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Repository for continued development of GENESIS 2.4 neural simulator
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genesis-2.4

Repository for continued development of the GENESIS 2.4 neural simulator

The files here have been updated from the November 11, 2014 public release of GENESIS 2.4, from http://genesis-sim.org/GENESIS. The directory 'genesis' contains these, with any changes made since that time.

The 'pgenesis' directory contains the official (May 2019) release of parallel GENESIS (PGENESIS) version 2.4, updated from the December 2014 preliminary release.

The most recent update of this repository contains the May 2019 GENESIS 2.4 update and the official PGENESIS 2.4 release. This is a significant update that has now been packaged as 'genesis-pgenesis-2.4-05-2019.tar.gz' on the GENESIS web site http://genesis-sim.org/GENESIS. Further updates to GENESIS and PGENESIS will continue to appear here.

The May 2019 Update

Recent updates to GENESIS and a merge of the GENESIS/PGENESIS development branch from the U.S. Army Research Laboratory have addressed a number of issues in order to increase its scalability for modeling very large networks of multicompartmental neurons on supercomputers.

Optional installation of a garbage collector library drastically reduces memory usage, allowing for models of millions of neurons. Various run-time errors and integer overflow issues were eliminated. Changes in PGENESIS insured the repeatability of random connections between simulation runs. Updates of GENESIS allow the fast "hsolve" solver to be used with new synaptic plasticity models and measurements of cortical field potentials. The efficient delivery of spike events when hsolve is used with large network models results in increases in simulation speed by factors of 10 to 20.

Previous updates to GENESIS 2.4 are:

The December 6, 2014 update contains new documentation and compiled binaries for using GENESIS under MS Windows with Cygwin.

The December 11, 2016 update contains source code (in genesis/src/newconn) for 'facdep_rules', a new hsolveable short term facilitation/depression synaptic plasticity object. Documentation is in genesis/Doc/facdep_rules.txt.

The July 8, 2017 update contains source code and documentation for 'facdep_rules2', an improved version of 'facdep_rules'.

A new version of genesis/src/sys/system.c fixes compilation problems with recent versions of glibc.

The October 29, 2018 update contains two new objects and documentation for calculating extracellular field potentials when the sources are cells that have been taken over by the fast hsolve solver object. See Doc/efield2.txt and Doc/efield_cells.txt for details.

Python analysis scripts in Scripts/gpython-tools are updated to use either Python 2 or 3.

The 'genesis-binaries' directory contains pre-compilied binary distributions, such as 'genesis-binaries/genesis-2.4-Cygwin-bin.tar.gz'.

Upgrading GENESIS 2.4

If you have an installed GENESIS 2.4 distribution, you can simply download the new files into the appropriate 'genesis' directories. Then, do the usual sequence of 'make clean; make; make install' in genesis/src.

If you would like to download the entire package, click on 'Clone or Download' for genesis-sim/genesis-2.4 then "Download Zip" this will give genesis-2.4-master.zip with:

genesis genesis-binaries pgenesis README.md

Unless you want to install pgenesis also, you can delete it and the genesis-binaries tree.

Alternatively, if you are familiar with using git and want to clone your own copy of the repository, you may do that.

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