= !BioHackathon 2009 = [[PageOutline]] == About the 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 are usually spread around the world, accelerates communication and collaboration to exchange their ideas. !BioHackathon 2009 is sponsored by the Database Center for Life Science ([http://dbcls.rois.ac.jp/en/ DBCLS]) and the Okinawa Institute of Science and Technology ([http://www.irp.oist.jp/ OIST]), and will be held in Tokyo and Okinawa, Japan. * !BioHackathon 2009 http://hackathon2.dbcls.jp/ * !BioHackathon 2008 http://hackathon.dbcls.jp/ * DBCLS http://dbcls.rois.ac.jp/en/ * OIST http://www.oist.jp/ The DBCLS is being accepted as a national center for the sustainable life science databases in Japan. The OIST is the graduate university of science and technology and aiming to create a leading intellectual hub in the Asian-Pacific region. == Objectives == In the [http://hackathon.dbcls.jp/ BioHackathon 2008], we focused on the standardization of bioinformatics web services and the exchange data formats to create bioinformatics workflows. To make these global efforts to be fully utilized by the biologists, we need to integrate these services into the various end-user applications. For this purpose, we will organize the second !BioHackathon gathering software developers of mash-up services and web service providers. Additionally, we will also involve semi-wet biologists to apply their data for testing these services and applications in combination to address the real world use cases. Our goal is to develop stable and usable platforms for emerging demands, such as * Workflow for the massive sequence annotation (Galaxy, !BioMart, Taverna, MOWserve etc.) * Automatic genome sequence assembly and mapping (GMOD/GBrowse, UTGB etc.) * Visualization of the large scale data sets (Cytoscape, Processing etc.) * Interoperable web services and database resources (BioMOBY, TogoWS, TogoDB etc.) and test these infrastructures with several biological use cases. For example, the Marine Genomics Unit in OIST is equipped with Roche 454 sequencers and they are hoping to start environmental genomics of the coral reef in Okinawa. We have been working on the integration of our database resources into the Galaxy, and would like to offer them to use the services provided by the DBCLS. Additionally, we will start to select some suitable use cases to deal with, based on the discussion in the mailing list. == Expected outcomes == * Improve end-user applications like Galaxy or Taverna by testing with the use cases. * Document how to solve the biological problems using these software and resources based on the hands-on seminar. * Issue a manifesto and guidelines for creating interoperable web services with SOAP and/or REST. * Publication of the meeting report. == Mailing list == * http://kml.dbcls.jp/pipermail/biohack2/ * biohack2_at_kml.dbcls.jp == Meeting organizers == * [http://www.linkedin.com/in/toshiakikatayama Toshiaki Katayama] ([http://togodb.dbcls.jp/ TogoDB], [http://togows.dbcls.jp/ TogoWS], [http://www.genome.jp/kegg/soap/ KEGG API], [http://bioruby.org/ BioRuby]; [http://www.hgc.jp/ HGC], Japan) * [http://www.linkedin.com/in/shuichikawashima Shuichi Kawashima] ([http://www.genome.jp/kegg/soap/ KEGG API]; [http://www.hgc.jp/ HGC], Japan) * [http://www.linkedin.com/pub/5/137/71b Takeshi Kawashima] (Marine Genomics Unit, OIST, Japan) * [http://www.linkedin.com/in/nakaomitsuteru Mitsuteru Nakao] (TogoWS, !BioRuby, Galaxy i18n, [http://genome.kazusa.or.jp