Search found 10 matches
- Wed Oct 13, 2021 3:02 pm
- Forum: Adding new mechanisms and functions to NEURON
- Topic: undersampling curves
- Replies: 9
- Views: 19033
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.
- Wed Oct 13, 2021 8:38 am
- Forum: Adding new mechanisms and functions to NEURON
- Topic: undersampling curves
- Replies: 9
- Views: 19033
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...
- Mon Oct 11, 2021 9:08 am
- Forum: Adding new mechanisms and functions to NEURON
- Topic: undersampling curves
- Replies: 9
- Views: 19033
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...
- Fri Oct 08, 2021 2:58 pm
- Forum: Adding new mechanisms and functions to NEURON
- Topic: undersampling curves
- Replies: 9
- Views: 19033
Re: undersampling curves
Thank you! That's exactly what I need and seems very easy
- 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: 10310
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...
- Thu Oct 07, 2021 4:40 pm
- Forum: Adding new mechanisms and functions to NEURON
- Topic: undersampling curves
- Replies: 9
- Views: 19033
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...
- Thu Oct 07, 2021 7:39 am
- Forum: Adding new mechanisms and functions to NEURON
- Topic: undersampling curves
- Replies: 9
- Views: 19033
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 ...
- Thu May 21, 2020 2:58 pm
- Forum: Optimization
- Topic: how to fit channel parameters
- Replies: 5
- Views: 10121
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...
- Wed May 20, 2020 6:42 am
- Forum: Optimization
- Topic: how to fit channel parameters
- Replies: 5
- Views: 10121
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...
- Tue May 19, 2020 5:37 pm
- Forum: Optimization
- Topic: how to fit channel parameters
- Replies: 5
- Views: 10121
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...