"Requirement of an allosteric kinetics of NMDA receptors for spike-timing-dependent plasticity"

H. Urakubo, M. Honda R.C. Froemke, S. Kuroda, J Neurosci 28(13) pp 3310-3323 (2008)

Supplmentary Information

The source codes of an allosteric STDP model are provided here ("tar zxvf Urakubo2008.tar.gz" for uncompression), and detailed model description is here . The source codes Urakubo2008.tar.gz (modified on 9/Feb/2010) contain the demonstration programs of voltage-dependent synaptic plasticity (Volt, Fig 2), spike-timing-dependent plasticity (STDP, Fig 4) and burst-dependent plasticity (BURST, Fig 7). All models were built on the GENESIS/kinetikit (version 2.2.1 or 2.3) with X86-Linux. To execute the demonstration programs, the GENESIS simulator (version 2.2.1 or 2.3) must be installed from source codes to your LINUX/UNIX system appropreately. The contruction of directories of the source codes is shown as follows.

newgenesis Extended GENESIS. The extended GENESIS is executable on X86-64 redhat Enterprise Linux ES ver 4 with appropriate ~/.simrc, kkit, etc. Otherwize, create your own "newgenesis" as described in MODEL/genesis_customizing/.
Volt.out, STDP.out, BURST1.out, BURST2.out, BURST3.out

Scripts for simulations (csh/tcsh is assumed). Execute the files by "csh Volt.out". Note that the execution time is very long. It takes about 1 hour for one parameter simulation with 2.4 GHz AMD Opteron.

Volt_PBSPro.out, STDP_PBSPro.out, BURST1_PBSPro.out, BURST2_PBSPro.out, BURST3_PBSPro.out If your system has the job scheduler "PBS professional" ver 7 or above, you can use the scripts instead of Volt.out, STDP.out etc. to execute multiple simulations in parallel. Edit the files to fit your system.
Data strage for spike-timing-dependent plasticity (STDP, Fig 4). The subdirectories 0-17 store the simulation results of 100 pre- and post-spike pairing at Tpost-Tpre = -256, -128, -64, -32, -16, -8, ..., 256 ms, respectively.
Data strage for voltage-dependent plasticity (Volt, Fig 2). The subdirectories 0-9 store the simulation results of 100 pre-spiking with holding -115, -105 -95, ..., 25 mV, respectively.
Data strage for burst-dependent plasticity (BURST, Fig 7A-C). The subdirectories POST1_PRE5, PRE5_POST1 and PostPrePost4 store the correspondent simulation results.
tmp1/ - tmp5/
Temporal file strage of the GENESIS programs.
PROGRAMS/ GENESIS subroutines.
Graph plot files (Matlab m-files). VoltMolcProf.m draws Fig 2A-E, VoltMolcTot.m draws Fig 2G VoltCond.m draws Fig 2HI ,STDPCond.m draws Fig 4DE, STDPMolc.m draws Fig 4FG, BURST1.m draws Fig 7A, BURST2.m draws Fig 7B, and BURST2.m draws Fig 7C.
Kkit file of signaling cascade and AMPAR trafficking models. The model must be executed with initials33.g or initials_VoltageClamp33.g on the extended GENESIS.
Initial file loader for simulation of STDP and BURST.
Initial file loader for simulation of Volt.
Initial files.
A postsynaptic neuron model with a sample program. Execute "./newgenesis main_Poirazi.g" with your own "newgenesis."

Extension on the GENESIS simulator. The extension "newgenesis" of your own system is required for successful execution of the sample programs. To create "newgenesis" of your own system:

  1. Check the versions of ${GENESIS_SOURCE}/Usermake and ${GENESIS_SOURCE}/Libmake by reading the first lines of the files. If the versions are different from ${Urakubo2008}/MODEL/genesis_customizing/Makefile and ${Urakubo2008}/MODEL/genesis_customizing/*/Makefile, this may cause problems. Replace the files with your GENESIS files, if the problems occur.
  2. Modify the system configuration variables (line 57, lines 64-73) of ${Urakubo2008}/MODEL/genesis_customizing/Makefile for your own system. You can refer to ${GENESIS_SOURCE}/src/Makefile.
  3. Fill the user configuration variables of ${Urakubo2008}/MODEL/genesis_customizing/Makefile if you replaced the files with ${GENESIS_SOURCE}/Usermake.
  4. Fill the user configuration section of ${Urakubo2008}/MODEL/genesis_customizing/*/Makefile if you replaced the files with ${GENESIS_SOURCE}/Libmake.
  5. "make" in the directory "${Urakubo2008}/MODEL/genesis_customizing".
  6. If the programs are compiled successfully, "cp ./newgenesis ./../../" and enjoy the sample programs!