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Resources of the IOSSIM



IOSSIM (Insect Olfactory System Simulator) is a software system developed for K computer. This system was developed as one of the projects for "Research and Development of Next-Generation Integrated Life-Science Simulation Software (ISLiM)" supported by Next-Generation Supercomputer Project of MEXT.

IOSSIM contains following one series of database and three softwares
1.Bombyx Neuron Database; BoND/IVBPF)
2.KNEWRiTE: sofotware for extracting neural structure of individual neurons
3.NEUROREGISTER: software for generating a neural network in a standard brain
4.NEURON_K+: software for simulating a large-scale neural network


        Figure 1. Structure of IOSSIMの構成

■BoND/IVBPF
This database contains physiological and morphological properties of more than 1600 brain neurons of male silkmoths (Bombyx mori).This database is partly open for public. Publised database

■KNEWRiTE
Extraction software of neuron structure. PC based software. Working on windows/linux conditions.


Download: Source Cord

■NEUROREGISTER

Software for mapping neurons (SWC format) into a standard brain using FIJI. Fiji is an image processing package. It can be described as a distribution of ImageJ (and soon ImageJ2) together with Java,

Download: Source Cord

■NEURON_K+
NEURON_K+ is a simulation environment for modeling individual neurons and networks of neurons based on NEURON, which is tuned for K computer.


Download: Source Cord 2012/05

Download: Soruce Cord 2012/09

How to install NEURON_K+

1. Uncompress NEURON_K+.
  > tar xvzf neuron_kplus_release[version].tar.gz

  > mv neuron_kplus_release[version].tar.gz neuron_kplus

2. Download original NEURON source codes and move.

  > wget http://www.neuron.yale.edu/ftp/neuron/versions/v7.2/nrn-7.2.tar.gz"
  >http://www.neuron.yale.edu/ftp/neuron/versions/v7.2/nrn-7.2.tar.gz%3C/a%3E%3Cbr />

  > tar xvzf nrn-7.2.tar.gz

  > mv nrn-7.2 neuron_kplus/nrn


3. Apply the patch to the NEURON.

  > cd neuron_kplus

  > patch -p0 < neuron_kplus_release[version].diff


4. Make MOD file compiler.

  > cd nrn

  > ../config_sh/config_mod_[machine].sh

  > make

  > make install


5. Make NEURON.

  > ../config_sh/config_nrn_[machine].sh

  > make

  > make install

Source Cord Page

+++Compile including custum mode

1. special (nrniv+追加mod(adding ion channel model)の実行ファイル)の作成
1a) nocmodl(GCC mod>C translater)のnrn/sparc64/binへのコピー

For example,
/home/group010/user0046/k+/v3/nrn/sparc64/bin

cp ../../x86_64/bin/nocmodl . 

1b) modファイルの準備
任意の場所で
tar –xvf mod.tar.gz

1c) コンパイル (Compiling)
mod内で
make_mod.sh
を実行

1d) 結果 (Results)
mod/sparc64/Special」ができているはず

2.Job Processing

2a) 解凍(Extraction)
適当な場所で(一応ルートを想定)

tar xvf hocjobs.tar.gz

2b) スクリプト書き換え
cd hocjobs
nkjob.shの
パスを書き換え

2c) 実行(Run)
pjsub nkjob.sh



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