[Comp-neuro] NEURON 7.3 release, and a new Programmer's Reference

Ted Carnevale ted.carnevale at yale.edu
Wed Apr 3 15:16:37 CEST 2013

1.  The latest standard distribution of NEURON is version 7.3, which is
now availiable from
In addition to lots of internal bug fixes and performance enhancements
over prior versions, NEURON 7.3 has many new features that users will
find helpful.  Below are just a few examples; for a more complete list
see http://www.neuron.yale.edu/phpBB/viewtopic.php?f=22&t=2793

2.  We are transitioning from the old Programmer's Reference (the
"Quick Index", "index", and "contents" links at
which is no longer being updated. For the most up-to-date
documentation on NEURON, see the _new_ Programmer's Reference--
home page http://www.neuron.yale.edu/neuron/static/new_doc/index.html
alphabetical index 

New features in NEURON 7.3

Model specification

* Reaction diffusion in one dimension can now be specified using Python
classes and methods described in the new Programmer's Reference under
Programmatic Model Specification / Basic Reaction-Diffusion. This is a
very active area in NEURON development, and we are working to extend
this to two- and three-dimensional reaction-diffusion. Previously it
was necessary to use NMODL for reaction-diffusion. We expect that
interpreter-based specification of reaction-diffusion will eventually
replace this application of NMODL.


* PtrVector is a new hoc class that implements fast scatter/gather from 
a Vector to other hoc variables.


* The NEURON+Python help system has been much expanded so that the same 
information used to generate the Programmer's Reference is immediately 
available from within a live NEURON session.

Network models and parallel simulations

* NEURON now offers the Random123 pseudorandom sequence generator,
which uses 4 integers to define the random sequence. This is an
excellent random number generator for parallel problems, even better
than MCellRan4.

* Inter-host communication can now use the
ParallelContext.py_alltoall() to send distinct arbitrary Python objects
to all the other ranks.

NEURON Installers

* A single OS X version of NEURON works for lion and mountain lion,
regardless of whether OpenMPI and/or Python has been installed.

* A 64bit version of NEURON is available for MSWin.

Items of particular interest to developers

* The nonvint_block_supervisor is an API to NEURON's internal
algorithms that allows new equations, currents, and conductances to be
introduced by Python and solved by fixed step and adaptive integration.

* LinearMechanism has been extended to allow a Python callable as an
optional first argument that can change the b and g terms in equations
of the form c*dy/dt + g*y = b. This makes it possible for b to become
essentially a nonlinear function of t and y, i.e. allows
LinearMechanism to be used with nonlinear equations.

* neuron.nrn_dll() gives Python access to the C-language internals of
NEURON. This makes all internal NEURON functions, variables, etc.,
available through a ctypes object.

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