//genesis //net_func.g /* This file sets the netowork of SP cells up by calling the function that sets up the SP-SP inhibitory network and calling the functions that connect extrinsic input to the SP network.This file also has the include statements for the file that prints out the connection of the SP-SP network. */ /* function include_net (net) str net addglobal str cellPath setglobal cellPath "/library/"{net}"cell" if ({net} == "SP") include MScell/MScellSyn.g // Single SP neuron model with synaptic channels makeMScellSyn {getglobal cellPath} "MScell/MScell.p" else end if ({net} == "FS") include FScell/FScellSyn.g // Single FS neuron model with synaptic channels makeFScellSyn {getglobal cellPath} "FScell/FScell.p" else end make_spike {cellPath}/soma add_field {cellPath} setfield /library/{net}cell/soma/spike thresh 0 abs_refract 0.004 output_amp 1 end */ /****************************Begin Network description****************************************************/ function rannum_new2 (tablename) str tablename int i int last={getfield {tablename} X_A->xmax} //get the index of last element from the value of xmax //echo "last=" {last} int index={ round {rand -0.499 {last+0.499}} } //choose a random index int filenum={getfield {tablename} X_A->table[{index}]} //return filenum associated with index selected above setfield {tablename} X_A->table[{filenum}] {getfield {tablename} X_A->table[{last}]} //replace selected filenum with last element setfield {tablename} X_A->xmax {last-1} //set xmax to be {last-1} return {filenum} end function chan_mod (net, channame, perc) //function that modulates the channel of choice in order to create heterogeneous cells str net, channame float std_val, std_val_D1, std_val_D2, perc, g, g_soma, g_prim, g_sec, g_tert, g_a, std_val_D1_soma, std_val_D2_soma, std_val_D1_prim, std_val_D2_prim, std_val_D1_sec, std_val_D2_sec, std_val_D1_tert, std_val_D2_tert int i, d1_num, d2_num d1_num = {getfield /SPnetwork/SPcell/soma d1_cnt} //get the number of D1 neurons in the network (stored in d1_cnt) d2_num = {getfield /SPnetwork/SPcell/soma d2_cnt} //get the number of D2 neurons in the network (stored in d2_cnt) // MAKE IT COMPARTMENT DEPENDENT if ({net}=="SP") if ({channame}=="NR2A") std_val_D1 = {getfield /library/{net}cell_D1/soma/{channame} gmax} std_val_D2 = {getfield /library/{net}cell_D2/soma/{channame} gmax} else std_val_D1_soma = {getfield /library/{net}cell_D1/soma/{channame}_channel Gbar} std_val_D2_soma = {getfield /library/{net}cell_D2/soma/{channame}_channel Gbar} std_val_D1_prim = {getfield /library/{net}cell_D1/primdend1/{channame}_channel Gbar} std_val_D2_prim = {getfield /library/{net}cell_D2/primdend1/{channame}_channel Gbar} std_val_D1_sec = {getfield /library/{net}cell_D1/secdend1/{channame}_channel Gbar} std_val_D2_sec = {getfield /library/{net}cell_D2/secdend1/{channame}_channel Gbar} std_val_D1_tert = {getfield /library/{net}cell_D1/tertdend1/{channame}_channel Gbar} std_val_D2_tert = {getfield /library/{net}cell_D2/tertdend1/{channame}_channel Gbar} end else std_val = {getfield /library/{net}cell/soma/{channame}_channel Gbar} end float mod_D1 = {perc*std_val_D1} float min_D1 = {std_val_D1 - mod_D1} float max_D1 = {std_val_D1 + mod_D1} float m_D1 = {min_D1} float dm_D1 = ({max_D1 - min_D1})/({d1_num}) float mod_D2 = {perc*std_val_D2} float min_D2 = {std_val_D2 - mod_D2} float max_D2 = {std_val_D2 + mod_D2} float m_D2 = {min_D2} float dm_D2 = ({max_D2 - min_D2})/({d2_num}) float mod_D1_soma = {perc*std_val_D1_soma} float min_D1_soma = {std_val_D1_soma - mod_D1_soma} float max_D1_soma = {std_val_D1_soma + mod_D1_soma} float m_D1_soma = {min_D1_soma} float dm_D1_soma = ({max_D1_soma - min_D1_soma})/({d1_num}) float mod_D2_soma = {perc*std_val_D2_soma} float min_D2_soma = {std_val_D2_soma} float max_D2_soma = {std_val_D2_soma + mod_D2_soma} float m_D2_soma = {min_D2_soma} float dm_D2_soma = ({max_D2_soma - min_D2_soma})/({d2_num}) float mod_D1_prim = {perc*std_val_D1_prim} float min_D1_prim = {std_val_D1_prim - mod_D1_prim} float max_D1_prim = {std_val_D1_prim + mod_D1_prim} float m_D1_prim = {min_D1_prim} float dm_D1_prim = ({max_D1_prim - min_D1_prim})/({d1_num}) float mod_D2_prim = {perc*std_val_D2_prim} float min_D2_prim = {std_val_D2_prim} float max_D2_prim = {std_val_D2_prim + mod_D2_prim} float m_D2_prim = {min_D2_prim} float dm_D2_prim = ({max_D2_prim - min_D2_prim})/({d2_num}) float mod_D1_sec = {perc*std_val_D1_sec} float min_D1_sec = {std_val_D1_sec - mod_D1_sec} float max_D1_sec = {std_val_D1_sec + mod_D1_sec} float m_D1_sec = {min_D1_sec} float dm_D1_sec = ({max_D1_sec - min_D1_sec})/({d1_num}) float mod_D2_sec = {perc*std_val_D2_sec} float min_D2_sec = {std_val_D2_sec} float max_D2_sec = {std_val_D2_sec + mod_D2_sec} float m_D2_sec = {min_D2_sec} float dm_D2_sec = ({max_D2_sec - min_D2_sec})/({d2_num}) float mod_D1_tert = {perc*std_val_D1_tert} float min_D1_tert = {std_val_D1_tert - mod_D1_tert} float max_D1_tert = {std_val_D1_tert + mod_D1_tert} float m_D1_tert = {min_D1_tert} float dm_D1_tert = ({max_D1_tert - min_D1_tert})/({d1_num}) float mod_D2_tert = {perc*std_val_D2_tert} float min_D2_tert = {std_val_D2_tert} float max_D2_tert = {std_val_D2_tert + mod_D2_tert} float m_D2_tert = {min_D2_tert} float dm_D2_tert = ({max_D2_tert - min_D2_tert})/({d2_num}) echo "m_d1" {m_D1_soma} echo "m_d2" {m_D2_prim} echo "dm_d1" {dm_D1_sec} echo "dm_d2" {dm_D2_tert} if (!{exists val_D1}) create tabchannel val_D1 // else end disable val_D1 int tablemax_D1 = {getfield /SPnetwork/SPcell/soma d1_cnt} call val_D1 TABCREATE X {{tablemax_D1}-1} 0 {{tablemax_D1}-1} call val_D1 TABCREATE Y {{tablemax_D1}-1} 0 {{tablemax_D1}-1} call val_D1 TABCREATE Z {{tablemax_D1}-1} 0 {{tablemax_D1}-1} for (i=0; i<{tablemax_D1}; i={i+1}) setfield val_D1 X_A->table[{i}] {m_D1} // setfield val_D1 X_B->table[{i}] {m_D1_soma} // setfield val_D1 Y_A->table[{i}] {m_D1_prim} // setfield val_D1 Y_B->table[{i}] {m_D1_sec} // setfield val_D1 Z_A->table[{i}] {m_D1_tert} // m_D1 = {m_D1 + dm_D1} m_D1_soma = {m_D1_soma + dm_D1_soma} m_D1_prim = {m_D1_prim + dm_D1_prim} m_D1_sec = {m_D1_sec + dm_D1_sec} m_D1_tert = {m_D1_tert + dm_D1_tert} end if (!