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NSF-Simons NITMB Fellows Program Applications due October 15, 2024 NITMB is seeking early-career researchers who have interest in transforming biological research and inspiring new mathematical discoveries. This opportunity is open to researchers who want to develop mathematical, theoretical, and c...

The Python tutorials illustrate a lot of useful things that can be done with code, and a particular approach to writing code that scales well as program complexity increases. But the KISS principle has its own advantages. Writing less code automatically means writing fewer typos and user-created bug...

Calcium is a key signal in many phenomena, some of which involve calcium diffusion from the site of ca entry (or site of release from organelles) to the site of ca action. Calcium accumulation mechanisms for such cases add even more overhead because more ODEs (or more complex kinetic schemes) are in...

Relax. Numerical integration is computationally expensive. Merely "READing" cai costs nothing by comparison. You could insert hundreds of mechanisms that READ cai into every section of a model cell, with no noticeable effect on run time--unless at least one of those mechanisms involved an ...

Start with a clear concept of what you're trying to do. For your purpose, is it sufficient to represent neurites as right cylinders, or is it important that a neurite's diameter may vary, and its centroid diverge from a straight line, from one end to the other? This decision should be strictly on a ...

I'm working on converting some NML files created in Webknossos into a format that I can import into NEURON. I did not find any ready-made solutions that seemed to give me what I need Have you considered https://github.com/nathantspencer/webknossos_toolkit ? Hard to know the quality and actual utili...

I guess I wasn't sufficiently explicit. By "simple test" I meant dirt simple--no dependence on anything (other than e.g. MPI and your operating system) that that isn't built into NEURON. That means no ion channels other than pas and HH. And no reference to 3rd party modules e.g. "sett...

Documentation says "The cell or artificial cell object is returned that is associated with the global id." Says "cell or artificial cell object", not "(top level) section" (that is, it doesn't say "a section that is not encapsulated in an object"). Is this the...

The electric field at any location p with coordinates (x,y,z) is the gradient of electric potential v at that location. You need to discover the locations of the internal nodes (segment centers) of all sections in your model cell, and then use that information to get COMSOL to tell you what the fiel...

the cell I create is composed of h.SectionList() and not a neuron cell() object First, a bit of terminological clarity. NEURON has no such thing as a "neuron cell() object". It's up to the user to decide what types of cells are to be represented in a network model, then for each of those ...

Wrapping up the example from my post of Thu Aug 22, 2024--during the stimulus, the membrane potentials for compartments A and C approach 0.5 mV and -0.5 mV, respectively. Immediately after the end of the stimulus, the membrane potentials reverse polarity and then decay toward 0 as time advances. The...

The limitations are such as . . . only if the electrotonic length is small enough to neglect longitudinal currents Not so. The mathematical derivation and discussion that are presented in justification of the activating function approach make the tacit assumption that the axon / nerve fiber / neuri...

if anybody reads this post, I suggest the following for discussion about this topic and other interesting ones: 10.1016/j.jphysparis.2011.10.003 An excellent suggestion. For those who don't immediately recognize the DOI, the citation is Joucla S, Yvert B. Modeling extracellular electrical neural st...

Why? Because you don't understand the limitations of the "activating function" approach. Frank Rattay was quite explicit about those limitations in at least one of his many articles, but he didn't reiterate them in all. Your task, if you are willing to accept it, is to track down those lim...

Yes, that's the imprecision of fixed precision floating point arithmetic. Then I remember that few parameters of any biological system are known to more than two significant figures and shudder after looking at the documentation again I ran the following test and see that I can just supply a time h....