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.txt, NewGenesis.txt, and NewObjects.txt for instructions on compiling these libraries into GENESIS.
This is a library of biochemical reaction objects for modeling calcium concentration, contributed by K. T. (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.
The latest version is available from
http://www.gmu.edu/departments/krasnow/CENlab/chemesis.html
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.
The randomspike2 object was implemented as an alternative to the the randomspike object, which generates different random number sequences when the time step is changed. The randomspike2 object avoids this time step dependent behavior.
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 "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. (NOTE: This object was originally created for use with GENESIS 1. It will require some small changes in the Makefiles (derived from Usermake and Libmake) for use with GENESIS 2.)