Program at a Glance

      [Click the blue text in the table for more information]

1st workshop day, Dec. 21 (Fri)
Time Event place

Reception Desk Open

Okochi Hall

Opening Remarks

Okochi Hall

Keynote Lecture 1:  Dr. E. CHESLER

Okochi Hall

Keynote Lecture 2:  Dr. K. KAIBUCHI

Okochi Hall



Organized Session 1: Large Scale Mouse Brain Data

Okochi Hall

Group Photo

Okochi Hall

Lunch Break


Poster Session

  Core time: 14:00 Odd; 14:30 Even

C61, 2F



Organized Session 2: Neuroinformatics and Drug Discovery

Okochi Hall



Organized Session 3: Neuroinformatics in INCF Japan Node

Okochi Hall



Social Gathering

C72, Hirosawa Club


2nd workshop day, Dec. 22 (Sat)
Time Event place

Reception Desk Open

Okochi Hall            

Keynote Lecture 3:  Dr. N. KOBAYASHI

Okochi Hall

Keynote Lecture 4:  Dr. B. URIA

Okochi Hall



Organized Session 4: Challenges in Data Analysis for Innovation in Neuroscience

Okochi Hall

Closing Remarks

Okochi Hall



Tutorial Courses

C61, 2F    

Course 1: Description of EEG data


Course 2: Creating the Insect Brain


Course 3: Collaborative Large-Scale Modelling


Closing of Tutorial Courses

<Note to poster presenters>
Put up posters  9:00 - 13:20, Dec. 21
Remove posters  15:00, Dec 21 - 9:30, Dec. 22

Opening Remarks 

9:30 - 9:45, Dec.21

Shun-ichi AMARI   (RIKEN Center for Brain Science)

Keiji TANAKA        (RIKEN Center for Brain Science)

Taishin NOMURA   (Osaka University)

Keynote Lectures back to page top

Keynote Lectures                    Dec. 21

KL-1 9:45 - 10:25 Elissa J. CHESLER (The Jackson Laboratory, USA)

'Finding relations among genes, brain and behavior in heterogeneous functional genomics data'

KL-2 10:25 - 11:05 Kozo KAIBUCHI (Nagoya University, JP)

'KANPHOS (Kinase-Associated Neural PHOspho-Signaling), a comprehensive database for specific substrates of kinases'

Keynote Lectures                    Dec. 22

KL-3 9:30 - 10:10 Norio KOBAYASHI (RIKEN ISC, JP)

'Novel trends in research data utilisation based on open science'

KL-4 10:10 - 10:50 Benigno URIA (Google DeepMind, UK)

'Vector-based Navigation using Grid-like Representations in Artificial Agents'


Organized Sessions back to page top

OS 1: Large Scale Mouse Brain Data               Dec. 21

 Organized by Tsuyoshi MIYAKAWA, Akira SATO

OSⅠ-1 11:25 - 11:50  Tsuyoshi MIYAKAWA (Fujita Health University)

'Endophenotype in the brain: A key concept for understanding the relationships between genes and behavior'

OSⅠ-2 11:50 - 12:15  Akira SATO  (Tokyo University of Science)

'Brain Transcriptome Database (BrainTx)'

OSⅠ-3 12:15 - 12:40  Hiroshi MASUYA  (RIKEN BRC)

'RDF-based data integration of mouse phenotype'

OS 2: Neuroinformatics for Drug Discovery        Dec. 21

 Organized by Junichiro YOSHIMOTO and Yoshiyuki ASAI

OSⅡ-1 15:10 - 15:30 Junichiro YOSHIMOTO  (Nara Institute of Science and Technolgy)

'Potential of KANPHOS Platform for drug discovery'

OSⅡ-2 15:30 - 15:55 Samik GHOSH  (Systems Biology Institute)

'Towards creating an engine of scientific discovery'

OSⅡ-3 15:55 - 16:20 Masahito OHUE (School of Computing, Tokyo Institute of Technology)

'High performance computing drug discovery- Toward Targeting Protein-Protein Interactions'

OS 3:Neuroinformatics Infrastructure and Platforms in INCF Japan Node   Dec. 21

Organized by Yoko YAMAGUCHI

OSⅢ-1 16:40 - 16:55 Yoko YAMAGUCHI (RIKEN)

'Neuroinformatics and FAIR in INCF Japan Node'

OSⅢ-2 16:55 - 17:10 Yuko OKAMURA-OHO (Jissen Woman's University)

'ViBrism DB: data and platforms'

OSⅢ-3 17:10 - 17:20 Shinobu MASAKI (Brain Activity Imaging Center, ATR Promotions, Inc.)

