requirement of an allosteric kinetics of nmda receptors for spike-timing-dependent plasticity
Note from the ModelDB Administrator: the below is a copy of the author's web
site at
http://www.bi.s.u-tokyo.ac.jp/kuroda-lab/info/STDP/index.html
"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
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_STDP/
|
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_Volt/
|
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_BURST/
|
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. |
|
GRAPHS/
|
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. |
|
MODEL/
|
core33.g
|
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. |
|
initials33.g
|
Initial file loader for simulation of STDP and BURST. |
|
initials_VoltageClamp33.g
|
Initial file loader for simulation of Volt. |
|
initial_routines/
|
Initial files. |
|
Poirazi_cell/
|
A postsynaptic neuron model with a sample program. Execute
"./newgenesis main_Poirazi.g" with your own "newgenesis." |
|
genesis_customizing/
|
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:
- 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.
- 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.
- Fill the user configuration variables of ${Urakubo2008}/MODEL/genesis_customizing/Makefile
if you replaced the files with ${GENESIS_SOURCE}/Usermake.
- Fill the user configuration section of ${Urakubo2008}/MODEL/genesis_customizing/*/Makefile
if you replaced the files with ${GENESIS_SOURCE}/Libmake.
- "make" in the directory "${Urakubo2008}/MODEL/genesis_customizing".
- If the programs are compiled successfully, "cp ./newgenesis ./../../"
and enjoy the sample programs!
|
|
