jsherfey

% Minimal multi-layer PFC model with Poisson-based inputs
% wd: ~/models/dynasim/mechanisms
% gist: https://gist.github.com/jsherfey/8010719b0461ddc961829251389a4f0b

% Purpose: shareable basis for extended PFC-related models
% Default model: "L2/3" (E-Ed,FS,LTS) -> "L5/6" (E-Ed,FS), with Poisson-based inputs.
% Easily extends to more layers with different populations per layer.

% move to directory storing mechanism files and associated function PFC_cell_specification
mechanism_dir='~/models/dynasim/mechanisms';

jsherfey

% Explore soft WTA and persistence in spiking network with RNN-based assemblies 
% wd: ~/models/dynasim/sandbox
% gist: https://gist.github.com/jsherfey/987453dccf5135631456

% Purpose: simulate injected currents (steady or ramping) to two competing 
% assemblies E1 & E2 in E/I network with goal of determining factors controlling 
% persistence and competition.

% ** transition to competition: I->E.gGABA=(.5-1) and E->I.gAMPA=(.5-1) ** 

jsherfey

% matfiles={'ACd-net_Etype2_PFCcell_homo_tauI5ms_Estim3_f0-10-60Hz_10realizations.mat',...
%           'ACd-net_Etype2_PFCcell_homo_tauI13ms_Estim3_f0-10-60Hz_10realizations.mat',...
%           'ACd-net_Etype7_PFCcell_hetero_tauI5ms_Estim3_f0-10-60Hz_10realizations.mat',...
%           'ACd-net_Etype7_PFCcell_hetero_tauI13ms_Estim3_f0-10-60Hz_10realizations.mat'};

matpath='/home/jason/models/dnsim/SparsePINB/resonance';
% scripttag='ACd-net'; batchtag='f0-10-60Hz_5realizations_2sec';
%scripttag='ACd-net'; batchtag='f0base35Hz_f0shift-10-10Hz_2realizations';
%scripttag='ACd-net'; batchtag='f0base20-50Hz_f0shift-15-15Hz_1realization';
% scripttag='ACd-net'; batchtag='f0base35Hz_f0shift-15-15Hz_5realizations';

jsherfey

simulation.json:

{"ProjName":"GammaRhythm","StudyName":"sPING-inhibdecay2","scope":"I-E","variable":"tauDx","values":"[2.5:2.5:10]","sim_start":"0","sim_stop":"200","sim_solver":"Euler","sim_dt":".01","sim_target_fs":"20000","sim_host":"ip84.ucsd.edu","sim_cluster_flag":"1","sim_cluster":"mmilcluster.ucsd.edu","sim_qsubscript":"qmatjobs2","sim_rootoutdir":"/space/mdeh3/9/halgdev/projects/jsherfey/research/projects/ProjName/simulation/StudyName/SetName","sim_file_prefix":"biosim_experiment","sim_report_address":"jssherfey@gmail.com","sim_codepath":"/space/mdeh3/9/halgdev/projects/jsherfey/code/hhnetsim","sim_driver":"/space/mdeh3/9/halgdev/projects/jsherfey/code/hhnetsim/biosim/simdriver.m","result":"(ex. ts_sync)","result_keyvalue":"{}","figure":"trace","figure_keyvalue":"{'vars':'V,Iext,output'}","project_id":"1","model_id":"1098","study_id":"13"}

{"ProjName":"GammaRhythm","StudyName":"sPING-noise","scope":"E","variable":"V_noise","values":"[0:25:100]","sim_start":"0","sim_stop":"200","sim_solver":"Euler",