This describes some GENESIS 2 single cell and channel models that have been converted to G-3 NDF format for inclusion in the '/usr/local/neurospaces/models/library' directory. The list of model categories may be seen with the g-shell command 'library_show'. The cells and channels are listed with the commands 'library_show ndf cells' and 'library_show ndf channels'.
The NDF format files in the cells/ directory were produced with the gshell 'sli_load" and 'ndf_save' commands from GENESIS 2 SLI scripts that create a cell '/cell' from prototpe compartments in '/library'. A typical set of commands to generate the file 'simplecell-nolib.g would be:
sli_load simplecell-nolib.g delete /proto delete /output delete /library ndf_save /cell simplecell-nolib.ndf quit
Presently, the command ndf_save /cell or ndf_save /cell/** saves not only the '/cell' element tree, but also the '/library' and the elements created by default in GENESIS 2 '/proto' and '/output'. These trees were deleted before the models were saved.
simplecell-nolib.ndf - The basic two compartment 'simplecell' model that is used in the tests in test-simplecell directory of:
~/neurospaces_project/ns-sli/source/snapshots/0/tests/scripts
and in the GENESIS Modeling Tutorial section "Building a cell the easy way" (http://www.genesis-sim.org/GENESIS/UGTD/Tutorials/genprog/simplecell-tut.html).
The soma compartment contains "squid-like" Na and K channels formed from the channel prototype script 'hh_tchan.g' in GENESIS 2 neurokit/prototypes library. The gate tables of these channels are filled using the 'setupalpha' command with no added options. The dendrite compartment contains and excitatory synchan 'Ex_channel' and an inhibitory synchan 'Inh_channel'. Because of its simplified morphology, this is useful model for testing variations of GENESIS 2 scripting commands that are used in more complex models, and testing their conversion to G-3.
traub91-nolib.ndf - The 'traub91' model is a burst-firing CA3 region hippocampal pyramidal cell, using a linear arrangement of 19 compartments containing active conductances in all compartments.
traub94-nolib.ndf - A burst-firing hippocampal pyramidal cell using 64 asymmetric compartments in a branched geometry, containing active conductances in all compartments. The channels are very similar to the ones used in the 'traub91' model.
traub95-nolib.ndf - A fast spiking hippocampal interneuron, using 51 branched asymmetric compartments containing active conductances in all compartments.
RScell-nolib.ndf - RScell is a single compartment cell used in the RSnet simulation and GENESIS Modeling Tutorial section "Creating large networks with GENESIS" (http://www.genesis-sim.org/GENESIS/UGTD/Tutorials/genprog/net-tut.html).
The channels used are GENESIS 2 adaptations of NEURON models by Destexhe and Par (1999). The functions defining the channels are implemented with a straightforward use of setupalpha to create Na, K, and a muscarinic M current. 'sli_run' and 'ndf_load' plus 'run' both give results that are indistinguishable from GENESIS 2 when plotted.
BDK5cell2-nolib.ndf - The 'BDK5cell2' model is a branched layer 5 cortical pyramidal cell with 9 compartments and 9 voltage or calcium activated channels in the soma.
The original version of this model can be found in the genesis-sim.org Models archive under 'corticalcells' (http://genesis-sim.org/node/110). The detailed description of the channel models and the fitting of parameters was given by Bernander, Douglas and Koch (1992) in the unpublished Caltech CNS Memo 16 (Bernander_etal_CNSmemo16_1992.pdf).
The original GENESIS 2 implementation used symmetric compartments and filled the gate tahles by using the 'setuptau' command. The 'BDKcell2' model is a transformation using appropriately sized asymmetric compartments to give equivalent passive properties. The gate tables are filled using 'setupalpha'. This version produces results consistent with the GENESIS 2 version.
The 'channels' directory contains the files 'Na_hh_tchan.ndf' and 'K_hh_tchan.ndf'. These represent the Hodgkin-Huxley squid fast Na and delayed rectifier K channels used in the 'simplecell' model and many tutorial scripts. The files were generated with sli_load/ndf_save in the same manner as the cell NDF files, with a SLI script that created the two channels. As with the cells, all other elements except the channel to be saved were deleter before saving the channel to NDF.