[Comp-neuro] NEURON v. 6.2 available

Ted Carnevale carnevalet at sbcglobal.net
Tue Aug 12 19:35:52 CEST 2008

The newest standard distribution of NEURON is version 6.2, which is
available from http://www.neuron.yale.edu/neuron/install/install.html

This is principally a "bug fix" release, but there have also been
some improvements of features and functionality.  Of the latter, the
most noteworthy have to do with Python.

Changes that affect Python

All communication with hoc from Python is now accomplished uniformly
via the neuron.h object.  In other words, do this first
   import neuron
   h = neuron.h
Then, for example,
   h.Section() returns new section
   h.cas() returns currently accessed section
   h.allsec() is an iterator over all sections

Python allows use of a nrn.Segment object as the argument to a
PointProcess constructor or loc function. That is, IClamp(section(x))
is an alternative to IClamp(x, sec = section).
Also, section(0.5).sec is the section, and section(0.5).x is the arc
location value 0.5.

The following new Vector functions are much (> 50 times !) faster than
a Python loop over the elements:
--Vector.from_python(source) fills the Vector with doubles from a
   Python list or NumPy 1-d array. The Vector is resized and returned.
--Vector.to_python() returns a Python list of doubles.
--Vector.to_python(target) fills the target with doubles from the
   hoc Vector and returns the target object.  Note that if the target
   is a NumPy 1-d array, it must already be sized the same as the Vector.

Other changes that deserve mention

CellBuild.cexport() is public and can be used from hoc with an argument
of 1 (or 0) to force (or prevent) writing the cell info to the
simulation instance.

Vector.play in continuous mode uses linear extrapolation of the last
two time points when a value is requested outside the time domain of
the vector.  This allows more efficient variable time step approach
to a discontinuity as it keeps the first derivative continuous when
cvode asks for a value past the next discontinuity (the discontinuity
event will cause a retreat to the proper time).

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