This is the readme for the models associated with the paper:
Mäki-Marttunen T, Krull F, Bettella F, Hagen E, Næss S, Ness TV, Moberget T, Elvsåshagen T, Metzner C, Devor A, Edwards AG, Fyhn M, Djurovic S, Dale AM, Andreassen OA, Einevoll GT (2018) Alterations in schizophrenia-associated genes can lead to increased power in delta oscillations. Cerebral CortexThis code was contributed by Tuomo Maki-Marttunen, 2015-2018 with the license: CC BY 4.0 Python and NEURON scripts (NEURON is freely available from https://neuron.yale.edu) for running network simulations of layer V pyramidal cells (L5PCs). This ModelDB entry includes two directories each of which contains a readme with usage instructions:
approxhaynet # The main directory with the Python and HOC scripts for simulating the network of L5PCs. Includes files for simulations # with both stationary and oscillatory Poisson background inputs. haymod # An auxiliary directory with similar content as our ModelDB entry 169457. Includes scripts for scaling the variants, # calculating the f-I curves and prepulse-inhibition windowsThe codes have been tested on macOS 10.13.3 running Python 2.7.14 and NEURON 7.5 and Linux 2.6.32-696.18.7.el6.centos.plus.x86_64 running Python 2.7.3, NEURON 7.4 and 7.5 (the LFP simulations cannot be run using NEURON 7.4), and mpirun (Open MPI) 1.6.2. The reduced-morphology L5PC model is based on
Maki-Marttunen et al. 2018 "A stepwise neuron model fitting procedure designed for recordings with high spatial resolution: Application to layer 5 pyramidal cells", J Neurosci Methods. Jan 1;293:264-283HOC-commands for simulations including in vivo-like synaptic firing based on
Hay & Segev 2015, "Dendritic excitability and gain control in recurrent cortical microcircuits", Cerebral Cortex 25(10): 3561-3571and the full-morphology model is based on
Hay et al. 2011, "Models of neocortical layer 5b pyramidal cells capturing a wide range of dendritic and perisomatic active properties", PLoS Comput Biol 7:e1002107Library of variants based on
Maki-Marttunen et al. 2016, "Functional Effects of Schizophrenia-Linked Genetic Variants on Intrinsic Single-Neuron Excitability: A Modeling Study", Biol Psychiatry Cogn Neurosci Neuroimaging. Jan 1;1(1):49-59.