Locked History Actions

Events/Tokyo2015





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)

-

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)

-

-

-

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!

Twitter

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


http://www.rcast.u-tokyo.ac.jp/index_en.html

http://www.ims.riken.jp/english/

http://dbcls.rois.ac.jp/en/

https://aws.amazon.com/