commit: 793710fde6c3d193a249b5ab6a943a1c596b6abe Author: Andrei Zavada <johnhommer <AT> gmail <DOT> com> AuthorDate: Wed Feb 18 01:10:53 2015 +0000 Commit: Christoph Junghans <ottxor <AT> gentoo <DOT> org> CommitDate: Wed Feb 18 01:10:53 2015 +0000 URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=793710fd
initial ebuild for sci-biology/cnrun CNrun is a neuronal network simulator, with these features: * a conductance- and rate-based Hodgkin-Huxley neurons, a Rall and Alpha-Beta synapses; * a 6-5 Runge-Kutta integration method: slow but precise, adjustable; * Poisson, Van der Pol, Colpitts oscillators and interface for external stimulation sources; * NeuroML network topology import/export; * logging state variables, spikes; * implemented as a Lua module, for scripting model behaviour (e.g., to enable plastic processes regulated by model state); * interaction (topology push/pull, async connections) with other cnrun models running elsewhere on a network, with interactions (planned). --- sci-biology/cnrun/ChangeLog | 6 ++++++ sci-biology/cnrun/cnrun-2.0.2.ebuild | 23 +++++++++++++++++++++++ sci-biology/cnrun/metadata.xml | 29 +++++++++++++++++++++++++++++ 3 files changed, 58 insertions(+) diff --git a/sci-biology/cnrun/ChangeLog b/sci-biology/cnrun/ChangeLog new file mode 100644 index 0000000..34e6696 --- /dev/null +++ b/sci-biology/cnrun/ChangeLog @@ -0,0 +1,6 @@ +# ChangeLog for sci-biology/cnrun +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 18 Jan 2015; Andrei Zavada <johnhom...@gmail.com> cnrun-2.0.2.ebuild: + Initial packaging for gentoo. diff --git a/sci-biology/cnrun/cnrun-2.0.2.ebuild b/sci-biology/cnrun/cnrun-2.0.2.ebuild new file mode 100644 index 0000000..dd02af2 --- /dev/null +++ b/sci-biology/cnrun/cnrun-2.0.2.ebuild @@ -0,0 +1,23 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI="5" + +DESCRIPTION="A NeuroML-enabled, neuronal network simulator w/ conductance- and rate-based HH neurons" +HOMEPAGE="http://johnhommer.com/academic/code/cnrun"; +SRC_URI="http://johnhommer.com/academic/code/cnrun/source/${P}.tar.xz"; + +LICENSE="GPL-2+" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +RDEPEND="dev-libs/libxml2 + dev-lang/lua + sci-libs/gsl" + +DEPEND="${RDEPEND}" + +src_configure() { + econf --bindir="${EPREFIX}"/bin +} diff --git a/sci-biology/cnrun/metadata.xml b/sci-biology/cnrun/metadata.xml new file mode 100644 index 0000000..48dcd97 --- /dev/null +++ b/sci-biology/cnrun/metadata.xml @@ -0,0 +1,29 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>johnhom...@gmail.com</email> + <name>Andrei Zavada</name> + </maintainer> + <longdescription> + CNrun is a neuronal network simulator, with these features: + + * a conductance- and rate-based Hodgkin-Huxley neurons, a Rall and + Alpha-Beta synapses; + * a 6-5 Runge-Kutta integration method: slow but precise, adjustable; + * Poisson, Van der Pol, Colpitts oscillators and interface for + external stimulation sources; + * NeuroML network topology import/export; + * logging state variables, spikes; + * implemented as a Lua module, for scripting model behaviour (e.g., + to enable plastic processes regulated by model state); + * interaction (topology push/pull, async connections) with other + cnrun models running elsewhere on a network, with interactions + (planned). + + Note that there is no `cnrun' executable, which existed in cnrun-1.*. + Instead, you write a script for your simulation in Lua, and execute + it as detailed in /usr/share/lua-cnrun/examples/example1.lua. + </longdescription> +</pkgmetadata>
