Network Version 1_40
Contents
1. Network 1 40 User Manual Page 6 Name_Ca_hpower 1 must be an ae Name_Ca_hinf 1 1 exp x 50 3 Name_Ca_htau 100 200 1 exp ee S Name_K_Gmax 120 0 ns Name_K_Erev 80 0 mV mAlphaBeta K 7 i e_K_mpower 4 must be an integer e_K_malpha 0 01 v 55 exp v 55 10 Name_K_mbeta 0 125 exp v 65 80 Name_Na_Gmax 36 0 ns Name_Na_Erev 50 0 mV Name_Na_mpower 4 must be an integer mhAlphaBeta Na Name_Na_malpha 0 01 v 55 exp v 55 10 Name_Na_mbeta 0 125 exp v 65 80 Name_Na_hpower 1 must be an integer Name_Na_halpha 0 07 exp v 67 100 Name_Na_hbeta 1 exp v 37 10 1 Parameter definitions for synaptic currents are given in the Table 5 x X v and V are equivalent synapse Pre Post Nothing is necessary yet Pre_Post_S1_Gmax 10 0 nS GradedmiInst S1 Pre Post_S1l_Erev 80 0 mV Pre_Post_S1_minf 1 1 exp x 55 3 Pre_Post_S2_Gmax 10 0 nS Pre_Post_S2_Erev 80 0 mV GradcomTa tnt 32 Pre_Post_S2_minf 1 1 exp x 55 3 Pre_Post_S2_mtau 10 20 1 exp SASS 73 GapJunction Elec Pre_Post_Elec_Gmax 10 0 nS Pre_Post_S3_Gmax 10 0 nS Pre_P2. 1 40 User Manual Page 9 3 Tutorials Tutorial 1 A passive cell Make a file called passive cfg containing the following eel P Passive L Make a file called passive par containing the following P_Text 0 pA P_Cm 200 pE P_L Gmax 10 nS P_L Frev 60 mV Make a file called passive ics containing the following P_Vm 60 At the command line type S network passive gt out The program will inform you that it is parsing compiling and running The file out should contain 1000 lines On each line there should be 2 entries the first is time and the second is 60 Now create a new file called par2 this name is arbitrary that contains P_Iext 1000 pA At the command line type cp last passive ics network r b 100 e 300 par par2 passive gt gt out cp last passive ics network r b 300 e 500 passive gt gt out You just injected a 1 nA pulse of duration 200 ms into the cell The result is in the file out and can be plotted with gnuplot Tutorial 2 The Morris Lecar cell Tutorial 3 The Hodgkin Huxley cell Tutorial 4 A Passive Cable Tutorial 5 An Active Cable Tutorial 6 Reciprocal Inhibition
3. option files The options that may be included in the option files are the following in Table 1 These options should be included in the file as option value with no space in between The sign at the beginning of the line comments out that option Network 1 40 User Manual The Configuration File Page 3 The contents of the file project cfg are necessary for determining the structure of the model The configuration file is a list of statements one per line that describe the structures of the cells or compartments their connections and the names and types of intrinsic and synaptic currents without specifying any parameters Empty lines and anything following a symbol on each line is ignored Additional spaces and tabs are also ignored The program is case sensitive REMOVEFILES rm 0 1 remove non executables ERRORFILE dev null filename less serious errors errorfile dev stderr filename more serious errors outputfile dev stdout filename output parse parse 1 0 parse or not run r 1 0 run or not compile c 1 0 compile or not tabulat 4 0 1 tabulate inf and taus speeds up integration tO b 0 any number begin time tmax e 100 ay aumiler end time gt t0 dt h 0 1 any number integration dt any skip S 10 positive print one point every skip integer pipe output through dd bs 10000 to dd 0 1 3 speed up write to disk par2 par ie filename a
4. symbol on each line is ignored Additional spaces and tabs are also ignored The program is case sensitive The units are arbitrary and the user should be careful to balance the units Parameter definitions for intrinsic currents are given in the following Table 4 x X v and V are equivalent cell Name Name_Text 0 0 pA or Name_Cm 100 0 pF compartment Name Name_Ga 100 0 nS If more than 1 compartment See Name_L_Gmax 10 0 nS Name_L_Erev 60 0 mV Name_Nal_Gmax 100 0 ns Name_Nal_Erev 50 0 mV mInst Nal Name_Nal_mpower 3 must be an se Name_Nal_minf 1 1 exp x 45 2 Name_Na2_Gmax 120 0 nS Name_Na2_Erev 50 0 mV mTauInf Na2 Name_Na2_mpower 3 must be an Name_Na2_minf 1 1 exp x 55 3 Name_Na2_mtau 1 10 1 exp x 55 a Name_K1_Gmax 120 0 ns Name_K1_Erev 80 0 mV Name_K1_mpower 4 must be an integer mInst_hTauInf K1 Name_K1_minf 1 1 exp x 51 12 Name_K1_hpower 1 must be an Name_K1_hinf 1 1 exp x 50 3 Name_K1_htau 10 100 1 exp S 3 mhTaulInf Ca Name_Ca_Gmax 11 0 nS Name_Ca_Erev 80 0 mV Name_Ca_mpower 2 must be an Name_Ca_minf 1 1 exp x 47 2 Name_Ca_mtau 10 12 1 exp x 52 5