{exists val_D2}) create tabchannel val_D2 // else end disable val_D2 int tablemax_D2 = {getfield /SPnetwork/SPcell/soma d2_cnt} call val_D2 TABCREATE X {{tablemax_D2}-1} 0 {{tablemax_D2}-1} call val_D2 TABCREATE Y {{tablemax_D2}-1} 0 {{tablemax_D2}-1} call val_D2 TABCREATE Z {{tablemax_D2}-1} 0 {{tablemax_D2}-1} for (i=0; i<{tablemax_D2}; i={i+1}) setfield val_D2 X_A->table[{i}] {m_D2} // setfield val_D2 X_B->table[{i}] {m_D2_soma} // setfield val_D2 Y_A->table[{i}] {m_D2_prim} // setfield val_D2 Y_B->table[{i}] {m_D2_sec} // setfield val_D2 Z_A->table[{i}] {m_D2_tert} // m_D2 = {m_D2 + dm_D2} m_D2_soma = {m_D2_soma + dm_D2_soma} m_D2_prim = {m_D2_prim + dm_D2_prim} m_D2_sec = {m_D2_sec + dm_D2_sec} m_D2_tert = {m_D2_tert + dm_D2_tert} end int tablemax = {getglobal numCells_{net}} if (!{exists ind}) create tabchannel ind //create a table to contain the indices of the filenames else end disable ind tablemax = {getglobal numCells_{net}} call ind TABCREATE X {{tablemax}-1} 0 {{tablemax}-1} for (i=0; i<{tablemax}; i={i+1}) setfield ind X_A->table[{i}] {i} //indices of unique filenames end str cN int inCtr, ctr, d2Ctr, d1_numC = {{d1_num}-1} for(i = 0; i < {getglobal numCells_{net}}; i = {i + 1}) inCtr = {rannum_new2 ind} if ({inCtr}>{d1_numC}) //echo "inctr" {inCtr} "d1" {d1_num} d2Ctr = {{inCtr}-{d1_num}} //echo "diff" {inCtr-d1_num} "d2Ctr" {d2Ctr} g = {getfield val_D2 X_A->table[{d2Ctr}]} g_soma = {getfield val_D2 X_B->table[{d2Ctr}]} g_prim = {getfield val_D2 Y_A->table[{d2Ctr}]} g_sec = {getfield val_D2 Y_B->table[{d2Ctr}]} g_tert = {getfield val_D2 Z_A->table[{d2Ctr}]} //echo "g D2" {g} else g = {getfield val_D1 X_A->table[{inCtr}]} g_soma = {getfield val_D1 X_B->table[{inCtr}]} g_prim = {getfield val_D1 Y_A->table[{inCtr}]} g_sec = {getfield val_D1 Y_B->table[{inCtr}]} g_tert = {getfield val_D1 Z_A->table[{inCtr}]} //echo "g D1" {g} end if ({channame}== "NR2A") g_a = {g/2.75} else end ctr=0 foreach cN ({el /{net}network/{net}cell[{i}]/##[TYPE=compartment]}) ctr = {ctr+1} if ({channame}=="NR2A") setfield {cN}/{channame} gmax {g} setfield {cN}/AMPA gmax {g_a} else if (({ctr}<32 && {net}=="FS") || {net}=="SP") // if exists{{cN}/{channame}_channel} if ({getfield {cN} position}==1.599999996e-05) setfield {cN}/{channame}_channel Gbar {g_soma} elif ({getfield {cN} position}==3.599999764e-05) setfield {cN}/{channame}_channel Gbar {g_prim} elif ({getfield {cN} position}==6.022999878e-05) setfield {cN}/{channame}_channel Gbar {g_sec} elif ({getfield {cN} position}>7.0e-05) setfield {cN}/{channame}_channel Gbar {g_tert} // setfield {cN}/{channame}_channel Gbar {g} end // setfield /library/{net}cell_D1/soma/{channame}_channel Gbar else end end end end end // chan_mod function end function chan_mod_FS (net, channame, perc) //function that modulates the channel of choice in order to create heterogeneous cells //created separate function for FS because there were places where having all three (D1,D2,FS) in one //function made it more cumbersome. Can possible still integrate into one file str net, channame float std_val, std_val_FS, perc, g, g_soma, g_prim, g_sec, g_tert, g_a, std_val_FS_soma, std_val_FS_prim, std_val_FS_sec, std_val_FS_tert int i, FS_num FS_num = {getglobal numCells_{net}} // MAKE IT COMPARTMENT DEPENDENT std_val_FS = {getfield /library/{net}cell/soma/{channame}_channel Gbar} std_val_FS_soma = {getfield /library/FScell/soma/{channame}_channel Gbar} std_val_FS_prim = {getfield /library/FScell/primdend1/{channame}_channel Gbar} std_val_FS_sec = {getfield /library/FScell/secdend1/{channame}_channel Gbar} float mod_FS = {perc*std_val_FS} float min_FS = {std_val_FS - mod_FS} float max_FS = {std_val_FS + mod_FS} float m_FS = {min_FS} float dm_FS = ({max_FS - min_FS})/({FS_num}) float mod_FS_soma = {perc*std_val_FS_soma} float min_FS_soma = {std_val_FS_soma - mod_FS_soma} float max_FS_soma = {std_val_FS_soma + mod_FS_soma} float m_FS_soma = {min_FS_soma} float dm_FS_soma = ({max_FS_soma - min_FS_soma})/({FS_num}) float mod_FS_prim = {perc*std_val_FS_prim} float min_FS_prim = {std_val_FS_prim - mod_FS_prim} float max_FS_prim = {std_val_FS_prim + mod_FS_prim} float m_FS_prim = {min_FS_prim} float dm_FS_prim = ({max_FS_prim - min_FS_prim})/({FS_num}) float mod_FS_sec = {perc*std_val_FS_sec} float min_FS_sec = {std_val_FS_sec - mod_FS_sec} float max_FS_sec = {std_val_FS_sec + mod_FS_sec} float m_FS_sec = {min_FS_sec} float dm_FS_sec = ({max_FS_sec - min_FS_sec})/({FS_num}) echo "m_FS" {m_FS_soma} echo "dm_FS" {dm_FS_sec} if (!{exists val_FS}) create tabchannel val_FS end disable val_FS int tablemax_FS = {getglobal numCells_{net}} call val_FS TABCREATE X {{tablemax_FS}-1} 0 {{tablemax_FS}-1} call val_FS TABCREATE Y {{tablemax_FS}-1} 0 {{tablemax_FS}-1} call val_FS TABCREATE Z {{tablemax_FS}-1} 0 {{tablemax_FS}-1} for (i=0; i<{tablemax_FS}; i={i+1}) setfield val_FS X_A->table[{i}] {m_FS} // setfield val_FS X_B->table[{i}] {m_FS_soma} // setfield val_FS Y_A->table[{i}] {m_FS_prim} // setfield val_FS Y_B->table[{i}] {m_FS_sec} // m_FS = {m_FS + dm_FS} m_FS_soma = {m_FS_soma + dm_FS_soma} m_FS_prim = {m_FS_prim + dm_FS_prim} m_FS_sec = {m_FS_sec + dm_FS_sec} end int tablemax = {getglobal numCells_{net}} if (!{exists ind}) create tabchannel ind //create a table to contain the indices of the filenames else end disable ind tablemax = {getglobal numCells_{net}} call ind TABCREATE X {{tablemax}-1} 0 {{tablemax}-1} for (i=0; i<{tablemax}; i={i+1}) setfield ind X_A->table[{i}] {i} //indices of unique filenames end str cN int inCtr, ctr, d2Ctr, FS_numC = {{FS_num}-1} for(i = 0; i < {getglobal numCells_{net}}; i = {i + 1}) inCtr = {rannum_new2 ind} g = {getfield val_FS X_A->table[{inCtr}]} g_soma = {getfield val_FS X_B->table[{inCtr}]} g_prim = {getfield val_FS Y_A->table[{inCtr}]} g_sec = {getfield val_FS Y_B->table[{inCtr}]} //echo "g FS" {g} if ({channame}== "NR2A") g_a = {g/2.75} else end ctr=0 foreach cN ({el /{net}network/{net}cell[{i}]/##[TYPE=compartment]}) ctr = {ctr+1} if ({channame}=="NR2A") setfield {cN}/{channame} gmax {g} setfield {cN}/AMPA gmax {g_a} else if (({ctr}<32 && {net}=="FS") || {net}=="SP") if ({getfield {cN} position}==1.999999949e-05) setfield {cN}/{channame}_channel Gbar {g_soma} elif ({getfield {cN} position}>6.0e-05 && {getfield {cN} position}<12.0e-05) setfield {cN}/{channame}_channel Gbar {g_prim} end end end end end end // chan_mod function end function make_net (net,dopa) //read in by net.g //reads in network type and the ratio of d1 and d2 neurons to be modeled in the network str net int i, k, n_ctr, inCtr, tablemax float dopa,rand_num //following loop assigns D1 and D2 neurons randomly in the network based on 