The NEURON Book: errata and discussion

[neuromau]

What about this? P. 114, section 5.6.4: Working with range variables. It gives an example for iterating over each node including 0 and 1, and then a 'variant' that excludes 0 and 1, but the variant is the same as the original syntax:

Code: Select all

for (var) stmt

Thanks,
Marianne

[ted]

Another one! To exclude the nodes at 0 and 1, the statement should be

Code: Select all

for (var, 0) stmt

[ted]

Several NMODL listings with statements that extend over more than one line contain backslash characters ("\").* This will generate an error message about an "illegal block" when compiled with mknrndll or nrnivmodl--because NMODL does not use backslash or any other character as a "line continuation character." Just omit the backslash and the code will compile properly.

Thanks to nianwosuh for pointing out this error!

*--examples include:
Listing 9.8 on page 249
and
examples of LONGITUDINAL_DIFFUSION usage page 253
the revised KINETIC block on page 259
the code excerpt on page 279

[ted]

It appears that the code used to generate Fig. 10.2 in The NEURON Book (time course of presynaptic cai and other variables in a model of graded transmitter release) employed different values for L and diam of the presynaptic terminal than what is described on page 269.

preterm (name of the section that is the presynaptic terminal) is described as "a 1 um diameter hemisphere" so
volume = 1/2 * 4/3 * PI *(1/2)^3 = PI/12 um3
area = 1/2 * 4*PI*(1/2)^2 = PI/2 um2 (curved surface only; ignore the area of the flat face which in this model is presumed to be free of ion channels)

A section with length L and diameter diam has
volume = PI*L*(diam/2)^2 = PI*L*diam^2 / 4
area = PI*L*diam
so
diam = 4*volume/area = 2/3 um
L = area/PI/diam = 3/4 um
and surface/volume ratio is 6/um

But looking at the source code used to generate the figure I see that somehow the actual values employed were
diam = 1/PI/2 = 0.1591549 . . . um
L = 1 um
so the surface area of the presynaptic terminal was actually 0.5 um2
and its volume was 0.01989436 . . . um3
so surface/volume ratio was much larger--more than 25.

This means that the computational model generated peak calcium concentrations that were too large--maybe more than 4 times too large.

This will be corrected in the second edition of The NEURON Book.

[ted]

Page 151 paragraph 2 line 2
Fig. 1.27
should be
Fig. 1.29