5. synapse named S See Table 3 for available types of synapses The statement connect compl comp2 connects the compartment comp 1 to the compartment comp2 symmetrically GradedmTauInf graded single gated synapse GradedmInst graded single gated instantaneous synapse GapJunction gap junctional electrical synapse NOT SYMMETRIC GradedmTauInf_mpostTauInf graded single gated synapse with single gated activation dependence on the postsynaptic potential Gradedm Inst_mpostInst graded single gated instantaneous synapse with single gated activation instantaneous dependence on the postsynaptic potential AlphaFu nction spike mediated alpha function at e PulseSt im I does not define a true synapse but allows a set of square pulse currents of a fixed amplitude duration and frequency to be injected into the postsynaptic cell Network 1 40 User Manual Page 5 does not define a true synapse but allows a set of square pulse currents of a fixed amplitude duration and frequency to be injected into the postsynaptic cell depending on whether the presynaptic cell is above or below some fixed threshold ControlledPulse The Parameter File This section describes the contents of the file project par These contents depend on the cells and currents defined in the configuration file The values in the tables are just given as examples Empty lines and anything following a
6. Network 1 40 User Manual Page 1 Network Version 1 40 User Manual December 26 2001 Please send all comments and bug reports to Farzan Nadim farzan njit edu 0 Introduction Network is a neuronal network simulation software implemented in C Network can be used to model single neurons with Hodgkin Huxley type dynamics or networks of such neurons connected with synapses Network supports both a 4 order Runge Kutta and a variable time step integration method The current version of Network runs in UNIX and the parser is written in bash shell script and gawk Network is run from the command line and outputs to standard output There is no graphical interface At the command line network reads the name of the project e g project and looks in the current directory for a configuration file project cfg and a file containing the equations and parameters project par In this text the command line commands denotes the command prompt command and the contents of files are displayed using the Courier font 1 Running network The network command line is of the form bashsS network OPTIONS project The first argument on the command line is the user assigned name of the project Assignments of the cell synapse or network configurations are done in the file project cfg Assignments of the equations and parameters are done in the file project par The program searches for these 2 files in the current directory and gives an erro
7. ault nht same as notabulate par filename use this option to pass additional parameters to network This option is useful when changing parameters of the model without compiling Since this file filename is always read after project par itis a good way to modify parameters without touching the original project par file z run the executable runnetwork in the current directory without compiling the functions Note that using the options c and r together is superfluous since the latter option overrides the former To compile and run use neither of the two options rm remove the c and h files from the current directory after producing the executable file s skip only the first point of this many steps is printed to standard output Use this option when you have a small delta_time to keep the output small a run with tables This option makes look up tables for all the steady state activation and inactivation and time constant functions The tables are from 150 to 150 mV in increments of 1 mV Values in between are obtained by linear interpolation Values outside the range are set to the boundary values tabulate same as t V version version same as v All options may be included in the file SHOME network_options and or project opt in the project directory These files are read in order and latter assignments override the former ones Command line assignments are read last and override those in the
8. dditional parameter file tolerance gt 0 forces the program to use a any number tolerance 1 SO variable time step integrator for stiff equations Otherwise RK4 is used varfileoption keep val filename filename contains variables to be kept The statement compartment name declares a compartment called name The terms compartment and cell are equivalent Such a line also indicates that the lines immediately following will define the contents of this compartment The statements immediately following are usually definitions of intrinsic ionic currents see Table 2 for a list Passive L Network 1 40 User Manual mhTauInf Na mTauInf Kd These 3 lines define 3 ionic currents in the last defined compartment The first entry on each line defines the type of current and the second entry is the user assigned name Page 4 5 leak current Passive nTauInf single gated activation current oe single gated activation instantaneous current mhTauinf double gated activation inactivation current minst hTauIrnt double gated activation inactivation current with instantaneous activation The statement synapse compl comp2 declares a synaptic connection from the compartment cell comp1 to the compartment cell comp2 This statement is only meaningful when it is immediately followed by a new line containing the definition of the synapse For example GradedmTauInf S defines a graded