'dopa' ratio if ({net}=="SP") create neutral /{net}network int d1_count=0, d2_count=0 for(i = 0; i < {getglobal numCells_{net}}; i = {i + 1}) rand_num = {rand 0 1} if ({dopa}<{rand_num}) copy /library/SPcell_D1 /SPnetwork/SPcell[{i}] //Copy a D1 neuron here addfield /SPnetwork/SPcell[{i}]/soma D1 setfield /SPnetwork/SPcell[{i}]/soma D1 1 d1_count = d1_count + 1 else copy /library/SPcell_D2 /SPnetwork/SPcell[{i}] //Copy a D2 neuron here addfield /SPnetwork/SPcell[{i}]/soma D1 setfield /SPnetwork/SPcell[{i}]/soma D1 0 d2_count = d2_count + 1 end end addfield /SPnetwork/SPcell/soma d1_cnt setfield /SPnetwork/SPcell/soma d1_cnt {d1_count} addfield /SPnetwork/SPcell/soma d2_cnt setfield /SPnetwork/SPcell/soma d2_cnt {d2_count} int NX = {getglobal NX_{net}} int NX_2 = {pow {NX} 2} float x = 1.6e-5, y = 0, x_ze = 0, y_ze = 0 str cName setfield /{net}network/{net}cell[0]/ x 0 setfield /{net}network/{net}cell[0]/ y {y} //setfield /{net}network/{net}cell[0]/soma/ z {z} // echo "NX squared"{NX_2} //Now place the cells along the xy axis for(k = 1; k < {getglobal numCells_{net}}; k = {k + 1}) if ( {k%{NX}} == 0 ) x = 0 y = {y + 25e-6} elif ( {k%{NX}} != 0 ) x = {x + 25e-6} end foreach cName ({el /SPnetwork/SPcell[{k}]/##[TYPE=compartment]}) x_ze = {getfield {cName} x0} y_ze = {getfield {cName} y0} setfield {cName} x {x + x_ze} setfield {cName} y {y + y_ze} end end elif ({net}=="FS") createmap /library/{net}cell /{net}network {getglobal NX_{net}} {getglobal NY_{net}} -delta {getglobal SEP_X_{net}} {getglobal SEP_Y_{net}} -origin {getglobal origin_x_{net}} {getglobal origin_y_{net}} end end /* There will be NX cells along the x-direction, separated by SEP_X, and NY cells along the y-direction, separated by SEP_Y. The default origin is (0, 0). This will be the coordinates of /network/SPcell[0]. The last cell,SPcell[{NX*NY-1}], will be at (NX*SEP_X -1, NY*SEP_Y-1). */ ////////////////////////////////Connecting Inhibitory SP network///////////////////////////////////////////////// //1- soma, 2- primary dendrite, 3-secondary dendrite, 4- tertiary dendrite int cellCtr echo "Connecting Inhibitory SP_network." /* Call function that connects SP-SP neurons based on probability function that is exponential. Argument is the desired factor of the exponential funtion. */ function conn (net,net2) str net,net2, input_folder if ({net}=="FS" && {net2}=="SP") loops_SP=1 factor_SP = 100e-6 end if ({net}=="FS" && {net2}=="FS") weight_FS=1 end echo "fact1" {getglobal factor_{net}} echo "fact2" {getglobal factor_{net2}} if ({net2}=="FS") netconn {net} {net2} ""/{net}"network/"{net}"cell" ""/{net2}"network/"{net2}"cell" {getglobal factor_{net2}} {getglobal loops_{net2}} {getglobal weight_{net}} 1 0 0.75 0.3 2e9 elif ({net2}=="SP") //last 3 params - SP(1/0), FS(1/0), intrinsic percentage(0-1) netconn_SP {net} {net2} ""/{net}"network/"{net}"cell" ""/{net2}"network/"{net2}"cell" {getglobal factor_{net2}} 1 1 1 end // gap probs - a combination of Galarreta and Hestrin and striatal data if ({net}=="FS" && {net2}=="SP") echo "FS SP netconn done" elif ({net}=="SP" && {net2}=="SP") echo "SP SP netconn done" end ////////////////////Connecting FS and cortical input to SP network/////////////// /* FS