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Chapter 117 Neuroinformatics Japan Node and Platforms Chapter 117 Neuroinformatics Japan Node and Platforms Shiro Usui Abstract Since the establishment of NIJC in 2005 at the RIKEN Brain Science Institute, which represents the Japan Node of INCF, Japanese neuroinformatics activities has been enhanced to integrate outstanding research of neuroscience in Japan. We introduce the scheme and resources developed by NIJC. There are nine neuroinformatics platforms so far, including both already developed and under de- velopment. The J-Node portal has been accessed about 47,000 times per month on average inside and outside the country. We intend to increase the overseas users of the platforms on the J-Node site. Keywords Neuroinformatics · INCF · J-Node · platforms · XooNIps Introduction Neuroinformatics (NI) is concerned with integrating the diverse and complex neu- roscience data through information science in the inter/intranationally organized framework. The international framework is the International Neuroinformatics Co- ordinating Facility (INCF)1 established through the Global Science Forum of OECD on November 2005, while the intranational counterpart is the National Node of the INCF member country. The role of the National Nodes includes to coordinate neu- roinformatics activities within the country and to promote neuroinformatics devel- opment that supports the objectives of INCF. The Neuroinformatics Japan Center (NIJC) represents the INCF national Node of Japan (J-Node)2 . Together with the Japan Node Committee and the Platform Com- mittees, NIJC facilitates neuroinformatics research in Japan. Figure 117.1 shows J-Node in the center connected with nine platforms. Platform Committee members S. Usui RIKEN Brain Science Institute, Hirosawa 2-1, Wako, Saitama, 351-0198 Japan e-mail: [email protected] 1 http://www.incf.org/ 2 http://www.neuroinf.jp/ R. Wang et al. (eds.), Advances in Cognitive Neurodynamics, 679 C Springer Science+Business Media B.V. 2008 680 S. Usui Ministry of Education, Culture, Sports, Science and Technology INCF Request: Participation in INCF Paying the contributions Report INCF Support for drawing the framework Japan Node RIKEN BSI Committee Office Participation, JapanNode Paying the contributions Neuroinformatics Japan Center Establish Coordination Japanese-wide Framework for Maintenance of infrastructure Promoting research American European Support for developing and operating the system Node Nodes e vic NIJC Steering Committee Ad PF Coordinating Committee Committee Committee Committee Committee Committee Committee Committee Committee Committee Neuron CDT- Cerebellum NICT /Glia IVB BMI Visiome IBR NIMG DB PF PF PF PF PF PF PF PF Some platforms are under Neuroscience Researchers (Users) development and not released yet Fig. 117.1 Japan-Node scheme with INCF collaborate to develop their platforms. Each platform has been developed with a base platform system, XooNIps3 , which was developed by NI-Team at RIKEN BSI and is operated by NIJC. The registered users of a platform can freely download its contents and upload their own contents on it by a simple procedure with the approval of the platform Committee. These platforms are or will be accessible at the J-Node site. J-Node Platforms We here introduce each platform (PF) developed or under development at the J-Node portal site [1]. Cerebellar Development Transcriptome Database To elucidate the genetic basis for mouse cerebellar development, as a model sys- tem, the members analyze all of the transcriptional events (i.e., the transcriptome) responsible for developmental stages. CDT-DB has been developed to combine the large datasets of the expression profile information and the relevant bioinformatics, which not only allows us to delineate the complex genetic mechanisms underpinning cerebellar development but also provides a tool for sharing and mining of our large datasets. [PF head: Furuichi, Teiichi (RIKEN Brain Science Institute)] 3 http://xoonips.sourceforge.jp/ 117 Neuroinformatics Japan Node and Platforms 681 Neuron-Glia PF Focuses on how neuronal and glial cells and the networks of these cells work in a highly complex and dynamical system of brain and proposes to give math- ematical model descriptions to new findings and ideas on neural information pro- cessing. Neuron-Glia PF also provides the function to help collaboration of researchers. [PF head: Miyakawa, Hiroyoshi (Tokyo University of Pharmacy and Life Sciences)] Invertebrate Brain PF IVB PF allows us to share such resources as the physiological and behavioral data from insects and other invertebrate animals. For example, Invertebrate Brain Gallery - a collection of images of nervous systems in various invertebrates - is constructed and managed by the original XooNIps module. Original image data of invertebrate neurons, such as interneuron of antennal lobe of moth brain, are collected on the site. [PF head: Kanzaki, Ryohei (University of Tokyo)] Cerebellum PF Is a database of the all kinds