Simulation Platform: a test environment of computational models via web
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1
RIKEN Brain Science Institute, Neuroinformatics Japan Center, Japan
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2
University of Hyogo, Japan
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3
The University of Electro-Communications, Japan
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4
Aichi Prefectural University, Japan
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5
Chubu University, Japan
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6
Chukyo University, Japan
The importance of theoretical and computational approaches is rapidly growing in the neuroscience community. To date, a number of computational models have been developed, and many of them are going to be open-access for researchers to validate and reutilize. We are willing to support this trend: Neuroinformatics Japan Center (NIJC) has been hosting 8 neuroinformatics databases called platforms. Each platform contains a variety of computational models as well as research papers, experimental data, and analysis tools, that will enable the researcher to share knowledge on neuroscience and to accelerate their research.
Although a number of computational models are available on other platforms and databases, preparing the environment to carry out simulation using these models is still inconvenient. If a model is written for neural simulators such as NEURON or GENESIS, we have to install these simulators on our computers. If a model is written in C or C++, we have to prepare developmental tools including gcc, g++, make and other scientific libraries. Furthermore, if a model is written in MATLAB, there is no way but to purchase MATLAB, even for a trial run. Here, we present our on-going efforts on launching a web service called Simulation Platform (SimPF). SimPF provides a test environment of computational models via the web. Users can run a trial of computational models that are registered on Neuroinformatics databases and platforms such as ModelDB. All procedure uses a web browser; there is no need to install any software on their computers. A user is asked to upload a script of a model to SimPF. 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 the VNC (Virtual Network Computing) protocol. A VM is a Linux box running Debian GNU/Linux, on which a variety of neural simulators and developmental tools are installed. The user can use these softwares to run the uploaded script and thereby carry out simulations on the VM. The VM is alive only for 5 minutes, after which a new VM is cloned to prevent the system from trojans or traps.
Summarizing, SimPF lets the users be free from preparing the environment to carry out simulations and thereby supporting and speeding up their neuroscience research. We hope it can be also utilized to validate models for journal reviews. We will present the detailed specification of our platform and perform some live demonstrations.
Conference:
Neuroinformatics 2009, Pilsen, Czechia, 6 Sep - 8 Sep, 2009.
Presentation Type:
Oral Presentation
Topic:
Large scale modeling
Citation:
Usui
S,
Yamazaki
T,
Ikeno
H,
Okumura
Y,
Satoh
S,
Kamiyama
Y,
Hirata
Y,
Inagaki
K,
Kannon
T,
Kamiji
NL and
Ishihara
A
(2019). Simulation Platform: a test environment of computational models via web.
Front. Neuroinform.
Conference Abstract:
Neuroinformatics 2009.
doi: 10.3389/conf.neuro.11.2009.08.047
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Received:
22 May 2009;
Published Online:
09 May 2019.
*
Correspondence:
Shiro Usui, RIKEN Brain Science Institute, Neuroinformatics Japan Center, Wako-shi, Japan, usuishiro@riken.jp