Code for Simulations in Jones SR, Pritchett DL, Sikora MA, Stufflebeam SM, Hamalainen M, Moore CI (2009) Quantitative Analysis and Biophysically Realistic Neural Modeling of the MEG Mu Rhythm: Rhythmogenesis and Modulation of Sensory-Evoked Responses. J Neurophysiol 102:3554-72 These files were contributed by Stephanie Jones. Here is a description of the files: File: sj10-cortex.hoc Creates cells and network (grid of layer 5 and layer 2/3 cells - 100 pyramidal neurons and 35 interneurons in each layer). Contains templates for multi-compartment Layer 5 and Layer 2/3 pyramidal neurons and single compartment inhibitory neurons, and all synaptic conductances in the SI cortical column model. Creates a template "FeedX" that is used to externally drive the network when simulating an "evoked response" (specified in Batch.hoc and scale_ep_thresh.hoc) and/or an "ongoing mu rhythm" (specified in MuBurst_10.hoc and E_FFFBx_fixed_10.hoc). Creates a 2-D grid of cells with all possible connections such that the inhibitory neurons are placed every 2 pyramidal neurons with procedure I_zig_zag. Creates a "dipole current" for each cell (defined in dipole.hoc) and each layer. File: wiring_proc_2Dv2.hoc Procedures for simulating synaptic connections across the local SI cortical column model. These are set up with a Gaussian decay profile for weight and delay from a center of mass in the network. The maximum weights, min delays, synapse type, and post-synaptic targeted dendritic compartment numbers are defined in wiring-SmlFeed-3_7.hoc. File: wiring-SmlFeed-3_7.hoc Defines the fixed connections within the SI network by specifying weights, delays, synapse type, and post-synaptic dendritic target compartments numbers. File noise2D_v2.hoc Procedures for simulating ongoing background noise to the network. The weights are defined in Batch.hoc. File: MuBurst_10.hoc Procedure (make_MuBursts) creates "feedforward (FF)" and "feedback(FB)" external driving input to the SI cortical column model (as FeedX objects) simulating an ongoing "mu" rhythms such that the SI network is driven ever 100ms for (starting at 150ms – to allow the network to reach a steady state – until 1450) by 10 spiking neurons (totaling 150 spike driving neurons over a 1500ms simulation, see Fig 2 in Jones et al. 2009). The weight of these inputs and the delay between FF and FB drive are set in E-FFFBx_10.hoc File: E_FFFBx_fixed_10.hoc Procedure (e_fffbx) defines the weight and delay between the ongoing FF and FB input to the SI network, with a different weight during the period in which an evoked response is simulated (550-850ms). File: scale_ep_thresh.hoc Defines the properties of the simulated "evoked response" input by specifying weights, delays, synapse type, and post-synaptic dendritic target compartments numbers. File dipole.hoc Creates a template that defines the "dipole current" for each cells. The dipole current is the measure of a magnetoencepholography (MEG) signal. File: batch.hoc Calls in all the necessary files, sets default parameters, initial conditions, and runs the simulations creating 26 runs of a 1500ms simulation of an ongoing mu rhythm with a simulated evoked response starting at 450ms. Folder: STATES Contains data files for all of the initial conditions. Folder: mod_files The .mod files. In addition the default hh mechanism is used. Usage instructions: This version of the model was parallelized by Michael Hines. Please check your NEURON version (the message that neuron outputs when started). For example, running nrniv might display NEURON -- VERSION 7.2 (499:91db257165c4) 2011-01-25. The number before the colon needs to be greater than or equal to 499 as above. After unzipping the attached file (on the parallel cluster master) and cd'ing to the created folder compile the mod files with the command nrnivmodl mod_files and then type mpirun -n 4 nrniv -mpi Batch.hoc replacing the 4 above with a number of processors that you have available. 20120409 euler method updated to cnexp in km.mod, kca.mod, cat.mod, ca.mod, and ar.mod; and updated to derivimplicit in cad.mod as per http://www.neuron.yale.edu/phpBB/viewtopic.php?f=28&t=592