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Python PipelinEs for 9ml (PyPe9) Installation/Demo
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Pype9


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:alt: Documentation Status

Introduction

"PYthon PipelinEs for 9ml (Pype9)" is a collection of software Python pipelines to
simulate networks of neuron models described in NineML (http://nineml.net)
using either Neuron (http://neuron.yale.edu) or NEST (http://nest-simulator.org)
as simulator backends.

Documentation

Brief documentation is available at http://pype9.readthedocs.io

Reporting Issues

Please submit bug reports and feature requests to the GitHub issue tracker
(http://github.com/CNS-OIST/PyPe9/issues).

Unsupported 9ML

9ML aims to be a comprehensive description language for neural simulation. This
means that it allows the expression of some uncommon configurations that are
difficult to implement in NEURON and NEST. Work is planned to make the NEURON
and NEST pipelines in Pype9 support 9ML fully, however until then the following
restrictions apply to models that can be used with Pype9.

  • synapses must be linear (to be relaxed in v0.2)
  • synapses can only have one variable that varies over a projection
    (e.g. weight) (to be relaxed in v0.2)
  • no analog connections between populations (i.e. gap junctions)
    (gap junctions to be implemented in v0.2)
  • only one event send port per cell (current limitation of NEURON/NEST)
  • names given to 9ML elements are not escaped and therefore can clash with
    built-in keywords and some PyPe9 method names (e.g. 'lambda' is a reserved
    keyword in Python). Please avoid using names that clash with C++ or Python
    keywords (all 9ML names will be escaped in PyPe9 v0.2).

Installation

Simulator Backends

Pype9 works with the following simulator backends

on MacOS
^^^^^^^^
On macOS, NEST and Neuron can be installed via the Hombrew package manager (https://brew.sh).
Before installing them with Homebrew it is preferable (but not essential) to install the
Homebrew version of Python with::

brew install python

NEST can be installed with::

brew install --with-python nest

and Neuron can be installed with::

brew install neuron

NB: If you have MPI installed and want to use it to spread your simulation over multiple compute
cores/nodes you should provide the --with-mpi option.

If you don't/can't use Hombrew then see the _from Source Code section below.

on Ubuntu/Debian
^^^^^^^^^^^^^^^^
NEST and Neuron packages are available in the NeuroDebian repository (http://neuro.debian.net),
otherwise please install from source (see _from Source Code).

on Windows
^^^^^^^^^^
Pype9 has not been tested on Windows (and NEST does not run on Windows), so
although Pype9/Neuron may run, it is recommended that you use the Docker
container to run simulations on Windows.

with Docker
^^^^^^^^^^^
There is a Docker image located at https://hub.docker.com/r/tclose/pype9/
that you can pull to run the simulations within a Docker container. See the instructions
in the comments of the Dockerfile in the Pype9 repo for instructions on how to do this.

from Source Code
^^^^^^^^^^^^^^^^
Instructions on how to install NEST from source can be found on official NEST
website, http://www.nest-simulator.org/installation/

Good instructions on how to install Neuron from source can be found in Andrew
Davisons notes here, http://www.davison.webfactional.com/notes/installation-neuron-python/.

In the prereq folder there are also scripts for installing the Neuron and NEST from
source on a Ubuntu image, which may serve as a good reference.

Python

Pype9 depends on the following Python packages

These requirements and the Pype9 package itself can be installed after the
simulator backends are installed (see _Simulator Backends) by downloading/cloning
this repository and using pip::

cd <pype9-repo-dir>
pip install -r requirements.txt .

If you cannot use pip or setuptools you will need to manually install the libninemlnrn
shared library, which contains wrappers for GSL random distribution functions, with::

cd <pype9-repo-dir>/pype9/neuron/cells/code_gen/libninemlnrn
CC=<your-Neuron-c-compiler> ./manual_compile.sh

After that you just need to ensure the root of the Pype9 package is symlinked to your
site-packages directory or on your PYTHONPATH environment variable.

:copyright: Copyright 20012-2016 by the Pype9 team, see AUTHORS.
:license: MIT, see LICENSE for details.

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