'Recent Activities of NeuroImaging-Platform'

OSⅢ-4 17:20 - 17:35 Taishin NOMURA  (Osaka University) 

'Open and sustainable repositories for sharing data and models in neuroscience are indispensable to deepening understanding dynamic information processing in the brain

Discussion 17:35 - 17:40

OS 4: Challenges in Data Analysis for Innovation in Neuroscience          Dec.22

Organized by Shinji KAKEI, Alexander WOODWARD and Yoshinobu KANO

OSⅣ-1 11:10 - 11:25 Shinji KAKEI  (Tokyo Metropolitan Institute of Medical Science)

Big data in neuroscience

OSⅣ-2 11: 25 - 11:40 Alexander WOODWARD  (RIKEN CBS) 

Automated Connectomics Pipelines on HPCs using A.I and Computer Vision'

OSⅣ-3 11:40 - 11: 55 Yoshinobu KANO  (Shizuoka University)

Natural Language Processing, Neuroscience, and “AI”’

Panel Discussion 11:55 - 12:10

Poster Session back to page top

13:20 - 15:00 Dec. 21
     Core Time I   14:00 - 14:30  Odd Poster Number
     Core Time II 14:30 - 15:00  Even Poster Number

Large Scale Mouse Brain Data

 PS-1 Hiroshi OKAMOTO (Dwango Artificial Intelligence Laboratory) et. al.

'Connectome informatics: Reverse engineering of whole brain networks'

 PS-2 Akira SATO (Tokyo University of Science) et. al.

'Current activities of BrainTx platform - Brain transcriptome and Neural gene ontology projects'

 PS-3 Morteza HEIDARINEJAD (Computational Engineering Application Unit, RIKEN) et. al.

'Development of simulation platform for multiple cortico-thalamic circuits using pyNEST'

Challenges in Data Analysis for Innovation in Neuroscience

 PS-4 Yuka UENOHARA (University of Hyogo) et. al.

'Construction of the honeybee standard brain for primary auditory center'

 PS-5 Hidetoshi URAKUBO (Kyoto University) et. al.

'Development of a unified environment for automated neuronal network reconstruction from EM images'

 PS-6 Ken NAKAE (Kyoto University) et. al.

'Individuality of macro-scale connectome of common marmoset with global fiber reconstruction by diffusion MRI'

 PS-7 Shinji KAKEI (Tokyo Metropolitan Institute of Medical Science)

'Issues in evaluation of movement disorders'

 PS-8 Rui GONG (RIKEN CBS) et. al.

'The Brain/MINDS Cortical Flat Map for Visualize Neuroimaging Data'

 PS-9 Hiromichi TSUKADA (Okinawa Institute of Science and Technology Graduate University) et. al.

'Analysis of Local Excitatory-Inhibitory Balance using Whole-Brain Model based on the Common Marmoset MRI Data'

 PS-10 Henrik SKIBBE (Kyoto University) et. al.

'MarmU-Net: Axon tracer signal detection using an artificial neural network'

 PS-11 Yasutaka FURUSHO (Nara Institute of Science and Technology) et. al.

'Non-asymptotic analysis of Fisher information matrices of Multi-layer perceptron, ResNet, and Batch-normalization'

 PS-12 Akihiro NAKAMURA (Osaka University) et. al.

'Postural and beta-band electroencephalogram responses to floor-surface perturbations during human quiet standing'

Neuroinformatics Infrastructure and Platforms in INCF Japan Node

 PS-13 Takeru HONDA (Tokyo Metropolitan Institute of Medical Science) et. al.

'New release of cerebellar platform'

 PS-14 Masahide MAEDA (RIKEN CBS) et. al.

'Brain/MINDS Database System Design for Large-Scale Dataset Registration, Sharing and Publication'

Computational modelling

 PS-15 Carlos GUTIERREZ  (Okinawa Institute of Science and Technology Graduate University) et. al. 

Spiking neural network model of the basal ganglia with realistic topological organization'

 PS-16 Hayeong LEE (The University of Tokyo) et. al.

'The Conductance-based model for neurons in the olfactory circuit of Bombyx mori'

 PS-17 Takahiro AIZAWA (Dwango Artificial Intelligence Laboratory) et. al.

