Search found 25 matches

by Robert Claar
Mon Jun 26, 2023 5:06 pm
Forum: NEURON + Python
Topic: h.continuerun() behavior different when cvode is active
Replies: 2
Views: 21053

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...
by Robert Claar
Sat Feb 25, 2023 4:19 pm
Forum: NEURON + Python
Topic: Using external file to set parameter value in MOD file
Replies: 3
Views: 21396

Re: Using external file to set parameter value in MOD file

Thank you for the response! I am not currently using cvode.event and FInitializeHandler, but I have the documentation flagged to look into it. If you could provide an example that would be great. In the meantime I will look into Vector.play and all cells will be exposed to the same concentration of ...
by Robert Claar
Fri Feb 17, 2023 9:05 am
Forum: NEURON + Python
Topic: Using external file to set parameter value in MOD file
Replies: 3
Views: 21396

Using external file to set parameter value in MOD file

Hello there, I am creating a multicell model of pancreatic islet cells using NEURON+Python. In this model there are 4 parameters for ATP sensitive potassium channel conductances (gKATP) whose values are changed to model changes in glucose levels throughout the islet. Ideally what we would like to do...
by Robert Claar
Sat Aug 28, 2021 3:50 pm
Forum: Reaction-diffusion in NEURON
Topic: Using NEURON to model a system of endocrine cells
Replies: 3
Views: 15010

Re: Using NEURON to model a system of endocrine cells

Thank you in advance for reading through this monster of a post/question. I am still working on the same project I posted about above a year ago and am now stuck on something different. We are again using NEURON to recreate and add to a model created using XPPAUT. We have replicated the results from...
by Robert Claar
Thu Jun 10, 2021 3:12 pm
Forum: Suggestions and Feedback
Topic: Repeated/Wrong Text in NEURON extension to NMODL Doumentation
Replies: 1
Views: 51304

Repeated/Wrong Text in NEURON extension to NMODL Doumentation

I'm not sure if this belongs here but wanted to point it out. I was reading to try and figure out some reaction diffusion processes in a model I'm working on and found this webpage https://www.neuron.yale.edu/neuron/static/py_doc/modelspec/programmatic/mechanisms/nmodl2.html. The Valence and Point_P...
by Robert Claar
Fri Jul 03, 2020 8:21 am
Forum: Reaction-diffusion in NEURON
Topic: Using NEURON to model a system of endocrine cells
Replies: 3
Views: 15010

Re: Using NEURON to model a system of endocrine cells

Thank you so much, this helps a lot. I will try to create my own script inserting the mechanisms I have created.
by Robert Claar
Tue Jun 30, 2020 2:58 pm
Forum: Reaction-diffusion in NEURON
Topic: Using NEURON to model a system of endocrine cells
Replies: 3
Views: 15010

Using NEURON to model a system of endocrine cells

Hello, I am new to NEURON (and programming in general) and I am working with my lab partner to build a model of pancreatic islet cells using previous models not created in the NEURON framework. These previous models didn't have a spatial component and my lab partner and I want to utilize NEURON to a...
by Robert Claar
Mon Jun 29, 2020 1:45 pm
Forum: NEURON hacks
Topic: Using NetCon where voltage is not the threshold variable
Replies: 3
Views: 16214

Re: Using NetCon where voltage is not the threshold variable

Thanks Ted, We would like the hormonal concentration across our endocrine cells to most closely resemble a continuum with every cell being both a source of a hormone and sink of 3 hormones/reaction diffusion species (the hormone the cell secretes + the hormones secreted from two other cell types). T...
by Robert Claar
Sun Jun 28, 2020 5:54 pm
Forum: Hot tips
Topic: NEURONS v is different than mine
Replies: 1
Views: 12826

NEURONS v is different than mine

Hello, I am in the process of replicating two models in the NEURON framework to extend them in certain ways. At first I wrote one of the models into a single mod file. I didn't use NEURONs built-n v (membrane voltage), I wrote my own differential equation to calculate membrane potential, and I didn'...
by Robert Claar
Thu Jun 25, 2020 8:52 am
Forum: NEURON hacks
Topic: Using NetCon where voltage is not the threshold variable
Replies: 3
Views: 16214

Using NetCon where voltage is not the threshold variable

Hello, I am an incoming graduate student building a model of a network of endocrine cells and how the hormones they secrete affect each other. Using the NetCon object seemed like a great way to connect the different cell types and weight the connections. I want the cells to read the hormone concentr...