www.neuron.yale.edu

Aha--Araya's lab just published another article that combines experimentation with modeling that involved the same model cell, so it is quite likely that they will be able to find the source code. Mitchell DE, Miranda-Rottmann S, Blanchard M, Araya R. Altered integration of excitatory inputs onto th...

The first author is not necessarily the "corresponding author" i.e. the one who takes primary responsibility for communications. Depending on the journal, the corresponding author's identity is usually indicated at the beginning of the paper e.g. near the author list or Abstract, or at the...

Avoid Euler

For clear guidance on what integration method to specify in NMODL code, see Integration methods for SOLVE statements in the NEURON Forum's Hot tips area.

Do what you like, but if your time and effort are worth anything, think hard before using this anatomical data in your models. Especially since so much morphometric data is available from NeuroMorpho.org that is not affected by these artifacts. And if you use flawed anatomical data, when it comes ti...

Most of the information appears not to have been updated in years. That's because most of what needed to be documented hasn't changed in decades. Many changes are expected in NEURON version 9, especially metadata features that will be particularly useful for code introspection; this will doubtless ...

That paper would correspond to ModelDB entry 2488 (modeldb.yale.edu/2488, modeldb.science/2488). The associated source code does not include any swc files. The "Overview" page of the ModelDB entry mentions http://www.cnl.salk.edu/~zach/methods.html and http://www.cnl.salk.edu/~zach/ , but ...

Tell your experimental collaborators the following: 1. There are large (in some cases, huge) discontinuities in the z direction. You can see this yourself--just look at the values in the fifth field of each data line. That alone would make these data not useful for computational modeling. 2. All dia...

Thanks for the quick followup on that. If that particular swc file is available on line, could you please point me to it? I thought that problems with "one point somas" had been resolved a while ago, but apparently not.

we would like to save the last timepoint values of our parameters for a previous simulation and then use those values to initialize a future simulation. For that you will want to use the SaveState class. This is documented in the programmers' reference--see https://nrn.readthedocs.io/en/8.2.2/pytho...

Well, "insert" isn't something that hapens to a segment--it happens to a section. Example: if soma is a section, this statement soma.insert('pas') would insert the pas mechanism into soma. If you try to insert a mechanism into a segment under Python, you should get an error message similar...

OK, this is where it starts to get complicated. If one starts building a model from scratch, one is responsible for all the decisions about the model's anatomical and biophysical properties. That includes, but is not limited to, what ion channels, buffers, pumps etc. it should include. AND the value...

The hoc template is complicated but presumably it worked and was of some interest to you. So let's go back to that and see how to use it from Python and do vector record. After that is working, we can return to the issue of how to implement a cell class with Python. It will be most efficient if you...

The diameter, specific membrane capacitance, and cytoplasmic resistivity of a freshly created section are based on squid giant axon. The paramters of the built-in hh mechanism are based on the famous papers by Hodgkin and Huxley. What else would you like to know about?

Sorry if some of my responses incorrectly estimate your knowledge and experience. While the Forum is a useful tool, in many ways it is quite inadequate compared to a live discussion because of its rather limited semantic bandwidth. A live discussion permits the rapid back-and-forth exchange that is ...

A more important error occurred two statements earlier: in HCN4current_1 = h.ifun(sec_pyr1(0.5)) The syntax for adding a distributed mechanism to a section is different from the syntax for attaching a point process to a section. I could just tell you the correct syntax for the former, but here's a r...