and cortical input are connected to the SP network by using MATLAB generated input trains. Functions are called that (i) Convert the MATLAB generated files into GENESIS timetables (ii) Connect the timetables to the SP network readInputFromFile connects the MATLAB generated files to timetables. The function is called once for AMPA and once for GABA. The files for the unique input are called within the loop and inputs for the duplicate input are called once outside the loop.The arguments for this function are: (i) Name of the timetable (ii) Name of the MATLAB file to read from (iii) Number of synaptic inputs (iv) Number of connections from unique or duplicate input files */ if ({net}=={net2}) if ({net}=="SP") input_folder = "INPUTDATA_SP" else input_folder = "INPUTDATA_FS" end echo "input_folder" {input_folder} for (inputs=0; inputs<{getglobal numCells_{net}}; inputs={inputs+1}) readInputFromFile {net2} "AMPAinsignal_u_"{inputs}"_" \ ""{input_folder}"/AMPAinsignal_"{{inputs}+1}"_" \ {getglobal nAMPA_{net}} {getglobal nUnique_a_{net}} if ({net2}=="FS") readInputFromFile {net2} "GABAinsignal_u_"{inputs}"_" \ ""{input_folder}"/GABAinsignal_"{{inputs}+1}"_" \ {getglobal nGABA_{net2}} {getglobal nUnique_g_{net2}} end end readInputdFromFile {net2} "AMPAinsignal_d_" \ ""{input_folder}"/AMPAinsignal_dup_" \ {getglobal nDups_a_{net}} if ({net2}=="FS") readInputdFromFile {net2} "GABAinsignal_d_" \ ""{input_folder}"/GABAinsignal_dup_" \ {getglobal nDups_g_{net}} end /* connectInsignalToCell connects the timetables created by the above function calls to the SP cell network using a tabchannel and randomly selecting the input name from this tabchannel. The arguments for this function are: (i) Name of SP cell to connect to (ii) Name of input file to connect the unique input from (iii) Name of input file to connect the duplicate input from (iv) Type of synaptic connection (v) Number of connections from unique and (vi) duplicate input files */ int weight_sp=1, weight_fs=1 for(cellCtr = 0; cellCtr < {getglobal numCells_{net}}; cellCtr = {cellCtr + 1}) //Cortical input connectInsignalToCell {net2} ""/{net}"network/"{net}"cell["{cellCtr}"]" "AMPAinsignal_u_"{cellCtr}"_" "AMPAinsignal_d_" "AMPA" {getglobal nUnique_a_{net}} {getglobal nDups_a_{net}} 0 0 if ({net}=="SP") connectInsignalToCell {net2} ""/{net}"network/"{net}"cell["{cellCtr}"]" "AMPAinsignal_u_"{cellCtr}"_" "AMPAinsignal_d_" "NR2A" {getglobal nUnique_a_{net}} {getglobal nDups_a_{net}} 0 0 end if ({net2}=="FS") connectInsignalToCell {net2} ""/{net}"network/"{net}"cell["{cellCtr}"]" "GABAinsignal_u_"{cellCtr}"_" "GABAinsignal_d_" "GABA" {getglobal nUnique_g_{net}} {getglobal nDups_g_{net}} {weight_fs} {weight_sp} end end end ///////////////////////////////////////////////////////////////////////////////////// // include the utilities that will print out the connections between the SP neurons ce / /* Set the axonal propagation delay and weight fields of the target synchan synapses for all spikegens. */ planardelay /{net}network/{net}cell[]/soma/spike -fixed {prop_delay} //planarweight /{net}network/{net}cell[]/soma/spike -fixed {syn_weight} if ({net}=="SP" && {net2}=="SP") echo "end of SP SP conn" end end