Simulation Platform: Quick and easy access environment of model simulation in computational neuroscience

    For various levels of study in neural modeling, it is effective to utilize multiple neural models described at different scales seamlessly. The Internet and database technology provide us a compelling environment for computational neuroscience, specifically for downloading and using neural models. However, conventional neuroinformatics databases used to be designed for archiving model program files. To reuse such models, users often face problems when installing the required simulators and tools, and in some cases, execution is not successful. Therefore, we have been developing a simulation environment named “Simulation Platform” that allows trial of such existing resources [1,2,3].

    The Simulation Platform provides a cloud of virtual machines running GNU/Linux for scientists to use and validate the models without downloading and installing them. Each virtual machine is equipped with various software including developer tools such as compilers and libraries, popular neural simulators such as GENESIS, NEURON, and NEST, and scientific software such as Gnuplot, R, and Octave.

    We developed and opened a pre-release site of the Simulation Platform (http://sim.neuroinf.jp/) (Figure 1). When a user posts a request on the platform, a virtual machine is assigned and the requested simulation is executed automatically. The user remotely accesses to the machine through a web browser. If you have a tablet or a smartphone with web browser capability, such as iPad and iPhone, you can get a test bed on your hand. Therefore, the Simulation Platform is expected to eliminate impediments to handle and share multiple neural models.

References:

[1] Usui, S., Yamazaki, T., Ikeno, H., Okumura, Y., Satoh, S., Kamiyama, Y., Hirata, Y., Inagaki, K., Kannon, T., Kamiji, N., & Ishihara, A. (2009). Simulation platform: a test environment of computational models via web. In Front. Neurosci. Conference Abstract: Neuroinformatics 2009. doi: 10.3389/conf.neuro.11.2009.08.047

[2] Usui, S., Yamazaki, T., Ikeno, H., Okumura, Y., Satoh, S., Kamiyama, Y., Hirata, Y., Inagaki, K., Ishihara, A., Kannon, T., Kamiji, N., & Akazawa, F. (2010). Simulation platform: Model simulation on the cloud. In Front. Neurosci. Conference Abstract: Neuroinformatics 2010. doi:10.3389/conf.fnins.2010.13.00100

[3] Yamazaki, T., Ikeno, H., Okumura, Y., Satoh, S., Kamiyama, Y., Hirata, Y., Inagaki, K., Ishihara, A., Kannon, T., Usui, S. (2011), Simulation Platform Beta: A Clound-Based Online Simulation Environment. Submitted to Neural Networks.