Currently available user-contributed objects

Please refer to the documentation in in the GENESIS Reference Manual Section
"Customizing GENESIS", and in the text files in the genesis/Doc directory,
Customizing.doc, NewGenesis.doc, and NewObjects.doc for instructions on
compiling these libraries into GENESIS.

chemesis - This is a library of biochemical reaction objects for modeling
    calcium concentration, contributed by Avrama Blackwell (avrama@gmu.edu).
    These were used in the paper:
    K.T. Blackwell (2000) Evidence for a Distinct Light-Induced
    Calcium-Dependent Potassium Current in Hermissenda Crassicornis,
    J. Computational Neuroscience, 9: 149-170.

fieldpotential- The 'fieldpotential.tar.gz' file will extract to the
    fieldpotential directory, which contains a description file in the format
    of the GENESIS Reference Manual, the source code files and the library
    startup script file for the two GENESIS objects 'fp-box' and fp_cylinder'.
    These objects, contributed by Armen Sargsyan, calculate the extracellular
    field potential generated by a large population of pyramidal-like cells
    that uniformly fill either a box-shaped or cylindrical shaped region.

    If the cells are identical and are simultaneously and uniformly activated,
    it is not necessary to model a large number of identical cells - it would
    be enough to model just one cell and add CURRENT messages from its
    compartments to fp_box or fp_cylinder object. In case there are several
    cell types (differing in their parameters or stimulation patterns, but
    still uniformly filling the same volume), one cell of each cell type
    should be modeled, and again CURRENT messages from all compartments of all
    modeled cells should be added to a single fp_box or fp_cylinder object.
    Further details are given in fieldpotential/README.

izcell - This directory contains a GENESIS implementation of the Izhikevich
    modified integrate and fire neuron.  With this model, four parameters
    A, B, C, and D can be used to produce a wide variety of action
    potential shapes and firing patterns, with greater computational speed
    than the usual compartmental cell models.  This contains documentation,
    instructions for compiling it into GENESIS, and demos of cell and
    network simulations using the 'izcell' object.

spike - This directory and its subdirectories contain the source code, a
    demonstration script, and documentation for five new GENESIS objects
    contributed by Dieter Jaeger.  These may be used for the generation,
    recording, and analysis of spike trains.  It also contains improved
    versions of the existing freq_monitor and peristim objects.
    (This replaces the older datanal and timetable directories.)

    NOTE: This library has now been included in GENESIS 2.2, as part of
    the device library, so these files are obsolete, unless you are still
    using an earlier version of GENESIS.

spiketools - This library, contributed by Thomas Natschlaeger, contains two
    objects. One object called SpikeTrain is able to produce spikes at
    predefined times as well as to read them from an ASCII file. The second
    object called SpikeRecorder is able to write resulting spike times from
    various spike generating objects into an ASCII file for further processing
    (e.g. with MATLAB).


The following libraries were originally created for use with GENESIS 1.  In
most cases, only small changes in the Makefiles (derived from Usermake and
Libmake) will be needed to use them with GENESIS 2.

ghk - This directory and the subdirectory "ghklib" contain an object which
    calculates the current through a membrane, the reversal potential, and
    the chord conductance of a single ionic species using the Goldman
    Hodgkin Katz equation (constant field equation).  Extensive
    documentation may be found in "ghk.doc" and "ghklib/ghklib.g".  This
    object was submitted by Subbakrishna Shankar.  (NOTE: This has since
    been incororated into GENESIS 2.1, with some modifications.)

spikeinterval - The "spikeinterval" object, submitted by Steve Nowlan,
    calculates interspike intervals.  The input may be either
    continuous-valued action potentials from a compartment, or true spikes,
    as produced by the "spike" or "random" objects.  In the later case, this
    object is more robust than the "freq_monitor" object, which can
    sometimes miss or double-count spikes which last for only a single time
    step.  The "spikeinterval" object also allows output of spike interval
    data to a file.