         'Construction of functional hypothesis about brain local circuit by integrating neuroscientific knowledge as a framework'

 PS-18 Hayato TSUNODA (The University of Tokyo) et. al.

'Creating real scale simulation model of optic lobe based on Drosophila’s neural information'

 PS-19 Jo TAKANO (Kobe University) et. al.

'Simulation for Simplified Neural Network Model of Ultrastructure within an Olfactory Sensory Unit for Nestmate and Non-nestmate Discrimination in the Japanese Carpenter Ant'

 PS-20 Zhe SUN (Dwango Artificial Intelligence Laboratory) et. al.

'Spatial property of excitation and inhibition in a spatial neural network of the rodent primary somatosensory cortex'

Closing Remarks

12:10 - 12:20, Dec. 22

Shiro USUI   (Professor Emeritus, Toyohashi University of Technology)

Yoko YAMAGUCHI       (RIKEN Center for Brain Science)


Tutorial Courses back to page top

13:30 - 16:30, Dec. 22

C1: Description of EEG Data in a Standard Format based on NIX/odML schemes

Lecturer: Hiroaki WAGATSUMA (Kyusyu Institute of Technology)

Overview: This tutorial will give a short lecture for the standardization of multi-time scale (different sampling rate) timeseries obtained in the simltaneous recording, which is expected to add annotations to data epoches by usuing with meta-data descriptions. Participants exprience and learn
 i) the procedure of the data conversion of the human EEG data (.mat) and Eye-Tracking data (.json) to a single package of the standard format based on NIX (.nix) with given annotations on odML,
ii) programming to extract a specific target data of interest (NIX data access method) and visualize it in plot,
iii)  data analysis of the target data, generation of a new meta data label depending on the interest and re-embed the new metadata into the NIX format data.

The data and sample codes will be provided in the session. MATLAB (nix-mx) and Java (nix-java) are also available in the system; however we are using the python software tools in the tutorial.

A limit in the number of participants:  possibly 20 (30 as maximum)

Requirements of participants:

  • Experience of the use of linux or mac and python programming.

(windows PC is acceptable under the following condition.)

  • Participants are recommended to install "nixio" (as follows) in their own laptops if the PC are unix or mac (the instration will be done for 5-10mins), while if it is windows, the setting of python environment, installations and the software dependency check is taking time a lot. Therefore, if it is windows, participants must complete to install "nixio" in their windows PCs by themselves according to the installation manual in the web (*).

The simplest way to install NIXPY is from PyPI using pip, like  

pip install nixio           #python2
pip3 install nixio         #python3

(*) Neuroscience information exchange format - NIX:
-data model for storing fully annotated datasets


NIX-odML Global Workshop & Hackathon 2017 in Japan (with References more in the site)

C2: Creating the insect brain

Lecturers: Hidetoshi IKENO (University of Hyogo) and  Tomoki KAZAWA (The University of Tokyo)

Overview: This tutorial will give basic skills for the image processing using the confocal image data for constructing a standard brain map of small insect brain. Its applications will be also presented. We are using several software tools for the image processing and visualization.

A limit in the number of participants: 10

Requirements of participants: 

  • Their notebook PC needed on the day.

Note: The tutorial will be conducted in Japanese and used a Japanese text book “昆虫の脳をつくる”.  We will prepare materials based on the book for the day.


  • 神崎亮平(編)『昆虫の脳をつくる』朝倉書店,2018 (in Japanese)

C3: Introduction of Collaborative Large-Scale Modeling for High-Performance Computing

Lectures: Keiichiro INAGAKI (Chubu University), Takayuki KANNON (Kanazawa University) and Yoshihiro OKUMURA (RIKEN CBS)

Overview: This tutorial will give a short lecture for collaborative large-scale modeling and a hands-on using computer cluster. In the lecture, we/participants parallelize the several program code for brain system, connecting them using neuroinformatics tools, and simulate as one large-scale model in the computer cluster.

A limit in the number of participants:  We expect 5-8 participants. If we have received more applications that expected, we will select the participants based on background and experience.

Requirements of participants:

  • Participants must have laptop with installing ssh to log onto our computer cluster.
  • Experience of the use of linux and c/c++ programming.

Note: Part of lecture might be performed in Japanese.


  • T. Kannon, K. Inagaki, N.L. Kamiji, K. Makimura, S. Usui, PLATO: Data-oriented approach to collaborative large-scale brain system modeling, Neural Networks, vol.24, 9, pp.918-926, 2011.



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