of information on a cerebellum with an unique structure and role in motor learning. The platform will provide a history of the cerebellar research and the basic concepts of the cerebellar structure and function, references and images, experimental data for the modeling, source codes of neural network models, and other tools for the study of the cerebellum. The members will focus on the two important cerebellum-dependent experimental paradigms, i.e., adaptation of the eye movements and eyeblink conditioning. [PF head: Nagao, Soichi (RIKEN Brain Science Institute)] Brain-Machine Interface PF BMI is the interface in which mechanical devices provide sensory input to the brain, or are controlled by the motor output signals recorded in the brain. BMI PF is a database of BMI researches covering the research fields of neuroscience, compu- tational theory, robotics etc. It provides organically linked information about BMI to researchers of the field inside and outside the country and support researches to develop their study or understanding of BMI. By using a clickable map of re- search sites about BMI, users can figure out trends of BMI studies around the world. [PF head: Iijima, Toshio (Tohoku University)] 682 S. Usui Visiome PF is a vision science neuroinformatics platform, which was developed by NRV project [2]. Since reproducibility is a key principle of the scientific method, published re- sults must be testable by other researchers using the same methods. The platform collects various kinds of reference files and makes them organized and packaged as a single item in Visiome Binder, which is useful for providing a reading list for students, a collection of models and data with a particular interest, a collection of ed- ucative movies in vision science. [PF head: Kamiyama, Yoshimi (Aichi Prefectural University)] Integrative Brain Research PF The IBR project is comprised of about 300 principal investigators (PIs) from dif- ferent neuroscience areas. The database committee is planning both top-down and bottom-up types of databases. For the former, the database committee will collect the outcomes of the research of individual PIs and will publish these research out- comes on IBR PF. Although the activity of the project will finish in 5 years, the content will be maintained and updated by the IBR-PF committee under the J-Node afterwards. [PF head: Isa, Tadashi (National Institute for Physiological Sciences)] Neuroimaging PF NIMG-PF committee members are registering bibliographies, tutorial materials, software contents, experimental data and other information and links related to var- ious neuroimaging technologies such as MRI, MEG, EEG, PET, and NIRS, and their integrations. They are also developing convenient visualization functions for neuroimaging databases, which are capable of an easy-to-use display of 3D brain images and a function of search by pointing locations on the images. In addition, there is a plan of registering MEG multi-dipole analysis software and raw data of MRI and MEG. [PF head: Suzuki, Ryoji (Kanazawa Institute of Technology)] Neuroinformatics Common Tools PF NICT PF aims to share mathematical theory, algorithm, analytical tool and NI- supporting environment. At present, software tools and NI-supporting environment developed by NI-Team for neuroscientists are being registered, such as (1) Cus- tomizable base platform; XooNIps, (2) Personal database software; Concierge, (3) System analysis total environment; SATELLITE, and (4) Visualization tools; Samurai-Graph. [PF head: Usui, Shiro (RIKEN Brain Science Institute)] 117 Neuroinformatics Japan Node and Platforms 683 Concluding Remarks We have kept track of the access log to the J-Node site regularly since it was revised in July 2006. Figure 117.2 shows the records on monthly basis as of May 31 2007. The average number of site access is approximately 47,000 per month. This number has much increased because the portal was revised to be easier to find the informa- tion of users’ interests and to provide information in English as well. Figure 117.2 also reveals that the site is accessed not only from jp domain but also from other country domains (us, au, eu, de, and so on). It is necessary to collect significant resources to attract users and promote the J-Node site over the countries. 60,000 50,000 40,000 30,000 Non JP Access JP 20,000 10,000 0 e ly g ct v c b n u u O e Jan e Ju J A Sep No D F Mar Apr May Month 2006 2007 Year Fig. 117.2 The number of access to the J-Node portal site (June ’06 - May ’07) Acknowledgements I would like to thank Dr.Amari, Shun-ichi at RIKEN BSI and all members of the PF Committees for their supports and collaborations. References 1. Usui, S., Furuichi, T., Miyakawa, H., Ikeno, H., Nagao, S., Iijima, T., Kamiyama,Y., Isa, T., Suzuki, R., Ishikane, H.: Japanese Neuroinformatics Node and Platforms. ICONIP2007 Pro- ceedings, (2007). 2. Usui, S.: Visiome: Neuroinformatics research in vision project. Neural Networks, 16 (2003) 1293–1300..
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