BhallaLab/thalamocortical
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This is the PyMOOSE version of Single-column thalamocortical model by Traub et al 2005 with enhancements to add variability in single cell properties as well as synaptic condctances. Code is organized into four directories according to language/simulation system: for: original fortran code g77traub: My update of the g77 port to compile and run on mpif77. nrn: neuron model with additional scripts/updates for dumping information and testing. py: pymoose version. This evolved with moose from 2009 till 2013 when a drastic overhaul in te API was made (dh_branch). By the time the new stuff stabilized, it was too much work to convert the entire model into this new API. Still, the single cell models and ion channels have been translated and are available as part of moose-examples. They are yet to be extensively tested. The files in this diectory are as follows: {Cell}.p - prototype file for cells of type {Cell}. These are in GENESIS prototype format and are read by moose to create the prototype cell model. The prototype is copied in moose to make the cell population. py - channel.py: channel base class {cell}.py - Script defining the Python class for Cell. The __init__ method can take an existing object and a path and make a copy of the existing object in the specified path. trbsim.py - main script for running the simulation. It takes a large number of options. trbnetdata.py: network information from Traub et al 2005. trbnet.py - class TraubNet in this script creates the actual thalamocortical network based on specified cell-to-cell or celltype-to-celltype graphs or with default values from the original Traub et al 2005 model. connection.py - superseeded by trbnet.py kchans.py : all K+ channel definitions nachans.py: all Na+ channel definitions compartment.py: an extension of compartment class cachans.py: Ca2+ channels capool.py: extended version of CaConc archan.py: the combined cation current defaults.ini: default simulation configuration parameters. custom.ini: customizations to override the default simulation parameters. Currently py/data/<date> is where the python code dumps its data.
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