Rin Kuriyama*, Kaaya Akira*, Laura Green, Beatriz Herrera, Kael Dai, Mari Iura, Gilles Gouaillardet, Asako Terasawa, Taira Kobayashi, Jun Igarashi, Anton Arkhipov, Tadashi Yamazaki (*: equally contributed). Microscopic-Level Mouse Whole Cortex Simulation Composed of 9 Million Biophysical Neurons and 26 Billion Synapses on the Supercomputer Fugaku. in The International Conference for High Performance Computing, Networking, Storage and Analysis (SC ’25), November 16–21, 2025, St Louis, MO, USA. ACM, New York, NY, USA, 11 pages. doi: 10.1145/3712285.3759819.
Credits: Barry Isralewitz, with contributions by Kaaya Akira-Tamura, Kael Dai, Laura Green, Beatriz Herrera, Tadashi Yamazaki, and Anton Arkhipov.
Neulite is a light-weight neuron simulator for biophysically-detailed neuron models and their network models. It focuses on only neuron models registered on Allen Cell-Types Database, and can run models described in Brain Modeling ToolKit (BMTK) with a minimum rewrite. It consists of the frontend (Bionetlite module) and the backend (Neulite kernel) clearly separated, and the clear separation contributes to the portability of the kernel. As a result, the Neulite kernel runs on various architectures from Raspberry PI to the Supercomputer Fugaku. Furthermore, the Fugaku version of the kernel fully supports SIMD operations using Scalable Vector Extensions (SVE).
Neulite is developed to run the Allen V1 model on Fugaku. It is not planned to become a complete simulation environment such as NEURON and Arbor. Therefore, Neulite will not compete with them. Rather, Neulite focuses on the simplicity. In this respect, the development of Neulite is deeply influenced by the UNIX philosophy.
(Read more: The Neulite kernel as an MVP, Why isn’t the Neulite kernel written in C++?)
Source code
https://github.com/neulite/neulite/
This is the official version of the code, distinct from the one used for the SC’25 paper. The code for the paper originated from a prototype, which has been released along with the paper as Artifacts as part of the SC Reproducibility Initiative. An Artifact Description (AD) and Artifact Evaluation (AE) is appended to the paper, so please refer to those sections.
Technical Document
Members
Core team
Kaaya Akira-Tamura, Rin Kuriyama, Mari Iura, Tadashi Yamazaki
Advisors
Taira Kobayashi, Jun Igarashi
Collaborators
Whole mouse cortex simulation: Anton Arkhipov, Beatriz Herrera, Laura Green, Kael Dai (Allen Institute)
Advanced usage of Fugaku : Gilles Gouaillardet, Asako Terasawa (RIST)
Selected publications
- Rin Kuriyama*, Kaaya Akira*, Laura Green, Beatriz Herrera, Kael Dai, Mari Iura, Gilles Gouaillardet, Asako Terasawa, Taira Kobayashi, Jun Igarashi, Anton Arkhipov, Tadashi Yamazaki (*: equally contributed). Microscopic-Level Mouse Whole Cortex Simulation Composed of 9 Million Biophysical Neurons and 26 Billion Synapses on the Supercomputer Fugaku. in The International Conference for High Performance Computing, Networking, Storage and Analysis (SC ’25), November 16–21, 2025, St Louis, MO, USA. ACM, New York, NY, USA, 11 pages. doi: 10.1145/3712285.3759819.
- Kaaya Akira-Tamura, Rin Kuriyama, Mari Iura, Taira Kobayashi, Jun Igarashi, Tadashi Yamazaki. Development of a lightweight and customizable biophysical neuron simulator. Annual Meeting of Society for Neuroscience (Neuroscience2024) , October 5-9, 2024, Chicago, USA.
Press releases
Allen Institute:
https://alleninstitute.org/news/one-of-worlds-most-detailed-virtual-brain-simulations-is-changing-how-we-study-the-brain/
The University of Electro-Communications:
https://www.uec.ac.jp/eng/news/announcement/2025/20251118_7309.html