CHPC Workshop Morning Session
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The document discusses a workshop on using cloud computing solutions like Cloud BioLinux to overcome barriers in genomics research across institutions by providing pre-configured virtual machines with bioinformatics software on the Amazon EC2 cloud to enable genomic analysis without requiring local computational resources. The workshop will include presentations on cloud computing and Cloud BioLinux as well as hands-on sessions for installing and using Cloud BioLinux on laptops.
CHPC Workshop Morning Session
- 1. Cloud Computing Solutions for Genomics Across Geographic, Institutional and Economic Barriers Ntinos Krampis Asst. Professor J. Craig Venter Institute kkrampis@jcvi.org http://www.jcvi.org/cms/about/bios/kkrampis/
- 2. Workshop Schedule Morning Session: Background Presentations and Prep 11:00 – 11:45 Introduction to Cloud Computing for Bioinformatics 11:45 – 12:00 Questions and Answers 12:00 – 12:30 Using Cloud BioLinux on the Amazon EC2 Cloud 12:30 – 13:00 Preparation: install Cloud Virtual Machines on laptops Afternoon Session: Hands on Session 14:00 – 14:30 Preparation: install Cloud Virtual Machines on laptops 14:30 – 16:00 Bioinformatic Analysis using Cloud BioLinux 16:30 – 17:30 Customized Bioinformatics Solutions for Participants
- 3. A little bit of background information... ● Konstantinos (Ntinos) Krampis, started working at J. Craig Venter Inst. (JCVI) in 2009 ● Background training in Molecular Biology, PhD in Bioinformatics ● Research: cloud and high-performance computing, genome assembly ● Projects: Cloud BioLinux (cloudbiolinux.org) ● Taught Cloud BioLinux workshop at Univ. of Limpopo last May ● Slides available at http://www.slideshare.com/agbiotec ● Email me for slides, meeting, questions: kkrampis@jcvi.org
- 4. J. Craig Venter Institute (JCVI) Large-scale genome sequencing and bioinformatics computing ●Human Microbiome Project (HMP): genome sequencing of microbes living in and on the human body ● Global Ocean Sampling (GOS) survey: genome sequencing of microbes sampled from oceans around the world
- 5. JCVI: sequencing and computing infrastructure ● core sequencing laboratory: 454, Solexa, HiSeq, IonTorrent on the way ● dedicated bioinformatics department (57 bioinformaticians) ● large-scale computations, ~1000 node Sun Grid Engine (SGE) cluster
- 6. Low-cost sequencing instruments ● small-factor sequencers available: GS Junior by 454, MiSeq by Illumina ● bacterial, viral, small fungal genomes, sequencing for variant discovery ● sequencing as a standard technique in molecular biology and genetics ● RNAseq (instead of microarrays) and ChiPseq (instead of yeast 2-hybrid) http://www.gsjunior.com/ http://www.illumina.com/systems/miseq.ilmn
- 7. More small laboratories doing genome sequencing amount of sequencing number of labs acquiring the sequence data is only the first step...
- 8. Sequencing instruments shipped with minimal computational capacity ●Problem 1: sequencing data analysis requires high-performance and expensive computing hardware, for example: genome assembly, BLAST, genome annotation ●Problem 2: much of bioinformatics software are difficult to install by biologists, need technical expertise with operating systems, compiling source code etc.
