']


Thank you. 

[Arpit Shrimankar]

hi,

I hope after placing the mod file in the folder ,did you compiled it ?

Sincerely,

Arpit 

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[Reza]

Yes, I have. 

[Reza]

Hello guys!
While I am trying to have Izhikevich mechanism, I get the following error:


[

netParams.cellParams.keys(): odict_keys(['PYR', 'I', 'PYR_Izhi']) Start time: 2024-06-12 09:48:14.172004

Creating network of 2 cell populations on 1 hosts...: 0%| |

--------------------------------------------------------------------------- AttributeError Traceback (most recent call last) <ipython-input-24-5f9905b63eec> in <cell line: 225>() 223 netParams = netParams) 224 sim.net.createPops() # instantiate network populations --> 225 sim.net.createCells() # instantiate network cells based on defined populations 226 sim.net.connectCells() # create connections between cells based on params 227 sim.net.addStims() # add stimulation

---

6 frames

---

/content/netpyne/netpyne/cell/compartCell.py in _addPointProcesses(self, sectName, sectParams, cellType, cellVars) 485 sec['pointps'][pointpName] = Dict() 486 loc = pointpParams['loc'] if 'loc' in pointpParams else 0.5 # set location --> 487 Pointp = getattr(h, pointpParams['mod']) 488 pointpObj = Pointp(loc, sec=sec['hObj']) # create h Pointp object (eg. h.Izhi2007b) 489  

AttributeError: 'hoc.HocObject' object has no attribute 'izhi2007b']

The following shows how I compile this "izhi2007b.mod" file:

------------------------------------------------------------------------------------

%cd /content/

!nrnivmodl

/content INFO : Using neuron-nightly Package (Developer Version) /content cfiles = Mod files: "izhi2007b.mod" Creating 'x86_64' directory for .o files. MODOBJS= ./izhi2007b.o -> Compiling mod_func.cpp -> NMODL ../izhi2007b.mod Translating izhi2007b.mod into /content/x86_64/izhi2007b.cpp Notice: VERBATIM blocks are not thread safe -> Compiling /content/x86_64/izhi2007b.cpp => LINKING shared library "/content/x86_64/./libnrnmech.so" => LINKING executable "/content/x86_64/./special" LDFLAGS are: Successfully created x86_64/special

------------------------------------------------------------------------------------

This is how I added Izhi2007b:

PYR_Izhi = {'secs': {}}

PYR_Izhi['secs']['soma'] = {'geom': {}, 'pointps': {}} # soma params dict

PYR_Izhi['secs']['soma']['geom'] = {'diam': 10.0, 'L': 10.0, 'cm': 31.831} # soma geometry

PYR_Izhi['secs']['soma']['pointps']['Izhi'] = { # soma Izhikevich properties

'mod':'izhi2007b',

'C':1,

'k':0.7,

'vr':-60,

'vt':-40,

'vpeak':35,

'a':0.03,

'b':-2,

'c':-50,

'd':100,

'celltype':1}

netParams.cellParams['PYR_Izhi'] = PYR_Izhi

print('netParams.cellParams.keys(): ', netParams.cellParams.keys())

I would be grateful if you could help me with this.

Thank you. 

Reza