= !BioHackathon 2009 =

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

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== 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
[http://hackathon.dbcls.jp/ 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 ==

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

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

 * Publication of a meeting report.

== Mailing list ==

 * http://kml.dbcls.jp/pipermail/biohack2/
 * biohack2@kml.dbcls.jp

== Sponsor and organizers ==

This meeting is co-hosted by [http://dbcls.rois.ac.jp/en/ DBCLS]
and [http://www.irp.oist.jp/satoh/index.php 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)
 * 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)
 * Jan Christian Bryne (EMBRACE, ELIXIR; Bergen Center for Computational Science, 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.)

== 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: HND 14:40 - 17:30 OKA
  * ANA: HND 15:30 - 18:15 OKA

 * Transport from Naha airport to OIST

=== 3/17 - 3/20 ===

|| 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)

=== 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