J-Node / NIDM Joint Hackathon 2016 July

In July, We will have ‘J-Node and NIDM Joint Hackathon 2016 July’.

We invite guests from Neuroimaging Data Sharing (NIDASH) Task Force and hold tutorials of their philosophy and implementation of their NEUROIMAGING DATA MODEL (NIDM). We hope International collaborations and exchange between NIDASH and J-Node Hackathon activities will enhance the software development of neuroinfomatics data sharing and integrations.

All interested persons are welcome to participate.

The schedule is as follows.

On the first day, Ideathon as several tutorials and discussion is planned for the topics of Hackathon and grouping among participants. All participants will give a short presentation. Remaining schedule is for the development of source codes in each group. In the last session, all groups give presentations on their activities. Products of the hackathon are in principle to be devoted to open source.

The organizer will support accommodation and meals during the Hackathon.

We call for your proposal and participation to the J-Node and NIDM Joint Hackathon 2016 July and look forward to hearing from you.

The event was closed. Thank you everyone who participated.


Date: July 23(Sat) 10:30AM -25(Mon) 5:00PM, 2016 (Closed)


  • Jean-Baptiste Poline (University of California, Berkeley)   
  • Satrajit Sujit Ghosh (McGovern Institute for Brain Research)
  • David Keator (University of California, Irvine)
  • Nolan Nichols (SRI International)
  • Tomoki Kazawa (The University of Tokyo)
  • Hidetoshi Ikeno (University of Hyogo)
  • Alexander Woodward (RIKEN)

Venue: Shonan Village Center http://www.shonan-village.jp/english/   

        access http://www.shonan-village.jp/english/access.html

 Please take the bus from the followings.

  • From either JR Zushi or Keikyu Shin-Zushi station. (bus leaving JR Zushi station at 9:30am, Keikyu Shin-Zushi station at 9:32am)
    • Take bus no. 16 for Shonan Village, which leaves from bus stop number 1 at both stations (approx. 30 min.). A one way bus ticket costs JPY 350.
  • From Keikyu Shioiri station. (bus leaving at 9:33am)
    • Take bus no. 16 for Shonan Village, which leaves from bus stop number 2 (approx. 35 min.). A one way bus ticket costs JPY 380 All buses are The destination is Shonan Village Center.

Organized by:

  • J-Node Hackathon Working Group, INCF Japan Node
    • (Group Leader: Tomoki Kazawa (RCAST, The University of Tokyo))
  • INCF (International Neuroinformatics Coordinating Facility)

Committee: INCF Japan Node  J-Node Hackathon Working Group

  • Tomoki Kazawa(Chair) (The University of Tokyo)
  • Hidetoshi Ikeno(University of Hyogo)
  • Teiichi Furuichi (Tokyo University of Science)
  • Yoshiyuki Asai (OIST)
  • Akira Sato (Tokyo University of Science)
  • Yoshihiro Okumura (RIKEN BSI)
  • Yukiko Nota (ATR-Promosions Brain Activity Imaging Center)
  • Yoko Yamaguchi (RIKEN BSI)

Number of participants: 30 at most

Deadline of registration submission: July 4 (Mon), 2016  Deadline is extended to July 7(Thu) AM Registration finished.

Contact: office@nijc.brain.riken.jp

  • In principle, organizer shall support accommodation fee for 2 nights, 3 lunches and 2 dinner. Please contact us if you need accommodation on the previous night of this hackathon.
    • We ask you to pay for your own travel expenses, however several participants may be supported.
    • To apply, please fill in the application form and send it to J-Node office. After it has been reviewed you will be notified the result around a week after the deadline.
  • We would be very grateful if your affiliation could support for your travelling fee. If so please fill in the check box.
  • We will have a social gathering after the dinner on the 24th. We ask for all the participants to pay the fee of 2,100 yen on-site at the venue.
  • 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.
  • Both presentation and documents will be in English.  As for the achievement reports, we may ask you to submit them or make presentations 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) or INCF 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.