CyanoBase]; Kazusa DNA Res, Japan) * [http://www.linkedin.com/pub/10/859/63b Yasunori Yamamoto] (DBCLS, Japan) * Hong-Woo Chun (DBCLS, Japan) * [http://www.linkedin.com/pub/b/773/6a3 Atsuko Yamaguchi] (DBCLS, Japan) * [http://www.linkedin.com/pub/10/8a0/247 Shin Kawano] (DBCLS, Japan) * Keiko Sakuma (DBCLS, Japan) * Eiji Ueda (DBCLS, Japan) * [http://www.irp.oist.jp/satoh/ Noriyuki Satoh] (Director of Marine Genomics Unit, OIST, Japan) * [http://dbcls.rois.ac.jp/en/staff/index.html Toshihisa Takagi] (Director of DBCLS, Japan) == Confirmed participants == * [http://www.linkedin.com/in/jamespetertaylor James Taylor] (Galaxy; Emory Univ, US) * [http://www.linkedin.com/pub/0/263/342 Greg von Kuster] (Galaxy; Penn State Univ, US) * [http://www.linkedin.com/in/tomoinn Tom Oinn] (Taverna2; UK) * [http://www.linkedin.com/pub/4/807/22 Arek Kasprzyk] (!BioMart; OICR, Canada) * Syed Abbas Haider (!BioMart/GMOD; EBI, UK) * [http://www.linkedin.com/in/twharris Todd Harris] (GMOD) * [http://www.linkedin.com/in/albertolabarga Alberto Labarga] (Dasty3, Elsevier Grand Challenge, EBI; scientifik.info, Spain) * [http://www.linkedin.com/pub/11/1b2/47a Yulia Kovarskaya] (Elsevier GC; Univ of Granada, Spain) * [http://www.linkedin.com/pub/11/3a/b8a Oswaldo Trelles] (MOWserv, mAPI, jORCA, Magallanes; Universidad de Málaga, Spain) * José M. Fernández (MOWserv; CNIO, Spain) * [http://www.linkedin.com/pub/1/674/665 Mark Wilkinson] (BioMoby, Canada) * [http://www.linkedin.com/pub/2/579/779 Martin Senger] (IRRI, Philippines) * [http://www.linkedin.com/in/lindenbaum Pierre Lindenbaum] ([http://plindenbaum.blogspot.com/ mash-up, visualization]) * Nicholas Putnam (Genome assembly; Rice University) * Isaac Ho (Cytoscape/GenMAPP; JGI) * [http://www.linkedin.com/in/brunoaranda Bruno Aranda] (PSIQUIC; EBI) * [http://www.linkedin.com/pub/6/418/161 Keiichiro Ono] (Cytoscape; UCSD, U.S.) * [http://www.linkedin.com/in/jandot Jan Aerts] (Sanger, UK) * [http://www.linkedin.com/pub/5/569/123 Raoul Bonnal] (!BioRuby, BioSQL) * [http://www.linkedin.com/in/rutgervos Rutger Vos] (NEXML) * [http://www.linkedin.com/in/paulmkgordon Paul Gordon] (Genome Canada Bioinformatics Platform, Canada) * [http://www.linkedin.com/pub/b/b92/8b1 Jan Christian Bryne] (EMBRACE, ELIXIR, EuTRACC; The University of Bergen, Norway) * [http://www.linkedin.com/in/vachiranee Vachiranee Limviphuvadh] ([http://www.bii.a-star.edu.sg/research/bfd/psa.php ANNOTATOR]; Bioinformatics Institute, A*STAR Singapore) * [http://www.linkedin.com/in/tobiasgattermayer Tobias Gattermayer] ([http://www.bii.a-star.edu.sg/research/bfd/ann.php ANNOTATOR]; Bioinformatics Institute, A*STAR Singapore) * Keun-Joon Park (NIH, Korea) * Yunsun Nam (NIH, Korea) * Young Joo Kim (Professor at [http://www.ust.ac.kr/ UST], [http://www.kribb.re.kr/ KRIBB], Korea) * Yasumasa Shigemoto (DDBJ, Japan) * [http://www.linkedin.com/pub/11/b02/a61 Akira Kinjo] (PDBj, Japan) * Chisato Yamazaki (BIRC, Japan) * [http://www.linkedin.com/pub/9/645/914 Kiyoko F. Aoki-Kinoshita] (RINGS; Soka Univ, Japan) * [http://www.linkedin.com/pub/11/b66/319 Shujiro Okuda] (Glycoinfomatics; Ritsumeikan Univ, Japan) * [http://www.linkedin.com/pub/b/763/a65 Masumi Itoh] (Hokkaido Univ) * Jessica Severin (RIKEN, Japan) * [http://www.linkedin.com/in/hideyakawaji Hideya Kawaji] (RIKEN, Japan) * [http://www.linkedin.com/pub/9/bb1/766 Soichi Ogishima] (Tokyo Medical and Dental Univ, Japan) * Riu Yamashita (HGC, Japan) * [http://www.linkedin.com/pub/3/56a/437 Fumikazu