J-Node Hackathon 2018 March

J-Node Hackathon is a collaborative event organized by INCF Japan Node to facilitate the developments in neuroinfomatics field, which concerns with diverse and huge neuroscience data using database technology, computational tools and the various other software applications on local PC and on the internet.

Participants in our past hackathons are not only INCF Japan node members, but are national project members of SPPBS and Brain/MINDS, collaborative/cooperative neuroscientists, students and software engineers. We welcome anyone who are interested in Neuroinformatics. Please visit https://www.neuroinf.jp/program/j-node-hackathon.html for the details of our past hackathons. Our goal in this event are mainly collaborations, promotion and standardization of neuroscience databases. So far, we pursued themes mainly from two lines, the brain image standardization and ontology. However, we welcome new ideas and suggestions how to organize big data using new framework for making comparison between data, new UI, new modeling methods, some applications of your daily neuroinformatics work and so on.


Leaflet (English)  Leaflet (Japanese)

The event was closed. Thank you everyone who participated.



 Ideathon     March 6 (Tue) 10:00AM - 5:00PM , 2018

 Hackathon   March 18 (Sun) 10:00AM -20 (Tue) 6:00PM, 2018


   Ideathon       RIKEN BSI East Building 1F Seminar room  http://www.brain.riken.jp/en/access/

        Wako-shi Station (Tobu Tojo line / Subway Yurakucho line /Subway Fukutoshin line) 20 minutes' walk

   Hackathon    Φcafe https://phi.cafe/ (Japanese only)  * Free Wi-Fi is available.

        Hongo-sanchome Station (Subway Oedo line) 3 minutes' walk / Hongo-sanchome Station (Subway Marunouchi line) 5 minutes' walk

U R L: https://www.neuroinf.jp/hackathon2018/march.html (We will update from time to time)

Organized by: Neuroinformatics Japan Center, RIKEN BSI

Committee: J-Node Hackathon Working Group

  • Tomoki KAZAWA(Group Leader) (The University of Tokyo)
  • Hidetoshi IKENO(University of Hyogo)
  • Teiichi FURUICHI (Tokyo University of Science)
  • Yoshiyuki ASAI (Yamaguchi University)
  • Akira SATO (Tokyo University of Science)
  • Yukiko NOTA (ATR-Promosions Brain Activity Imaging Center)
  • Yoshihiro OKUMURA (RIKEN BSI)
  • Itsuko ISHII (RIKEN BSI)

Number of participants: 30 at most

Application method: Please fill in the application form and send it to J-Node Hackathon secretariat

Contact: info@nijc.brain.riken.jp (J-Node Hackathon secretariat)

Deadline of registration submission: February 15 (Thu), 2018  Deadline is extended to February 22(Thu)
                  Registration is now closed

  • Support for travelling expenses will be considered with priority to the students. Please consult us if you have the request. However please be advised that we may not be able to accommodate in full. 
  • Students need to get permission from their supervisors. Please fill in the application form including your supervisor’s name and the contact information. Also, please include your supervisor’s e-mail address to CC.
  • The presentation can be made in either in English or Japanese, but please prepare the materials in English.
  • The policy on research achievements for the Hackathon is as shown below:
    • When an achievement involves alteration of an existing software platform, licensing is subject to the original software.
    • When an achievement is newly developed by an individual, it is released and managed in an open source public repository, such as J-Node software center or GitHub.
      • In some circumstances, full disclosure may not be available due to research ethics.
    • Copyright of an achievement belongs to the developer, but it will be treated as a result of J-Node (NIJC) activity.
    • Lecture materials presented at Ideathon etc. will be disclosed at this website in the possible range, just like other developed achievements.
  • If you wish to participate this workshop partially, please consult us.
  • We will have a social gathering on 3/18(Sun) after the Hackathon. Please join us (fees at your own expense).


Day Hour Title Presentors  


9:30~ Venue : RIKEN BSI East Building 1F Seminar room  
10:00~10:05 Opening Remark Tomoki KAZAWA(The University of Tokyo) PDF
10:05~10:15 "Development of standards for open neuroscience at INCF Japan Node" Yoko YAMAGUCHI (RIKEN) PDF
10:15~10:45 "Trial use of mathematical models and applications on a cloud computing system: Simulation platform" Hidetoshi IKENO (University of Hyogo) PDF
10:45~11:15 "Towards brain data utilisation promotion by ontology-based data integration amongst various research fields" Norio KOBAYASHI (RIKEN) PDF
11:15~11:45 "XooNIps Now - Introducing case studies of data migration from CosmoDB to XooNIps" Yoshihiro OKUMURA (RIKEN)Tomoki KAZAWA (The University of Tokyo) PDFPDF
11:45~12:45 Lunch  
12:45~13:15 "A proposal of “WebLab”~Reform of 'research community' from journal reference databases~" Yoshihide TAMORI (NeuroCreative Lab) PDF
13:15~13:45 "Using the U-Net Deep Network Architecture to Segment Brain Image Data" Alexander WOODWARD (RIKEN)  
13:45~15:00 Flash talk  
15:00~16:45 Group discussion  
16:45~17:00 Report of Discussion  

【Flash Talk】
1. Yoshiyuki ASAI (Yamaguchi University)PDF
2. Hayeong LEE (The University of Tokyo)PDF
5. Kaoru SUZUKI (RIKEN BSI) 6. Meikei SHU (Xincor miXell Co.,Ltd.) 7. Mayu KUBOTA (Xincor miXell Co.,Ltd.)


Day Hour Title Presentors


9:30~ Venue : Φcafe
10:00 Opening Remark Tomoki KAZAWA(The University of Tokyo)
10:10~10:30 Self-introduction
10:30~12:00 Grouping, Development
12:00~13:00 Lunch
13:00~19:00 Development
19:30~ Social Gathering


10:00~12:00 Development
12:00~13:00 Lunch
13:00~19:00 Development


10:00~12:00 Development
12:00~13:00 Lunch
13:00~16:00 Development
16:00~18:00 Presentation time (Report of activity in the hackathon)
18:00 Closing  

【Wrap up】

Title Member Wrap up
Development of an image registration scheme for construction of the honey bee standard brain Hidetoshi IKENO PDF
Segmentation of honey bee brain images Kazuaki GOTO, Yuka UENOHARA, Satoshi TANAKA, Hidetoshi IKENO PDF
Online data analysis using Simulation Platform Keiichiro INAGAKI, Yoshihiro OKUMURA PDF
Document sharing on Software Center Takayuki KANNON, Yoshihiro OKUMURA PDF
Ontology development for G-Node odml Norio KOBAYASHI, Yoko MORII PDF
Tuning simulation execution speed up for NEURON K + Mayu KUBOTA, Tomoki KAZAWA PDF
Data migration ~from IVB -PF to CNS -PF~ Meikei SHU, Tomoki KAZAWA PDF
Data Analysis Pipeline Hayeong LEE, Tomoki KAZAWA PDF
Use of NinaPro Database in Myo controlled Prosthetic arm Sanjay DWIVEDI, Vishal GAURAV, Krati SAXENA, Harry BOLINGOT PDF
Update of Simulation Platform Infrastructure Yoshihiro OKUMURA, Yoko MORII, Hidetoshi IKENO PDF
  Yoshihide TAMORI  

Other Documents

Questionnaire results

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