[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
http://www.neuron.yale.edu/neuron/download
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
http://www.neuron.yale.edu/neuron/static/docs/help/contents.html)
which is no longer being updated.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 
http://www.neuron.yale.edu/neuron/static/new_doc/genindex.html

==========================
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.

hoc

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

NEURON+Python

* 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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