Day Hour Title Presentors




Venue : Shonan Village Center

Conference Room 2




Tomoki Kazawa(The University of Tokyo)
10:30~11:00 Estimation of gene expression pattern by registration of ISH images into the 3D standard brain atlas Hidetoshi Ikeno (University of Hyogo)
11:00~11:30 Brain Image Analysis Pipeline on NIJC’s Brain/MINDS Research Platform

Alexander Woodward (RIKEN)

11:30~12:00 ①NIDM Motivation and examples (linked data - why for neuroimaging?) 
(short break)
  ・ RDF / (mention OWL)  
  ・ SPARQL  (example of a hard query with SQL)

1. Jean-Baptiste Poline

2. Nolan Nichols, Satrajit Sujit Ghosh

12:30~13:30 Lunch
13:30~14:30 short presentation
1. Terms and internationalization
 ‐A quick intro to ontologies
 ‐How to take Japanese vocabulary and link to other lexicons - how do you use standard ontologies
 -Create an interface to have people contribute with new terms / curate terms
2. How to turn an excel spreadsheet into a query-able data model
‐Data sources -> NIDM/RDF object models
  ‐Examples SimpleData example:
  ‐Example ABIDE/FBIRN assessment example:
  ‐Linking Data/Integration Queries
3. NIDM workflow
 ‐An example of how provenance is captured
 ‐Taking Dave’s output and launch a workflow
 ‐Show how to construct your own workflow provenance
 ‐What are the vizualization tools for RDF graphs ?

1. Satrajit Sujit Ghosh

2. David Keator

3. Nolan Nichols, Satrajit Sujit Ghosh


Flash Talk


Group discussion


16:30~17:00 Presentation  of each group about the direction of the development  and training in the hackathon
17:00~18:00 Development or Training
18:00~19:00 Dinner
19:00~ Development or Training (seminar room can be used during night time)



7:30~9:00 Breakfast
9:00~12:00 Development
12:00~13:00 Lunch
13:00~17:00 Development
17:00~18:00 Short presentations for those who want to present updates on the projects
18:00~19:00 Dinner
19:00~21:00 Social Gathering
21:00~ Development (seminar room can be used during night time)



7:30~9:00 Breakfast
9:00~12:00 Development
12:00~13:00 Lunch
13:00~15:00 Development
15:00~16:45 Presentation time (Report of activity in the hackathon)
17:00 Closing


Team Member Wrap up
Integration of Database Catalogue in RDF among NIDM, NIJC and RIKEN Hiroshi Masuya, Norio Kobayashi, Yoko Morii, Nolan Nichols, Daivd Keator, JB Poline PDF
ISH Image Processing Kosuke Arase, Daisuke Miyamoto PDF
Team Registration Hidetoshi Ikeno, Daisuke Miyamoto PDF
JP Linker for IVB-PF Yusuke Mori, Hideki Kashioka, Takeshi Takeuchi PDF
Ontology-Based Search Server team Yoshiyuki Asai, Kyota Kamiyoshi PDF
RDFisation of existing brain databases Norio Kobayashi PDF
RDF Data Integration Experiments David Keator, Nolan Nichols, JB Poline PDF
Overlay approach to reconstruct noisy motion data Satoshi Oota PDF
Improvement of Japan Node Software Center Yoshihiro Okumura, Takayuki Kannon(Online) PDF
Web 3D brain viewer team Tomoyuki Kubota, Mitsuaki Tsukamoto, Keiji Matsuda PDF
Electron Microscopy Image Segmentation using Nipype and OpenCV on an HPC Torsten Bullmann, Alexander Woodward PDF
Nipype training and provenance Satrajit Ghosh, Shuntaro Aoki, Daisuke Miyamoto, Alexander Woodward, Torsten Bullman PDF
Automatic database manipulation team Tomoki Kazawa, Yoshihiro Okumura PDF
Nipype Users team Shuntaro Aoki, Daisuke Miyamoto PDF

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