First Asia-Pacific Bioconductor Developer’s Meeting

Tokyo, Japan

2015-09-08 ~ 2015-09-08

Instructors

• Matt Ritchie
• Martin Morgan

Description

Asia's first Bioconductor developer meeting.

Materials

Overview

The Bioconductor project is a widely used collection of over 1000 R packages for high-throughput genomic analysis and recently surpassed the milestone of 100,000 commits to its svn repository. Many popular software tools from the project are developed by researchers based in the Asia-Pacific region. To enhance collaborations and provide an avenue for networking, the region’s first developers’ meeting will be held directly preceding GIW/InCoB 2015. This event will bring together both current and prospective package developers to provide a forum for exchanging ideas and future plans for software in the project. The meeting will consist of a number of longer talks selected from abstracts as well as short ‘lightning’ presentations to maximize the opportunities for participants to highlight their work. A Developer workshop on ‘Turning great ideas into Bioconductor packages with impact’ will also be held.

Organisers

Dr Matt Ritchie, Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia

Dr. Martin Morgan, Bioconductor / Program in Computational Biology Fred Hutchinson Cancer Research Center, Seattle, WA USA

Venue

AIST Tokyo Waterfront Bio-IT Research Building 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan

Key dates

Email proposals for longer talks / lightning talks or posters to gustin.s near wehi.edu.au (Title and abstract of up to 300 words) by Friday 31st July 2015.

Registration

Registration is handled as part of the GIW/InCoB 2015 registration process. Alternatively email gustin.s near wehi.edu.au if you will be attending.

Tentative schedule

10:00am - 10:50am	Project Updates (Dr Martin Morgan)
10:50am - 11:50am	Getting to know you session: Contributed ‘lightning talks’
11:50am - 1:00pm	Lunch
1:00pm - 2:40pm	Contributed talks session I (4 x 25 minute talks)
2:40pm - 3:15pm	Coffee break
3:15pm - 4:15pm	Developer workshop “Turning great ideas into Bioconductor packages with impact”
4:15pm - 5:15pm	Poster session/social hour
6:00pm - 8:00pm	Dinner

Scholarships

A number of scholarships (up to $400 USD each) are available for students and Bioconductor package developers to help with the cost of travel to attend the meeting.

To apply for a scholarship, please submit a brief statement (200 words of less) describing your interest in the meeting. If you are a package developer or maintainer please tell us the package(s) you work on. The due date for applications is August 21st. Please send applications to gustin.s AT wehi DOT edu DOT au and put SCHOLARSHIP in the subject line.

Materials

• Introduction HTML

  Rmd

  R

• Data Representations HTML

  Rmd

  R

• RNASeq HTML

  Rmd

  R

• Annotation HTML

  Rmd

  R

To launch an Amazon Machine Image (AMI) for this course:

• Create an Amazon Web Services (AWS) Account if you don’t already have one.
• Start the instance ami-c5472aa0; See the documentation for this. Make sure your security group has port 80 accessible.
• Paste the Public DNS name of your instance into a web browser.
• Log in to RStudio with username ubuntu and password bioc .
• Be sure and terminate your instance when you are done using it, in order to avoid excessive charges.
• Inside RStudio, view the available vignettes with help(package="BiocAsiaPacific2015") and then click on “User guides, package vignettes and other documentation.”.
• For more information, see the Bioconductor AMI page.