6 Mar
2023
6 Mar
'23
9:45 p.m.
I'm trying to set the initial Calcium concentration for this model with no luck.
I've tried
self.model_params = {'tau_m': 10.0, # membrane time constant (ms)
...
'Ca': 0.1 #initial calcium concentration
}
This method doesn't throw an exception but it also doesn't change the initial
calcium concentration.
I've also tried self.nodes_e.set(Ca=0.1) which throws an exception
nest.lib.hl_api_exceptions.NESTErrors.DictError: DictError in SLI function
SetStatus_id: Unused dictionary items: Ca
Any suggestions?
7 Mar
7 Mar
12:18 a.m.
Hi,
Thank you for writing in. The neuron model having a calcium concentration is something of
a fluke, as it was originally introduced only as a component in simulating structural
plasticity. Therefore, I would recommend using this calcium value only if you are not
otherwise planning to use structural plasticity mechanisms.
I have created a pull request that makes the calcium concentration available for setting:
https://github.com/nest/nest-simulator/pull/2627 as it seems like this should anyway exist
as a feature. Please let me know if this works for you.
In the ideal case we would not use the calcium concentration from the structural
plasticity part of NEST, but track the concentration as part of the neuron model itself
(e.g. in models/iaf_psc....cpp,h). NESTML is a modelling language for NEST that was
created to allow you to easily express custom neuron (and synaptic) dynamics, and to
generate code for it and build an extension module for NEST. Please see here for writing
your neuron model in NESTML: https://nestml.readthedocs.org/
Yours,
Charl
On Mon, Mar 6, 2023, at 21:45, Abbey Durell wrote:
I'm trying to set the initial Calcium
concentration for this model with
no luck. I've tried
self.model_params = {'tau_m': 10.0, # membrane time constant (ms)
...
'Ca': 0.1 #initial calcium concentration
}
This method doesn't throw an exception but it also doesn't change the
initial calcium concentration.
I've also tried self.nodes_e.set(Ca=0.1) which throws an exception
nest.lib.hl_api_exceptions.NESTErrors.DictError: DictError in SLI
function SetStatus_id: Unused dictionary items: Ca
Any suggestions?
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18 Mar
18 Mar
10:40 p.m.
Thanks for this! This worked perfect.
I'm an undergrad doing some research. I'm not a CS major but I know enough to be
dangerous. I was able to compile your code and get it working. I'm curious, do you
know how I would change the connection rules as shown here
(https://nest-simulator.readthedocs.io/en/v3.4/synapses/connection_managemen…)
or should I open a new thread?
20 Mar
20 Mar
10:34 p.m.
Great to hear!
I'm not sure what exactly you mean by changing the connection rules, could you
elaborate? Perhaps a new thread for that would make the most sense.
Cheers,
Charl
On Sat, Mar 18, 2023, at 22:40, Abbey Durell wrote:
Thanks for this! This worked perfect.
I'm an undergrad doing some research. I'm not a CS major but I know
enough to be dangerous. I was able to compile your code and get it
working. I'm curious, do you know how I would change the connection
rules as shown here
(https://nest-simulator.readthedocs.io/en/v3.4/synapses/connection_managemen…)
or should I open a new thread?
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5:05 p.m.
Hi Abbey,
This is an open issue (stale). As far as I am aware, the solution hasn't been merged
with the latest issue. Check it out here:
https://github.com/nest/nest-simulator/issues/2212
In my work, I have been using NEST v2.20.2 as a temporary workaround---where it is quite
straight forward. Depending upon how urgently you need to control autapses and multapses
you can choose to use Sandra's test branch
(https://github.com/nest/nest-simulator/issues/2212#issuecomment-1178877744) or use NEST
v2.20.x.
Best,
Ady
On 3/28/23 2:46 AM, "Abbey Durell" <durell_abbey(a)wheatoncollege.edu>
wrote:
Thanks. I really appreciate the help. I just opened a
new thread.
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31 Mar
31 Mar
6:32 p.m.
Hi Ady,
Thanks for this. I was able to get allow_autapses and the other properties to work as
expected. I also wanted to change the p and rule settings for the node connections.
I've tried using the PR from listed above as a pattern like this:
In conn_builder.cpp I added
if (conn_spec->known(names::make_symmetric)){
updateValue< double >( conn_spec, names::p, p_ );
}
In sp_manager.cpp I added
if ( syn_spec->known( names::p ) )
{
def< double >( conn_spec, names::p, getValue< double >( syn_spec,
names::p ) );
}
Setting the "p" does not seem to make any changes though. Any suggestions?
Thanks,
Abbey
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6 comments
3 participants
participants (3)
-
aadhar.sharma＠saturn.uni-freiburg.de -
Abbey Durell -
Charl Linssen