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The main pagehttp://genesis-sim.org provideslinks to documentation and tutorials for the GENESIS 3 (G-3)project. This is intended to be a 21st century neural simulatorwithout the limitations of GENESIS 2 and other simulators that weredeveloped in the late 1980's and 90's. Presently, G-3 remains inthe development stage and its future is uncertain. However, the G-3documentation contains some rather general tutorials on creatingGENESIS GUIs with Python.

The November 2014 release of GENESIS 2.4 was intended to be the lastpackaged GENESIS 2 distribution for download from the GENESIS web site.Updates to GENESIS and PGENESIS are now obtained from the Repositoryfor Continued Development of the GENESIS 2.4 Neural Simulator(https://github.com/genesis-sim/genesis-2.4).

Although GENESIS 2 is user-suported, rather than being beingactively developed, users continue to contribute new libraries,documentation, and simulation scripts. GENESIS continues to bewidely used for large network models consisting ofmulticompartmental neurons, and for projects in modeling courses. Inparticular, there has been an increased use and extension of GENESISand PGENESIS for its original purpose of realistically modelingcortical networks on parallel computers.

What was intended to be a final release of the GENESIS 2 series hascontinued to evolve, with modifications needed to efficientlyimplement synaptic plasticity in large networks and with many contributionsfrom users. This has made it necessary for a new combined May 2019 GENESIS2.4 Update and the PGENESIS 2.4 Final Release.

Although the version number has not changed, recentuser-contributed updates are significant enough to warrant this newcombined packaged distribution. The official release of PGENESIS 2.4is much improved from the December 2014 preliminary release. Recentupdates to GENESIS and a merge of the GENESIS/PGENESIS developmentbranch from the U.S. Army Research Laboratory have addressed a numberof issues that limited its scalability for modeling very largenetworks on high performance computing resources. Optionalinstallation of a garbage collector library drastically reduces memoryusage, allowing for models of millions of neurons. Various run-timeerrors and integer overflow issues were eliminated. Changes inPGENESIS insured the repeatability of random connections betweensimulation runs. Updates of GENESIS since the 2014 release allow thefast "hsolve" solver to be used with new synaptic plasticity modelsand electric field measurements. The efficient delivery of spikeevents when hsolve is used with large network models results inincreases in simulation speed by factors of 10 to 20.

This official release of PGENESIS 2.4 is now available for running large-scalenetwork simulations on supercomputers at the Neuroscience GatewayPortal (NSG). For further information, see thehttps://www.nsgportal.org web page.

The Sourceforge genesis-sim-users mailing list is the best means ofobtaining help with GENESIS. You may subscribeathttps://lists.sourceforge.net/lists/listinfo/genesis-sim-users.Questions posted to the genesis-sim-usersmailing list usually receive a prompt response.

Further updates to GENESIS and PGENESIS 2.4 continue to be made and can be found at theRepository for the continued development of the GENESIS 2.4 neural simulator athttps://github.com/genesis-sim/genesis-2.4

Updates to the original GENESIS 2.4 release include:

• The objects facdep_rules' and an improved version, 'facdep_rules2',provide a new hsolveable short term facilitation/depression synapticplasticity object. These implement a simple phenomenological model ofshort term facilitation and or depression that is suitable for use inlarge network models.

• Two new objects 'efield2' and 'efield_cells' are used for calculatingextracellular field potentials when the sources are cells that havebeen taken over by the fast 'hsolve' solver object. These properlycalculate field potentials from morphologically realistic cells, usingall transmembrane and capacitive currents.

• The par_asc_file object (part of GENESIS, but used with PGENESIS) now hasOUT_OPEN and OUT_WRITE actions, as with serial asc_file.

• Python analysis scripts in Scripts/gpython-tools are updated for Python 3.

• The installation instructions and documentation for GENESIS and PGENESIShave been updated to cover use on supercomputer clusters with theoptional Boehm-Demers-Weiser conservative garbage collector.Its use with GENESIS and PGENESIS has allowed simulations of over onemillion cells, with little increase in memory usage with model size.

• Precompiled binary distributions and documentation for usingGENESIS under Windows with Cygwin

The original GENESIS 2.4 release includes:

• The 'stdp_rules' object, documentation, and Scripts for implementing spike timing dependent plasticity in networks of hsolved cells
• New network connection commands allow distance-dependent connection probabilities and/or weights, or the use of periodic boundary conditions for network connectivity.
• The chemesis library for modeling second messengers and calcium dynamics
• Various user-contributed bug-fixes, utilities, and improvements.
• A new autoconf-based build system, so that a simple "./configure"command will create the appropriate Makefile. This has been testedunder recent Linux and Mac OSX versions. The older method is alsoavailable for platforms not supported by autoconf.
• HTML indexing in the 'genesis' directory and subdirectories, for easybrowsing of the GENESIS directory system and documentation.
• New tutorial Scripts for chemesis, gpython-tools, purkinje, stdp_rules, VAnet2

Official release of PGENESIS (parallel GENESIS) version 2.4

• About PGENESIS 2.4 (README.pgenesis.html)

Some recently added GENESIS 2 tutorials and simulations

Ultimate GENESIS Tutorial Distribution

This is a complete self-paced GENESIS modeling course, combined withGENESIS binary and source distributions and installation instructions.It provides an easy way to get everything by downloading a singlepackage. The latest version may be browsed from this link.

This latest version was used as course materials for the tutorialConstructing biologically realistic neuron and network models withGENESIS at CNS 2014 presented by Hugo Cornelis.

You can download it as:

UGTD2-CNS.tar.gzorUGTD2-CNS.zip

VAnet2 - An efficient hsolvedGENESIS version of the Vogels and Abbott (2005) model that was usedin the Brette et al. (2007) review of network simulators. It serves as atutorial on the use of hsolve with network models in order to achievespeedups by a factor of 10 to 20. The 'VAnet2-batch.g' script isintended to be extended for testing GENESIS spike timing dependentplasticity (STDP) implementations with hsolve. This script would be agood starting point for models that use more realistic cells andconnections.

ACnet2 - An auditory cortexmodel that also serves as a tutorial and template for creatingneocortical network models.

fMRInet Is a variation of the ACnet2 model that illusrates how toprovide unusual stimuli, such as the effects of the electromagneticfields that are produced during an fMRI experiment. This is done by using a'script_out' object to provide the stimulus at clocked intervals.

This page contains older material relating to GENESIS 2.3

The GENESIS web site was established June 30, 1994.