NEURON 5.7.159

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NEURON 5.7.159

Post by ted »

On 4/22/2005 Michael Hines <> wrote:
Version 5.7.159 of NEURON is now available from

Some sticklers for detail may notice that the WWW site simply
calls it 5.7, but will then draw reassurance from the fact
that 159 appears in the name of the downloaded file. The
truly fastidious may even recall that the previous standard
release was actually 5.7.71, yet the WWW site called that
one 5.7 too. The rest of us are too busy to fret about
such minutiae.

Everyone, however, is likely to find comfort, if not delight,
in the new features, minor changes, and bug fixes that led
us to announce version 5.7.159. Below we present only the
most salient changes.

Partial List of New Features

1. Import3D tool
This GUI tool will be particularly helpful for modelers who work
with detailed morphometric data. It converts morphometric data
files into anatomically detailed models. The Import3D tool, which
can be brought up by
NEURON Main Menu / Tools / Miscellaneous / Import3D
reads Eutectic, SWC, and Neurolucida classic and Version 3 files,
and can export the data directly into the CellBuilder or generate
a "top level" instance of the model. Its controls and graphical
interface facilitate quick identification of orphan trees and
other errors. It also attempts, often with great success, to
deal intelligently with soma outlines.

2. Graph updating
This is roughly 10X faster than in prior versions. However,
this speedup can also let small models execute too fast for
a good visualization of how shape and space plots evolve.
If this happens, just use
NEURON Main Menu / Tools / MovieRun
to pop up a panel for doing an Init&Run in which each step
takes a specified real time.

3. ChannelBuilder
Many improvements, including
--stoichiometry for ligand-sensitive rates can now be specified
--Borg-Graham style voltage sensitive rates with control points
are available
--voltage sensitive rate tables
--fast fixed step hh rate tables can be used

4. CellBuilder
Improved support for inhomogeneous parameter specification
with the concept of functions over subset domain iterators.
That is, parameters in one or more sections can vary with
location according to a function of some independent variable
(the "subset domain iterator"). Subset domain iterators
provided are: arc distance from soma, physical distance
(radial distance) from a point, and projection onto a straight
line (distance along an axis).

5. Alias names for tool-generated parameters and states
Often, e.g. for graphing or optimization, it is desirable to
refer to a parameter or state that was generated by a tool
such as the LinearCircuitBuilder, NetBuilder, or ChannelBuilder.
Alias names allow the user to assign short, mnemonic names to
such parameters or states, which is much more convenient than
trying to keep track of arbitrary computer-generated strings.

6. hoc enhancements include:
--functions can return object references
--within a procedure, local object references can be declared
with scope limited to that procedure
--address arguments can take the address of local scalars

7. Timer class
This now works for Linux, OS X, and MSWin.
startsw() and stopsw() now have 0.01 sec resolution.

Includes demos of Dynamic Clamp Linear Circuit and
HH stochastic single channels.

9. NetStim.number is now fixed, independent of noise. Thus the
NetStim will turn off after "number" of events even with noise=1.
This differs from previous behavior where the NetStim would turn
off after an interval which was "number" times an individual random
interval. Since the most likely interval is 0, this often resulted
in a short total interval, thus producing far fewer than "number"

10. pt3dstyle()
pt3dstyle(1, x, y, z) introduces a new 3d point which defines
the location of the logical connection point of the section.
This introduces no electrical property change, but allows
correct visualization of the relative placement of a section
with respect to the parent (even when the parent is moved,
changes its length, or is scaled). This is most useful for
dendrites connected to the soma, which visually should have
their proximal ends on the edge of the soma diameter. Since
the connection point is generally 0.5, the x,y,z value should
be the midpoint of the soma centroid.
pt3dstyle(0) sets the old style mode where the section is
translated to the location of the parent connection point.
pt3dstyle() returns the style integer.

11. File class
Now has a flush() method.

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