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Development of an on-line simulation platform for neuroscience research

Hidetoshi Ikeno1*, Tadashi Yamazaki2, Yoshimi Kamiyama3, Akito Ishihara4, Keiichiro Inagaki5, Yutaka Hirata5, Yoshihiro Okumura6, Takayuki Kannon6, Shunji Satoh2, Hiroaki Wagatsuma7, Yoshiyuki Asai8, Yoko Yamaguchi6 and Shiro Usui9
  • 1 University of Hyogo, Japan
  • 2 The University of Electoro-Communications, Japan
  • 3 Aichi Prefectural University, Japan
  • 4 Chukyo University, Japan
  • 5 Chubu University, Japan
  • 6 RIKEN, Japan
  • 7 Kyushu Institute of Technology, Japan
  • 8 Okinawa Institute of Science and Technology, Japan
  • 9 Toyohashi University of Technology, Japan

Various data analysis algorithms and computational models have been proposed and utilized in neuroscience. Especially, theoretical approach to the neuronal system is indispensable for further advance in neuroscience. Recently, a number of software packages for data analysis and simulation of computational models have been provided on the Internet, and many of them are becoming open-access for researchers. However, we should to prepare the suitable computer environment where the numbers of software are installed for using these software resources. It will be sometimes caused problems by difference of operating system, version of software or lack of library files. In our project, we have been developing and providing a virtual machine environment for neuroscience research called Simulation Platform (Sim-PF, http://sim.neuroinf.jp) (Yamazaki et al., 2011) to use computational model and programs on the Internet without any barrier. The virtual machine based Linux is started by user demand, then executed script for downloading model file and running it on the virtual machine (VM) automatically. The server system managing VM is developed by Guacamole 0.8.4 and OpenNebula 4.12. Now, we are setting up for providing VM with Microsoft Windows OS. It is providing standard application software in neuroscience research, such as Fiji, vaa3D for image processing and 3D viewing; NEURON and GENESIS are for neuronal simulation. The Sim-PF provides not only utilities for visualization and simulation, but also the high-speed access to the registered data for retrieving and using large amount of data. It lets users be free from preparing the environment to carry out simulation, and lets users immediately get started on simulations for reviewing and analyzing existing models as well as for reviewing newly presented models submitted for publications. Up to now we have been developing online simulation pages for ModelDB contents, and the most of models registered on the ModelDB can be run on the web browser without installing any simulation software. As some of ModelDB contents are developing on MATLAB, one wishes to use these contents have to buy MATLAB license even just for evaluation. However, in the Sim-PF, these contents are registered after pre-compiling by MATLAB compiler and executed them for evaluation very easily. The platforms running by NIJC (http://www.neuroinf.jp/) supply various kinds of contents, such as data analysis program and experimental data. We are developing new contents, which can easily review these valuable resources on our platform. As an example of collaboration contents with other platform, users can review reconstruction process and results of neuronal morphological structure from confocal image data registered on the invertebrate brain platform (IVB-PF) on the Sim-PF. Registration of neuron model into the standard brain can be understand by following our contents. The tutorial movies for supporting users and education of students are making and uploading onto the Youtube. These are used to conduct a tutorial for newly joined students to the laboratory. In this moment, these movies are developed only in Japanese, but we are translating and uploading in English near future. The Sim-PF will be improved their functions and contents for further support education and research in neuroscience fields.

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References

Yamazaki, T., Ikeno, H., Okumura, Y., Satoh, S., Kamiyama, Y., Hirata, Y., Inagaki, K., Ishihara, A., Kannon, T., Usui, S. (2011). Simulation Platform: a cloud-based online simulation environment. Neural Netw. 2011 Sep;24(7):693-8. doi: 10.1016/j.neunet.2011.06.010. Epub 2011 Jun 23.

Keywords: simulation models, data visualization, Portal site, computational modeling, data analysis

Conference: Neuroinformatics 2015, Cairns, Australia, 20 Aug - 22 Aug, 2015.

Presentation Type: Demo, not to be considered for oral presentation

Topic: Infrastructural and portal services

Citation: Ikeno H, Yamazaki T, Kamiyama Y, Ishihara A, Inagaki K, Hirata Y, Okumura Y, Kannon T, Satoh S, Wagatsuma H, Asai Y, Yamaguchi Y and Usui S (2015). Development of an on-line simulation platform for neuroscience research. Front. Neurosci. Conference Abstract: Neuroinformatics 2015. doi: 10.3389/conf.fnins.2015.91.00029

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Received: 07 Apr 2015; Published Online: 05 Aug 2015.

* Correspondence: Prof. Hidetoshi Ikeno, University of Hyogo, Himeji, Japan, ikeno@shse.u-hyogo.ac.jp