The Galaxy Workshop Tokyo 2015 will be a great opportunity to participate in a full day of hands-on training, keynotes, lightning talks and discussions all about ways of using Galaxy for high-throughput biology, specially for human genome sequencing. This workshop will consist of two parts: The morning session is a hands-on training to learn how to run Pitagora-Galaxy, our Galaxy preconfigured virtual machine, on your laptop or on AWS cloud. The afternoon session includes keynotes and lightning sessions to explain actual workflows, which you can try immediately on Pitagora-Galaxy.


    This workshop is held as a part of activities of Galaxy Japan Community and aimed at potential users of Galaxy. We will welcome participants who are using workflow management systems other than Galaxy, and tool developers who are looking for such systems to offer their tools to a wider users. Also, we would like to share the status of new developments, interface to other systems, extensions and best practices in reproducible research.


    The preparation hands-on is optional. To attend this hands-on, please bring your laptops. The way to install Pitagora-Galaxy is described here.

    Time Title Speaker Workflow Slide Video
    09:30-10:00 (Registration) - - -
    10:00-12:00 Preparation Hands-on:
    Installling Pitagora-Galaxy
    Tazro Ohta (DBCLS, ROIS) - pdf video
    12:00-13:00 (Lunch) - - -
    Time Title Speaker Workflow Slides Videos
    12:30-13:00 (Registration) - - -
    13:00-13:05 Opening - - -
    13:05-13:25 Opening Remarks: Hiroyuki Aburatani (RCAST, Univ of Tokyo) - - video
    13:25-13:30 Message from Galaxy Team Dave Clements (Johns Hopkins University) - pdf video
    13:30-13:45 Introduction of Community Galaxy Ryota Yamanaka (RCAST, Univ of Tokyo) - pdf video
    13:45-14:00 Workflows: RNA-seq (1) Mika Yoshimura (ACCC, RIKEN) workflow pdf video
    14:00-14:15 Workflows: RNA-seq (2) Shinji Nakaoka (IMS, RIKEN) workflow pdf video
    14:15-14:30 Workflows: CAGE Makoto Nasuno (ASCADE) workflow pdf video
    14:30-14:45 (Coffee 1) - - -
    14:45-15:00 Workflows: ChIP-seq Ryo Nakaki (RCAST, Univ of Tokyo) workflow pdf video
    15:00-15:15 Workflows: BS-seq Yutaka Saito (CBRC, AIST) workflow pdf video
    15:15-15:30 Workflows: Variant Calling (1) Norio Shinkai (CBRC, AIST) workflow pdf video
    15:30-15:45 Workflows: Variant Calling (2) Makoto Ikeda (Percipere) workflow pdf video
    15:45-16:00 Workflows: Variant Calling (3) Hideki Nagasaki (NIG, ROIS) workflow pdf video
    16:00-16:15 (Coffee 2) - - -
    16:15-16:55 Keynote 2 (Overseas Galaxy Project):
    Genomics Virtual Laboratory
    Andrew Lonie
    (Life Sciences Computation Centre, VLSCI)
    - pdf video
    16:55-17:10 Infrastructure: Galaxy on AWS Cloud Yuichi Yoshiara (Amazon Data Service) - pdf video
    17:10-17:25 Infrastructure: Galaxy on PC Clusters Tomohiro Uchida (NABE International) - pdf video
    17:25-17:40 Platforms: Illumina BaseSpace Eri Kibukawa (Illumina) - pdf video
    17:40-17:55 Platforms: Garuda Alliance Nikos Tsorman (The Systems Biology Institute) - pdf video
    17:55-18:00 Closing - - -
    18:00-19:30 (Happy Hour) - - -


    RCAST, The University of Tokyo map
    (Komaba Research Campus)
    Building No.4, 2F Conference Hall


    Registration has been closed due to the hall capacity (100 max). Thank you!


    Please use #usegalaxyjp


    Ryota Yamanaka [1], Manami Kato [2], Tazro Ohta [3]
    Email: yamanaka [at]


    [1] Genome Science Division, RCAST, The University of Tokyo
    [2] Laboratory for Disease Systems Modeling, IMS, RIKEN
    [3] Database Center for Life Science, ROIS
    Also, supported by AWS in Education Research Grant award