Search found 25 matches

by Robert Claar
Tue Apr 23, 2024 11:47 am
Forum: Reaction-diffusion in NEURON
Topic: Setting concentrations in rxd.State nodes as a function of concentrations in other rxd.State nodes
Replies: 1
Views: 1114

Re: Setting concentrations in rxd.State nodes as a function of concentrations in other rxd.State nodes

Hello, Just following up on this. It is the last thing I need to figure out to set up my simulations. My other approach not using rxd is to use more POINTERs in my mod files and use of rxd in the way I explain above actually gave me a performance boost in some test simulations. Also the structure of...
by Robert Claar
Sun Apr 14, 2024 1:50 pm
Forum: Reaction-diffusion in NEURON
Topic: Setting concentrations in rxd.State nodes as a function of concentrations in other rxd.State nodes
Replies: 1
Views: 1114

Setting concentrations in rxd.State nodes as a function of concentrations in other rxd.State nodes

Hello, I have been using the rxd module to model paracrine signaling between pancreatic islet cells. While creating a simple example I have run into a problem. I have three cell (nrn.Section) types: A cells that secrete rxd.State G, B cells that secrete rxd.State I, and D cells that secrete rxd.Stat...
by Robert Claar
Wed Feb 21, 2024 7:06 am
Forum: NEURON + Python
Topic: Saving fixed timestep data using cvode variable timestep integration
Replies: 2
Views: 1034

Re: Saving fixed timestep data using cvode variable timestep integration

Thank you Ted for your quick reply! In case anyone wants to just grab some code to do this: NEURON Vectors t_resamp = h.Vector().indgen(start_time, end_time, Dt) v_resamp = h.Vector().interpolate(t_resamp, t_orig, v_orig) Python NumPy Arrays # You have to add Dt to end_time to include ent_time in yo...
by Robert Claar
Tue Feb 20, 2024 1:53 pm
Forum: NEURON + Python
Topic: Saving fixed timestep data using cvode variable timestep integration
Replies: 2
Views: 1034

Saving fixed timestep data using cvode variable timestep integration

Hello, I recently have had to do some filtering and additional processing of my model output that I didn't need to do before and now need to save my recorded data using a fixed timestep. However, I have a dramatic improvement in execution time using cvode compared to using a fixed timestep and I wou...
by Robert Claar
Thu Jan 18, 2024 11:23 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Units in NMODL
Replies: 6
Views: 15385

Re: Units in NMODL

Nevermind, I realized that you already answered my question regarding UNITSOFF and UNITON. I see now that I needed to use UNITSON and UNITSOFF in my BREAKPOINT block instead of ASSIGNED. I assumed that I would do it in ASSIGNED because that is where I declare the units but it makes sense that they c...
by Robert Claar
Wed Jan 17, 2024 1:16 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Units in NMODL
Replies: 6
Views: 15385

Re: Units in NMODL

Thanks for your response, I'll look into that chapter of the NEURON book. WRT to the UNITSOFF and UNITSON: I have plenty of variables in my model that don't have units for which I am using the approach foo () Just so it is explicit that I didn't forget to put units, but that the variable is dimensio...
by Robert Claar
Mon Jan 15, 2024 3:20 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Units in NMODL
Replies: 6
Views: 15385

Re: Units in NMODL

Also I have two follow-up questions regarding the proper way to use UNITSOFF and UNITSON and for best practices for defining custom units. Part of my computational model involves a large equation that has been broken up into several smaller equations for practicality reasons. These smaller equations...
by Robert Claar
Mon Jan 15, 2024 11:05 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Units in NMODL
Replies: 6
Views: 15385

Re: Units in NMODL

Understood, thank you Ted. As for the conversion factor syntax, I actually got that from the units tutorial from the NEURON documentation I linked in my original post. I found that it was the most readable and the tutorial stated it was the most clear way to define conversion factors. ...conversion ...
by Robert Claar
Sat Jan 13, 2024 2:42 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Units in NMODL
Replies: 6
Views: 15385

Units in NMODL

Hello, I have used NEURON to successfully replicate a model ran in XPPAUT. This model is the product of models going back to the 1970s and I have finally traced back through all the prior papers and have done a ton of dimensional analysis to get the units for all my model variables. When attempting ...
by Robert Claar
Tue Dec 19, 2023 2:27 pm
Forum: NEURON + Python
Topic: User defined function to set play vectors
Replies: 2
Views: 38333

Re: User defined function to set play vectors

Sorry, some of my code was incorrect which makes my question seem silly (maybe it still will be when I correct it). The initial chunk of code in my original post above should have been def set_play_vec(cell): data = h.Vector([0,5,17,2,4,38,22,43,1, 1]) time = h.Vector([1,2,3,4,5,6,7,8,9,10]) data.pl...
by Robert Claar
Wed Nov 22, 2023 3:39 pm
Forum: NEURON + Python
Topic: User defined function to set play vectors
Replies: 2
Views: 38333

User defined function to set play vectors

I wanted to make this post to get some clarification about the behavior I am observing and also in case anyone else runs into a similar issue. I am using the Vector.play method to set the values of a parameter inside one of my mod files. I started with a toy example that I found here in the forums h...
by Robert Claar
Tue Sep 12, 2023 11:47 am
Forum: NEURON + Python
Topic: MulRunFitter & Python
Replies: 3
Views: 15068

Re: MulRunFitter & Python

Yup, you are right. I was too narrowly focused. Running

Code: Select all

h.load_file("mulfit.hoc")
along with my other imports allowed me to call

Code: Select all

h.MulRunFitter
Thanks!
by Robert Claar
Sat Sep 09, 2023 1:03 pm
Forum: NEURON + Python
Topic: MulRunFitter & Python
Replies: 3
Views: 15068

MulRunFitter & Python

I have been scouring the forum for a way to use MulRunFitter programmatically in python. I found one post linking a model on modelDB that had a statement in their python code mrf = h.MulRunFitter[0] but when I import h from neuron and list its methods and attributes I do not see MulRunFitter listed....
by Robert Claar
Fri Aug 18, 2023 1:01 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Performing calculations involving values from multiple Sections and mod files
Replies: 0
Views: 49174

Performing calculations involving values from multiple Sections and mod files

Hello, I currently have created a framework built on NEURON to run simulations to investigate Islet of Langerhans cells with variable numbers of different cells/Sections under different conditions (e.g., glucose levels, 3D islet architectures, etc.). Each cell type has a corresponding mod file and e...