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INCF Japan-Node and Platforms

Usui Shiro1*
  • 1 Neuroinformatics Japan Center, RIKEN BSI, Japan

The INCF national node of Japan (J-Node) (http://www.neuroinf.jp/) is established at the Neuroinformatics Japan Center (NIJC), RIKEN Brain Science Institute (BSI). Based on the achievement of a Japanese pilot study on Neuroinformatics Research in Vision (1), we developed a base-platform XooNIps (http://xoonips.sourceforge.jp) and several neuroinformatics platforms (PFs). PF committee members collaborate to develop databases that are available for use online, and together with the J-Node committee, we promote domestic activities in neuroinformatics in Japan.

PFs currently running under the J-Node are as follows: Visiome, Brain Machine Interface, Invertebrate Brain, Cerebellar Development Transcriptome, Comprehensive Brain Science Network, Cerebellar, Neuro-Imaging, Dynamic Brain, BSI-NI (under development) and Simulation (under development) (2). We here describe 2 platforms which are under development. The rest of PFs are opened at the J-Node portal.

BSI-NI platform is a general term for several platforms which developed in BSI. RIKEN has been participating in the "Integrated Database Project" which MEXT launched from 2006 to develop and promote life science databases in Japan. To meet the same needs in the brain science, BSI established BSI-NI committee to promote neuroinformatics in April 2008. The following databases are under development to open.
•BSI Microarray Database
•Construction of 3-Dimensional brain atlas of novel experimental rodent "Degu"
•Construction of 3-Dimensional brain atlas of novel experimental primate "Common Marmoset"
•Multichannel EEG data for Brain Machine Interface (BMI) and/or Human Emotions (HE)

Simulation platform (SimPF) provides a common environment for testing, evaluating and sharing computational models via web browser. Users can run a trial of computational models that are registered on PFs and Neuroinformatics databases; no need to install any software on their computers. A user is asked to upload a script of a model to SimPF from a web browser. Once uploaded, SimPF assigns a virtual machine (VM) for the user from SimPF clouds, and connects the VM automatically to the user's browser via VNC (Virtual Network Computing) protocol. We are also providing MPI simulation environment for various kind of neuron and local-circuit simulation. The system consists of portal hosts, ganglia server and execution hosts. Linux and open source software are used for every host and server. Anyone can easily access and use our cloud simulation environment from browser. Install and configuration methods are provided by the PF.

Since the establishment of J-Node and PFs 5 years ago, top-page access statistics of unique users per day for each PF are shown in the Figure. The slopes at the initial phase are about 20 persons/day, which is mostly by the committee members to develop the PF. Once the URL is publicized at large, the slope becomes roughly 100 persons/day, rising by 5 times. This shows the importance of such PFs in neuroscience.

References

1. Usui S (2003) Visiome: Neuroinformatics research in vision project. Neural Networks 16:1293-1300

2. Usui S, Yamazaki S, Ikeno H, Okumura Y, Satoh S, Kamiyama Y, Hirata Y, Inagaki K, Ishihara A, Kannon Y, Kamiji NL (2010) Simulation Platform: Model simulation on the cloud. Neuroinformatics2010

Conference: Neuroinformatics 2010 , Kobe, Japan, 30 Aug - 1 Sep, 2010.

Presentation Type: Poster Presentation

Topic: General neuroinformatics

Citation: Shiro U (2010). INCF Japan-Node and Platforms. Front. Neurosci. Conference Abstract: Neuroinformatics 2010 . doi: 10.3389/conf.fnins.2010.13.00039

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Received: 10 Jun 2010; Published Online: 10 Jun 2010.

* Correspondence: Usui Shiro, Neuroinformatics Japan Center, RIKEN BSI, Saitama, Japan, usuishiro@riken.jp