function specification = assembleThalOnlyPoisson(numCellsScale)
% -------------------------------------------------------------------
%% 1. Make master equations and initialize
% -------------------------------------------------------------------
% Define equations of cell model (same for all populations)
eqns={
'dv/dt=(@current)/Cm'
'Cm = 1' % uF/cm^2
'spike_threshold = -25'
'monitor v.spikes(spike_threshold)'
'vIC = -68' % mV
'vNoiseIC = 50' % mV
'v(0) = vIC+vNoiseIC*rand(1,Npop)'
};
% Initialize DynaSim specification structure
specification=[];
% -------------------------------------------------------------------
%% 2. Assemble Cortex Model and Intracortical Connections
% -------------------------------------------------------------------
% % PY cells and intercompartmental PY connections:
% specification.populations(1).name='PYdr';
% specification.populations(1).size=round(numCellsScale*100);
% specification.populations(1).equations=eqns;
% specification.populations(1).mechanism_list={...
% 'CaBuffer_PYdr_JB12',...
% 'iAppliedCurrent',...
% 'iPoisson',...
% 'iHVA_PYdr_JB12',...
% 'iKCa_PYdr_JB12',...
% 'iNaP_PYdr_JB12',...
% 'iAR_PYdr_JB12',...
% };
% % Note that the soma mechanisms are somewhat sensitive to initial conditions
% specification.populations(2).name='PYso';
% specification.populations(2).size=round(numCellsScale*100);
% specification.populations(2).equations=eqns;
% specification.populations(2).mechanism_list={...
% 'iAppliedCurrent',...
% 'iLeak_PYso_JB12',...
% 'iNa_PYso_JB12',...
% 'iK_PYso_JB12',...
% 'iA_PYso_JB12',...
% 'iKS_PYso_JB12',...
% };
% specification.connections(1).direction='PYso<-PYdr';
% specification.connections(1).mechanism_list={...
% 'iCOM_PYso_PYdr_JB12',...
% 'iNaCurrs_PYso_PYdr_JB12',...
% };
% specification.connections(2).direction='PYdr<-PYso';
% specification.connections(2).mechanism_list={...
% 'iCOM_PYdr_PYso_JB12',...
% 'iAMPA_PYdr_PYso_JB12',...
% 'iNMDA_PYdr_PYso_JB12'};
% % IN cells and intercompartmental IN connections:
% % 'iPoisson',...
% specification.populations(3).name='IN';
% specification.populations(3).size=round(numCellsScale*20);
% specification.populations(3).equations=eqns;
% specification.populations(3).mechanism_list={...
% 'iAppliedCurrent',...
% 'iLeak_IN_JB12',...
% 'iNa_IN_JB12',...
% 'iK_IN_JB12',...
% };
% % PY<->IN connections/synapses
% specification.connections(3).direction='IN<-PYso';
% specification.connections(3).mechanism_list={...
% 'iAMPA_IN_PYso_JB12',...
% 'iNMDA_IN_PYso_JB12'};
% specification.connections(4).direction='PYso<-IN';
% specification.connections(4).mechanism_list={...
% 'iGABAA_PYso_IN_JB12'};
% specification.connections(5).direction='IN<-IN';
% specification.connections(5).mechanism_list={...
% 'iGABAA_IN_IN_JB12'};
% -------------------------------------------------------------------
%% 3. Assemble Thalamic Model and Intrathalamic Connections
% -------------------------------------------------------------------
specification.populations(1).name='TC';
specification.populations(1).size=round(numCellsScale*20);
specification.populations(1).equations=eqns;
specification.populations(1).mechanism_list={...
'iAppliedCurrent',...
'iPoisson',...
'iNa_TC_AS17',...
'iK_TC_AS17',...
'iLeak_TC_AS17',...
'iKLeak_TC_AS17',...
'CaBuffer_TC_AS17',...
'iT_TC_AS17',...
'iH_TC_AS17'};
specification.populations(2).name='TRN';
specification.populations(2).size=round(numCellsScale*20);
specification.populations(2).equations=eqns;
specification.populations(2).mechanism_list={...
'iAppliedCurrent',...
'iPoisson',...
'iNa_TRN_AS17',...
'iK_TRN_AS17',...
'iLeak_TRN_AS17',...
'iKLeak_TRN_AS17',...
'iT_TRN_AS17'};
specification.connections(1).direction='TC<-TRN';
specification.connections(1).mechanism_list={...
'iGABAA_TC_TRN_AS17',...
'iGABAB_TC_TRN_AS17',...
};
specification.connections(2).direction='TRN<-TRN';
specification.connections(2).mechanism_list={'iGABAA_TRN_TRN_AS17'};
specification.connections(3).direction='TRN<-TC';
specification.connections(3).mechanism_list={'iAMPA_TRN_TC_AS17'};
% % -------------------------------------------------------------------
% %% 4. Thalamo-cortical Connections
% % -------------------------------------------------------------------
% specification.connections(9).direction='PYdr<-TC';
% specification.connections(9).mechanism_list={'iAMPA_PYdr_TC'};
% specification.connections(10).direction='IN<-TC';
% specification.connections(10).mechanism_list={'iAMPA_IN_TC'};
% specification.connections(11).direction='TC<-PYso';
% specification.connections(11).mechanism_list={'iAMPA_TC_PYso'};
% specification.connections(12).direction='TRN<-PYso';
% specification.connections(12).mechanism_list={'iAMPA_TRN_PYso'};