BioHackathon 2009

Integration for the wet biologists - bring the cutting edge technologies to the bench.

Hackathon

The hackathon (hacking + marathon) basically is a camp where invited participants discuss about current issues and implement software to solve the problems on site collaboratively. This kind of meeting is very effective for the intensive development of projects, because face-to-face meeting of developers, who usually spread around the world, accelerates communication and collaboration to exchange their ideas instantly.

BioHackathon is a hackathon to implement bioinformatics software towards domain specific goals. This year, we will focus on end user applications to make our previous standardization efforts in  BioHackathon 2008 to be fully utilized by the primary consumers of our infrastructure. For this purpose, we will also involve semi-wet biologists working in an area where high throughput genome annotation is required. By knowing their demands, we will be able to find what kind of resource is missing and to prioritize our action items.

Objectives

Main objective of the meeting is to continue global efforts to standardize biological database resources and to improve usability and interoperability of bioinformatics services, which were proposed in the previous meeting.

The agenda of the previous meeting, BioHackathon 2008, is available at

 http://hackathon.dbcls.jp/

Additionally, we will collaborate with

• Organizations which have similar mission with us (e.g. ELIXIR) for the complementary efforts.
• Developers of integrated platforms like BioMart, GMOD, Galaxy etc.

to make our previous efforts to be utilized by the scientific researchers effectively.

Topics

Technology: Infrastructure and standardization

• Integration of the integrated databases - Unified API for distributed services
• Agreement on common exchange data formats, ontologies and semantics
• Provide stable and interoperable services with SOAP and REST
• Manifesto and guidelines for the next generation web services

Application: Mash-up and user friendly interface

• Improve end-user applications like Galaxy to utilize integrated databases and services
• What kind of resources are currently missing for science?
  • e.g. Genome-scale analysis: pipelines and visualization

Promotion: Outreach to the wet biologist

• Hands-on seminar
• Documentation

Goals

• Solve several use cases and summarize in tutorials during the hands-on seminar

• Discuss about the guidelines (manifesto) towards standardization of data types and protocols for the integration of databases and services.

• Improve Open Bio* libraries and other tools to apply real world issues.

• Publication of a meeting report.

Mailing list

•  http://kml.dbcls.jp/pipermail/biohack2/
• biohack2@…

Sponsor and organizers

This meeting is co-hosted by  DBCLS and  OIST, and flights and accommodation fees will be covered by their budget.

• Toshiaki Katayama (TogoDB, TogoWS, KEGG API, BioRuby?; HGC, Japan)
• Shuichi Kawashima (KEGG API; HGC, Japan)
• Takeshi Kawashima (Marine genomics; OIST, Japan)
• Mitsuteru Nakao (TogoWS, BioRuby?; Kazusa DNA Res, Japan)
• Yasunori Yamamoto (DBCLS, Japan)
• Atsuko Yamaguchi (DBCLS, Japan)
• Noriyuki Satoh (OIST, Japan)
• Toshihisa Takagi (Head of DBCLS, Japan)

Confirmed participants

• Alberto Labarga (Dasty3, Elsevier Grand Challenge, EBI; scientifik.info, Spain)
• Arek Kasprzyk (BioMart; OICR, Canada)
• Oswaldo Trelles (MOWserv; Universidad de Málaga, Spain)
• Tom Oinn (Taverna2; UK)
• James Taylor (Galaxy; Emory Univ, US)
• Jan Christian Bryne (EMBRACE, ELIXIR; The University of Bergen, Norway)
• Young J. Kim (KRIBB, Korea)
• Kiyoko Kinoshita (RINGS; Soka Univ, Japan)
• Hideaki Sugawara (WABI/SABI; DDBJ, Japan)
• Naohisa Goto (BioRuby?; Osaka Univ, Japan)
• Kazuharu Arakawa (G-language; Keio Univ, Japan)
• Keiichiro Ono (Cytoscape; UCSD, U.S.)
• Shinobu Okamoto (genoDive; Kazusa DNA Res, Japan)
• Yasukazu Nakamura (Kazusa DNA Res/DDBJ, Japan)

Venue

Places

• Tokyo (DBCLS) - for the 1st day (reception and symposium)
• Okinawa (OIST) - rest of the days (hack, hack, hack)

Our preliminary plan is to gather on Sunday in Tokyo for the reception (and symposium?), then fly together to Okinawa on Monday and back to Tokyo on Saturday after we tired of the hacking activities.

Date

• 2009/3/15-21

Schedule

3/15 (Sun)

• Arrival to Japan (Tokyo-Narita airport)
• Check into the hotel

• 17:00-21:00 Reception at DBCLS

3/16 (Mon)

• 9:00-12:00 Symposium in Tokyo
  • Invited talks
  • Lightning talks

• Flight from Tokyo-Haneda airport to Okinawa-Naha airport
  • JAL 923 : HND 14:40 - 17:30 OKA
  • ANA 131: HND 15:30 - 18:15 OKA

• Transport from Naha airport to OIST

3/17 - 3/20

Parallel sessions:

• software development (hack, hack, hack)
• use case driven hands-on seminar (try and record)

Time	3/17 (Tue)	3/18 (Wed)	3/19 (Thu)	3/20 (Fri)
8:00	breakfast	breakfast	breakfast	breakfast
9:00	hack, hack, hack	hack, hack, hack	hack, hack, hack	hack, hack, hack
12:00	lunch	lunch	lunch	lunch
13:00	hack, hack, hack	hack, hack, hack	excursion	summarize
17:00	progress report	progress report	progress report	overall presentation
18:00	dinner	dinner	dinner	dinner
20:00	hack, hack, hack	hack, hack, hack	hack, hack, hack	closing remarks

3/21 (Sat)

• Depature from Naha airport (taking flight for appropriate destination)

• Flight from Okinawa-Naha airport to Tokyo-Narita
  • ANA 2158: OKA 12:25 - 14:40 NRT

Housing

TO BE CONFIRMED

Access

TO BE DESCRIBED

Student scholarship

TO BE CONSIDERED

Publication

TO BE DISCUSSED

• Arek Kasprzyk for "Database"
• Alfonso Valencia for "Bioinformatics"
• Alex Bateman for "NAR"

Misc

What you should bring with you?

• Laptop computer
• Conversion plug for your AC adaptor (identical to the US type; 100 volt)

Photo album

IN PREPARATION

Streaming

IN PREPARATION

SVN repository

IN PREPARATION