Search found 24 matches
- 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: 0
- Views: 32
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...
- Wed Feb 21, 2024 7:06 am
- Forum: NEURON + Python
- Topic: Saving fixed timestep data using cvode variable timestep integration
- Replies: 2
- Views: 478
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...
- Tue Feb 20, 2024 1:53 pm
- Forum: NEURON + Python
- Topic: Saving fixed timestep data using cvode variable timestep integration
- Replies: 2
- Views: 478
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...
- Thu Jan 18, 2024 11:23 am
- Forum: Adding new mechanisms and functions to NEURON
- Topic: Units in NMODL
- Replies: 6
- Views: 14105
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...
- Wed Jan 17, 2024 1:16 pm
- Forum: Adding new mechanisms and functions to NEURON
- Topic: Units in NMODL
- Replies: 6
- Views: 14105
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...
- Mon Jan 15, 2024 3:20 pm
- Forum: Adding new mechanisms and functions to NEURON
- Topic: Units in NMODL
- Replies: 6
- Views: 14105
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...
- Mon Jan 15, 2024 11:05 am
- Forum: Adding new mechanisms and functions to NEURON
- Topic: Units in NMODL
- Replies: 6
- Views: 14105
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 ...
- Sat Jan 13, 2024 2:42 pm
- Forum: Adding new mechanisms and functions to NEURON
- Topic: Units in NMODL
- Replies: 6
- Views: 14105
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 ...
- Tue Dec 19, 2023 2:27 pm
- Forum: NEURON + Python
- Topic: User defined function to set play vectors
- Replies: 2
- Views: 25757
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...
- Wed Nov 22, 2023 3:39 pm
- Forum: NEURON + Python
- Topic: User defined function to set play vectors
- Replies: 2
- Views: 25757
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...
- Tue Sep 12, 2023 11:47 am
- Forum: NEURON + Python
- Topic: MulRunFitter & Python
- Replies: 3
- Views: 10091
Re: MulRunFitter & Python
Yup, you are right. I was too narrowly focused. Running along with my other imports allowed me to call
Thanks!
Code: Select all
h.load_file("mulfit.hoc")
Code: Select all
h.MulRunFitter
- Sat Sep 09, 2023 1:03 pm
- Forum: NEURON + Python
- Topic: MulRunFitter & Python
- Replies: 3
- Views: 10091
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....
- 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: 36581
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...
- Thu Jul 06, 2023 4:53 pm
- Forum: NEURON + Python
- Topic: h.continuerun() behavior different when cvode is active
- Replies: 2
- Views: 10982
Re: h.continuerun() behavior different when cvode is active
That makes sense, thank you!
- Mon Jun 26, 2023 5:06 pm
- Forum: NEURON + Python
- Topic: h.continuerun() behavior different when cvode is active
- Replies: 2
- Views: 10982
h.continuerun() behavior different when cvode is active
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...