April 28, 2015 @ [RCAST, The University of Tokyo](http://www.rcast.u-tokyo.ac.jp/index_en.html)
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.
Audience
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.
Program
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) | - | 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) | - | video | |
| 13:30-13:45 | Introduction of Community Galaxy | Ryota Yamanaka (RCAST, Univ of Tokyo) | - | video | |
| 13:45-14:00 | Workflows: RNA-seq (1) | Mika Yoshimura (ACCC, RIKEN) | workflow | video | |
| 14:00-14:15 | Workflows: RNA-seq (2) | Shinji Nakaoka (IMS, RIKEN) | workflow | video | |
| 14:15-14:30 | Workflows: CAGE | Makoto Nasuno (ASCADE) | workflow | video | |
| 14:30-14:45 | (Coffee 1) | - | - | - | |
| 14:45-15:00 | Workflows: ChIP-seq | Ryo Nakaki (RCAST, Univ of Tokyo) | workflow | video | |
| 15:00-15:15 | Workflows: BS-seq | Yutaka Saito (CBRC, AIST) | workflow | video | |
| 15:15-15:30 | Workflows: Variant Calling (1) | Norio Shinkai (CBRC, AIST) | workflow | video | |
| 15:30-15:45 | Workflows: Variant Calling (2) | Makoto Ikeda (Percipere) | workflow | video | |
| 15:45-16:00 | Workflows: Variant Calling (3) | Hideki Nagasaki (NIG, ROIS) | workflow | 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) |
- | video | |
| 16:55-17:10 | Infrastructure: Galaxy on AWS Cloud | Yuichi Yoshiara (Amazon Data Service) | - | video | |
| 17:10-17:25 | Infrastructure: Galaxy on PC Clusters | Tomohiro Uchida (NABE International) | - | video | |
| 17:25-17:40 | Platforms: Illumina BaseSpace | Eri Kibukawa (Illumina) | - | video | |
| 17:40-17:55 | Platforms: Garuda Alliance | Nikos Tsorman (The Systems Biology Institute) | - | video | |
| 17:55-18:00 | Closing | - | - | - | |
| 18:00-19:30 | (Happy Hour) | - | - | - |
Venue
RCAST, The University of Tokyo map
(Komaba Research Campus)
Building No.4, 2F Conference Hall
Registration
Registration has been closed due to the hall capacity (100 max). Thank you!
Please use #usegalaxyjp
Organizer
Ryota Yamanaka [1], Manami Kato [2], Tazro Ohta [3]
Email: yamanaka [at] genome.rcast.u-tokyo.ac.jp
Support
[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
 |
 |
 |
 |