Konishi] (Titech, Japan) * [http://www.linkedin.com/in/ngoto Naohisa Goto] (!BioRuby; Osaka Univ, Japan) * Takashi Hatakeyama (Eiwa Co., Japan) * Tatsuya Nishizawa (IMS Co., Japan) * [http://www.linkedin.com/pub/4/867/87 Kazuharu Arakawa] (G-language; Keio Univ, Japan) * Nobuhiro Kido (Keio Univ, Japan) * Kazuki Oshita (Keio Univ, Japan) * [http://www.linkedin.com/pub/11/5a2/323 Kozo Nishida] (NAIST, Japan) * [http://www.linkedin.com/pub/5/415/647 Kunihiro Nishimura] (genoDive; Univ of Tokyo, Japan) * Shinobu Okamoto (genoDive; Kazusa DNA Res, Japan) * Takatomo Fujisawa (Kazusa DNA Res, Japan) * Yasukazu Nakamura (DDBJ/Kazusa DNA Res, Japan) * Katsuhiko Murakami (BIRC, Japan) * Hideaki Sugawara (WABI/SABI; DDBJ, Japan) == Venue == Our preliminary plan is to gather on Sunday in Tokyo for the reception. On Monday morning, we will have a public symposium, then fly together to Okinawa on Monday afternoon. We'll be back to Tokyo on Saturday after we are tired of the hacking activities. * Tokyo (DBCLS) - for the 1st day (reception and symposium) * Okinawa (OIST) - rest of the days (hack, hack, hack) == Schedule == * 2009/3/15-21 === 3/15 (Sun) === * Arrival to Japan (Tokyo-Narita airport) * Check into the hotel ([http://www.uth.co.jp/ Ueno Terminal Hotel]) * 17:00-21:00 [http://dbcls.rois.ac.jp/en/access/index.html Reception at DBCLS (4F)] === 3/16 (Mon) === * 9:00-12:00 [http://www.u-tokyo.ac.jp/campusmap/cam01_04_16_e.html Symposium in Takeda Hall (5F)] || Toshiaki Katayama || Introduction to the !BioHackathon 2009 and integration efforts in DBCLS || || James Taylor || Integrated reproducible analysis with Galaxy || || Tobias Gattermayer || Biomolecular Function Discovery with the ANNOTATOR || || Jessica Severin || Accelerating experimentation and biological discovery within RIKEN OSC !LifeScienceAccelerator -- eeDB gLyphs || || Arek Kasprzyk || !BioMart and third party applications: Working towards better interoperability || || Tom Oinn || The Taverna 2 Workflow Engine API : Extensible, High Performance and Easy to Integrate || || Oswaldo Trelles || Multi-repository architecture for service integration || || Alberto Labarga || Integrating literature and annotation resources: the Elsevier Grand Challenge experience || || Hideaki Sugawara || Looking back on a WABI life for tomorrow || * Flight from Tokyo-Haneda airport to Okinawa-Naha airport * 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) === * Departure from Naha airport (taking flight for appropriate destination) * Flight from Okinawa-Naha airport to Tokyo-Narita * ANA 2158: OKA 12:15 - 14:40 NRT === Housing === * [http://www.oist.jp/seasidehouse.html OIST Seaside House] * [http://www.rizzan.co.jp/english/index.html Rizzan Sea Park Hotel Tancha Bay] === Access === * [http://dbcls.rois.ac.jp/en/access/index.html DBCLS] (Tokyo venue) * [http://www.oist.jp/access_1.html OIST] (Okinawa venue) == Misc == What should you bring with you? * Laptop computer * Conversion plug for your AC adaptor (identical to the US type; 100 volt) * Local liquor as always (for the Liquorthon at night :-) * [http://www.linkedin.com/ LinkedIn] account to share your contact address === SVN repository === * http://hackathon2.dbcls.jp/svn/ === Photo album === IN PREPARATION === Streaming and social networking === * http://www.ustream.tv/channel/biohackathon2009 * IRC: #biohackathon2009 on chat1.ustream.tv:6667 * http://friendfeed.com/rooms/biohackathon-2009 -- !FriendFeed room for !BioHackathon 2009