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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...

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...

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...

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...

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...

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...

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 ...

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 ...

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...

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...

Yup, you are right. I was too narrowly focused. Running along with my other imports allowed me to call Thanks!

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....

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...

That makes sense, thank you!

Hello, I have spent the last hour or so trying to find an old forum post relevant to my question, but can't seem to locate it. I need to run my model for a certain amount of time for it to reach stable outputs. I also am generating a lot of data from my simulations so I am "chunking" my si...