Search found 10 matches

by thitsa
Wed Oct 13, 2021 3:02 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: undersampling curves
Replies: 9
Views: 2495

Re: undersampling curves

Yes, I am using a Multiple Run Fitter, sorry I didn't specify that. With the VERBATIM seems to be working fine.
by thitsa
Wed Oct 13, 2021 8:38 am
Forum: Adding new mechanisms and functions to NEURON
Topic: undersampling curves
Replies: 9
Views: 2495

Re: undersampling curves

TITLE undersampling of cai COMMENT undersampling of the simulated cai to match the experimental speed ENDCOMMENT NEURON { SUFFIX undercai USEION ca READ cai RANGE cau,b, caund,tr } PARAMETER { tSta=0.5 } ASSIGNED { cai (milli/liter) cau (milli/liter) caund (milli/liter) b tr plp } INITIAL { b = 1 p...
by thitsa
Mon Oct 11, 2021 9:08 am
Forum: Adding new mechanisms and functions to NEURON
Topic: undersampling curves
Replies: 9
Views: 2495

Re: undersampling curves

load_file("nrngui.hoc") //set the compartment create dend dend{ nseg = 1 L = 5 diam = 2 insert ca12 } access dend //constants celsius = 37 dt = 0.1 steps_per_ms = 1/dt tstop = 8 v_init = -80 //import experimental input objref pulse1 objref InjectMatrix objref InjectFile, voltage InjectFil...
by thitsa
Fri Oct 08, 2021 2:58 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: undersampling curves
Replies: 9
Views: 2495

Re: undersampling curves

Thank you! That's exactly what I need and seems very easy
by thitsa
Fri Oct 08, 2021 8:50 am
Forum: Other questions
Topic: Simulating nanodomains to link SK/BK channels to specific Ca channels
Replies: 6
Views: 1227

Re: Simulating nanodomains to link SK/BK channels to specific Ca channels

Did you manage it? I am also trying to do the same thing. So far I have found that people couple Ca and BK channels by making BK recognize only the Ca coming from a specific channel. For example NEURON { SUFFIX cal USEION ca READ cai, eca WRITE ica USEION cal WRITE ical VALENCE 2: to use it in cal-s...
by thitsa
Thu Oct 07, 2021 4:40 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: undersampling curves
Replies: 9
Views: 2495

Re: undersampling curves

Yes it was indeed supposed to be und(i)=sum(y(n:n+4))/5 But why would it be necessary or desirable to average simulated cai over 0.5 ms intervals? Why not just pick the individual simulated cai values that correpond to integer multiples of 0.5 ms? It is not the same, during the experiment I dont mea...
by thitsa
Thu Oct 07, 2021 7:39 am
Forum: Adding new mechanisms and functions to NEURON
Topic: undersampling curves
Replies: 9
Views: 2495

undersampling curves

I have experimental traces of Ca fluorescent imaging that are sampled at 0.5 ms. I want to fit these recordings with my model but to do that I need to undersample the simulated cai. For example if my simulation dt is 0.1 ms and the duration is 8 ms, in matlab I would write y=cai(1:80) n=1 i=1 while ...
by thitsa
Thu May 21, 2020 2:58 pm
Forum: Optimization
Topic: how to fit channel parameters
Replies: 5
Views: 2262

Re: how to fit channel parameters

It finally works. Instead you... Multiple Run Fitter and nothing happened? Exactly,the model worked fine but wouldnt pop neither the MRF nor graphs when selected from the menu buttons. But then I removed a few things I was not interested in, such as half of the mosinit.hoc (the part I have bellow) a...
by thitsa
Wed May 20, 2020 6:42 am
Forum: Optimization
Topic: how to fit channel parameters
Replies: 5
Views: 2262

Re: how to fit channel parameters

I had a brief look in the tutorials but I could only see how to manualy call the MRF through the Tools button. I tried this with this specific model but nothing pops out when I push any button in the main menu. I was wondering if there is any hoc sample that calls MRF, reads the parameters and start...
by thitsa
Tue May 19, 2020 5:37 pm
Forum: Optimization
Topic: how to fit channel parameters
Replies: 5
Views: 2262

how to fit channel parameters

I am trying to fit my experimentaly measured somatic membrane potential with this model https://senselab.med.yale.edu/ModelDB/ShowModel?model=144526 . I would like to use as parameters the values na_ais, na_soma etc. from the file Cell parameters.hoc (bellow I put the interesting part of it) Not sur...