9. ditions are read from the file project ics if this file exists in the project directory The project ics file should contain each variable on a separate line and each line should be of the form variable lt value gt or variable lt value gt Each time network is run it creates a file called Last that contains the last point of integration This file could be renamed to project ics and used as initial conditions for the next run The UNIX Interface Network is run from the UNIX command line by typing network project gt outputfile All files associated with network are included in NETWORKHOME This directory should be included in the user path or alternatively there should be links to the executable files in usr local bin or usr bin Networks involves 3 executable commands network is the main script parse_network is the parser and tabulate_network builds the lookup tables for the t option Network 1 40 User Manual Page 8 2 Advanced Features The variables file option If keeping all the variables Keeping the current and conductance To keep the values of current cell_ion_I and conductance cell_ion_G the word keep should appear immediately after the name of the ion in the configuration file For example if project cfg contains cell Pyramidal mhTauInf Na keep the output of network project will contain two columns for Pyramidal_Na_G and Pyramidal_Na_lI The calcium dependent current Network
10. ost_S3_Erev 80 0 mV GradedmInst mpostInst 53 pre post 53 mint 1 lrexp x 55 3 Pre_Post_S3_mPosttinf 1 1 exp x 25 12 Pre _Post_S4_Gmax 10 0 nS Pre_ Post_S4_ Erev 80 0 mV GradedmTauInf_mpostTauInf S4 Pre_Post_S4_minf 1 14 ZP a2 3 Pre_Post_S4_mtau 10 20 1 exp es 3 Pre Post oA mPosiicidmi il Clase xto o Pre Post_S4_mPostttau 200 1 exp x 12 2 AlphaFunction A Pre_Post_A_Gmax 10 0 nS Pre_Post_A_Erev 80 0 mV Pre_Post_A_AlphaTau 25 ms Pre_Post_A_Threshold 20 mV presyn threshold Pre_Post_A_Slope 1 1 or 1 going through threshold up or down Network 1 40 User Manual Page 7 Pre_Post_A_ Tolerance le 3 defined by default to be le 3 This decides the tim tolerance to within which 2 events coincide ULL_Post_A_Period 1000 ms defined only if the presynaptic cell is NULL Determines the period of the synapse PulseStim I NULL_Post_A_ Period 50 ms defined only with NULL_Post_A_Duration 2 ms presyn cell NULL NULL_Post_A_Amplitude 1000 pA Pre_Post_I_Period 100 0 ms Pre_Post_I_Duration 80 0 mV Pre_Post_I_Amplitude 1000 pA ControlledPulse I Pc ToThresho ee A aes Post_I_Delay 10 0 ms delay after hold crossing amp before injection Post_I_Above 1 1 or 0 inject above hold or below The Initial Condition File The initial con
11. r message if these files are not found An optional file project ics can be provided in the current directory for assignment of initial conditions If this file exists network automatically reads it At the end of each simulation run network produces a file named last that contains the last point of integration This file can be renamed to project ics to be used as the initial condition in the next run If no option is passed to network by default it will produce the c and h files and a makefile in the current directory compiles them and runs the executable The output is directed to the standard output The output is currently formatted as a matrix where each row represents one time step The first element of the row is time and is followed by all the state variables in the order of definition Network 1 40 User Manual Page 2 Additional options must appear before the project name The order of the options is irrelevant The options are passed to network in the standard UNIX format with a hyphen Whenever the option requires an argument such as b begin_time the space between the 2 parts is required The current options are b begin_time generate the c and h files compile and produce an executable called runnetwork in the current directory and exit without running the executable e end_time h delta_time k filename keep only variables written in filename keep same as k notabulate run without tables def
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