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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



updating of the site
Copyright (C) 2018 Neuroinformatics Unit, RIKEN Center for Brain Science