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Bayes: Bioinformatics Analysis Environment Service on RIKEN Cloud
Bioinformatics Analysis Environment for Your
Laboratory Use
Itoshi NIKAIDO, Ph.D. <itoshi.nikaido@riken.jp>
Unit Leader, Bioinformatics Research Unit
RIKEN Advanced Center for Computer and Communication
http://bit.accc.riken.jp/
Notice: This service is an experimental project
Service
Providing bioinformatics analysis environment on cloud
computer
!
Collaboration
Implementation of user-interface for your bioinformatics
tools on Galaxy
Bioinformatics Evangelist Model for Data Analysis Infrastructure in RIKEN
Sequencing Core
Research Team/Unit
Research Team/Unit
Research Team/Unit
Bioinformatics Evangelist
Bioinformatics Research Unit Preventive medicine and applied genomics unit
Bioinformatics Research Group, RIKEN ACCC
Research Center
• Limitation
• few bioinformatics
researcher in your center
• 2, 3 collaboration/person
• Many bioinformatics tools
and combinations
• no root in RICC
• Plan
• Support for you and
bioinformatics evangelist at
each center
• Providing virtual machine
with pre-setting-up
bioinformatics analysis
environment
Providing bioinformatics analysis environment
Virtual machine with NGS Data analysis tools and pipelines
Bioinformatics Research Unit
Cloud Computer
User
(inside/outside RIKEN)
Browser, tools, Pipelines
Install and setup tools
(BioDevOps)
Development of tools
Browser & Pipelines
SSH, HTTPS
Calc.Result
Browser & Pipeline
Consultation
Tutorial
Providing data analysis environment for general NGS analysis on Cloud
computer system
User’s tools
• Cloud system is located at Wako campus
• You can access your virtual machine (Ubuntu 14.04 LTS)
• with root privileges
• via SSH and HTTP
• from only Wako, Yokohama, Kobe and Tsukuba
• We provide
• over 125 tools on Galaxy, 900 R/Bioconductor Packages and 600
command line tools (DebianMed)
• one virtual machine per one research group
• 10 virtual machines at drawing logs
• 8 CPU cores (2GHz), 64 GB RAM and 3 TB strage/VM
• NFS for mouse/human reference genome/transcriptome
Spec. of virtual machine
Bioinformatics Analysis Environment for Your Laboratory Use
Implementation of user-interface for your bioinformatics tools on Galaxy
Collaborative Service
• Experimental service with test users: 2015/04/01-
• bug check
• test of data transfer between VMs
• implement of your bioinformatics tools on Galaxy
• Galaxy and USCS Genome Browser work closely together on
Cloud system
• Release: ?
Roadmap
From experimental service to test service
!
• Please contact support-bayes@riken.jp
!
• References
• http://bit.accc.riken.jp/
• http://github.com/rikenbit/
• http://biodevops.org/
• http://genome.ucsc.edu/
• http://galaxyproject.org/
Bioinformatics Analysis Environment for Your Laboratory Use
Itoshi NIKAIDO, Ph.D. <itoshi.nikaido@riken.jp>
Unit Leader, Bioinformatics Research Unit
RIKEN Advanced Center for Computer and Communication
http://bit.accc.riken.jp/

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Bioinformatics Analysis Environment for Your Laboratory Use

  • 1. Bayes: Bioinformatics Analysis Environment Service on RIKEN Cloud Bioinformatics Analysis Environment for Your Laboratory Use Itoshi NIKAIDO, Ph.D. <itoshi.nikaido@riken.jp> Unit Leader, Bioinformatics Research Unit RIKEN Advanced Center for Computer and Communication http://bit.accc.riken.jp/
  • 2. Notice: This service is an experimental project
  • 3. Service Providing bioinformatics analysis environment on cloud computer ! Collaboration Implementation of user-interface for your bioinformatics tools on Galaxy
  • 4. Bioinformatics Evangelist Model for Data Analysis Infrastructure in RIKEN Sequencing Core Research Team/Unit Research Team/Unit Research Team/Unit Bioinformatics Evangelist Bioinformatics Research Unit Preventive medicine and applied genomics unit Bioinformatics Research Group, RIKEN ACCC Research Center • Limitation • few bioinformatics researcher in your center • 2, 3 collaboration/person • Many bioinformatics tools and combinations • no root in RICC • Plan • Support for you and bioinformatics evangelist at each center • Providing virtual machine with pre-setting-up bioinformatics analysis environment
  • 5. Providing bioinformatics analysis environment Virtual machine with NGS Data analysis tools and pipelines Bioinformatics Research Unit Cloud Computer User (inside/outside RIKEN) Browser, tools, Pipelines Install and setup tools (BioDevOps) Development of tools Browser & Pipelines SSH, HTTPS Calc.Result Browser & Pipeline Consultation Tutorial Providing data analysis environment for general NGS analysis on Cloud computer system User’s tools
  • 6. • Cloud system is located at Wako campus • You can access your virtual machine (Ubuntu 14.04 LTS) • with root privileges • via SSH and HTTP • from only Wako, Yokohama, Kobe and Tsukuba • We provide • over 125 tools on Galaxy, 900 R/Bioconductor Packages and 600 command line tools (DebianMed) • one virtual machine per one research group • 10 virtual machines at drawing logs • 8 CPU cores (2GHz), 64 GB RAM and 3 TB strage/VM • NFS for mouse/human reference genome/transcriptome Spec. of virtual machine Bioinformatics Analysis Environment for Your Laboratory Use
  • 7. Implementation of user-interface for your bioinformatics tools on Galaxy Collaborative Service
  • 8. • Experimental service with test users: 2015/04/01- • bug check • test of data transfer between VMs • implement of your bioinformatics tools on Galaxy • Galaxy and USCS Genome Browser work closely together on Cloud system • Release: ? Roadmap From experimental service to test service
  • 9. ! • Please contact support-bayes@riken.jp ! • References • http://bit.accc.riken.jp/ • http://github.com/rikenbit/ • http://biodevops.org/ • http://genome.ucsc.edu/ • http://galaxyproject.org/ Bioinformatics Analysis Environment for Your Laboratory Use Itoshi NIKAIDO, Ph.D. <itoshi.nikaido@riken.jp> Unit Leader, Bioinformatics Research Unit RIKEN Advanced Center for Computer and Communication http://bit.accc.riken.jp/