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)


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.

Organized by:

Committee: INCF Japan Node  J-Node Hackathon Working Group

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


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

Other Documents (Japanese Only)

● 開催後アンケート