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Bioinformatics Analysis Environment for Your Laboratory Use

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Bioinformatics Analysis Environment for Your Laboratory Use

  1. 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. 2. Notice: This service is an experimental project
  3. 3. Service Providing bioinformatics analysis environment on cloud computer ! Collaboration Implementation of user-interface for your bioinformatics tools on Galaxy
  4. 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. 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. 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. 7. Implementation of user-interface for your bioinformatics tools on Galaxy Collaborative Service
  8. 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. 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/

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