- 9. Each lab building their own informatics infrastructure ? ●small labs need additional funds to build computing clusters ●funds for bioinformaticians and software developers to maintain the clusters and software ● duplication of effort across labs ●sub-optimal utilization of the hardware due to small amounts of sequencing
- 10. Large sequencing centers offering bioinformatics analysis services ? ● Bioinformatic Resource Centers (BRC) ●bioinformatic analysis coupled with sequencing of an organism ● mostly provide data browsing and few analysis tools to the public ●cannot serve the bioinformatic needs of every small lab acquiring a sequencing instrument ●need end-to-end solutions, users submit sequence data and get final annotation
- 11. Solving Problem 1: using high-performance computing hardware available on the cloud ●cloud computing : high performance computers and data storage, remotely accessible through the Internet ●we are all using the cloud: Gmail, Google Docs, FaceBook; you store and access data on a remote computer ●cloud computers rented pay-as-you-go by service providers such as Amazon Elastic Compute Cloud (EC2)
- 12. The Amazon EC2 cloud computing service ● a subsidiary company of Amazon.com, rents computing pay-as-you go ● cloud computers cost $0.085 - $2 per hr (max 64GB memory and 8 processors) ● used by companies that need additional computers without investing on hardware ● physical locations US East / West regions, EU, Singapore, Japan researchers ● democratizes access to computing resources outside of institutional, economic or national boundaries 750 hours free for new users, sign up here: http://aws.amazon.com/free/ http://aws.amazon.com
- 13. How does cloud computing work ? ● cloud computing evolved from virtualization technology ● operating system, bioinformatics software and data, are installed on a Virtual Machine (VM) ● VM is emulation of a computer system, in the form of a single, executable binary file ● runs inside a physical computer such as a laptop ● why Virtualization: simplify IT maintenance
- 14. How does cloud computing work ? ● a VM is uploaded on the cloud remote Amazon EC2 cloud computing service service; runs by renting computing capacity from Amazon EC2 (up to VM VM VM 64GB RAM / 8 core computers) ● bioinformatics software can be executed from anywhere in the world through a desktop computer with Internet access Internet ● removes need for local computer clusters at each laboratory ● alternatively if you have a cluster locally it can run on a private cloud local computers
- 15. Solving problem 2: pre-installed and configured bioinformatics software on cloud Virtual Machines ●Cloud BioLinux: a publicly accessible Virtual Machine (VM) on the Amazon EC2 cloud ●100+ pre-configured and installed bioinformatics software tools Amazon EC2 cloud ●sequence analysis, genome assembly, annotation, phylogeny, molecular modeling, gene expression ●a researcher can initiate a practically unlimited number of VMs for large-scale data analysis and access them using a local computer
- 16. Cloud BioLinux for Bioinformatics ● how the Cloud BioLinux project came to be, what it can offers to small labs for genome sequence analysis ●where and how do I run Cloud BioLinux , especially if I am not a computer expert ● besides end-users, bioinformatics developers are provided a framework for modifying and sharing VM configurations and data
- 17. Creating Cloud Biolinux ● JCVI bioinformatics cloud computing research tinyurl.com/BioLinux-NEBC ● NEBC BioLinux software repository ● community effort at BOSC 2009 – 11 + ●initially: a VM on Amazon EC2 with the tools copied and installed from the NEBC repository ● now: developer's framework for creating customized cloud VMs = ● major contributors: http://www.cloudbiolinux.org
- 18. Research at JCVI with Cloud BioLinux ●Eucalyptus private cloud currently installed at JCVI, OpenStack on the way ●open-source cloud platforms, fully compatible with Amazon EC2 (identical API) ●easy to set up on a local computer cluster, comes with Ubuntu Linux server ●develop VMs in-house with complex bioinformatics pipelines pre-installed and upload to Amazon EC2 for public access ● free to use on your laptop with Virtualbox
- 19. 10 min of questions....
- 20. Research at JCVI with Cloud BioLinux ● bioinformatics data analysis pipelines have complex dependencies: operating system, software libraries, reference databases etc. ● approach: pre-install pipelines and all dependencies in a single binary VM file using a private cloud ●upload VM on Amazon EC2: pipelines ready to execute, no need to purchase hardware JCVI - GSC
- 25. Research at JCVI with Cloud BioLinux ● Funded by NIAID until 2013 ●port complex bioinformatic pipelines on the Amazon EC2 cloud ● focus on viral reads-to-annotation data pipelines ● benefits to small laboratories that lack resources if you own a cluster: download and run VM on your JCVI - GSC ● private Eucalyptus or Openstack cloud
- 26. Running Cloud BioLinux on the Amazon EC2 cloud Account on the Amazon EC2 cloud http://aws.amazon.com/ec2
- 27. Launch Cloud BioLinux through the EC2 cloud console http://tinyurl.com/cloud-biolinux-tutorial
- 28. Cloud BioLinux launch wizard: steps 1 & 2 1. go to the “Community AMIs” tab, specify the Cloud BioLinux VM identifier (most recent update: cloudbiolinux.org) 2. select computational capacity
- 29. Cloud BioLinux launch wizard: step 3 3. specify a password for login to Cloud BioLinux in the “User Data” box 10
- 32. Distributing Data Analysis Results with Cloud BioLinux
- 33. Distributing Data Analysis Results with Cloud BioLinux Whole System Snapshot Exchange ● how difficult is to share bioinformatics work on your computer with a collaborator ? ● capture the state of the computing system (OS + software), data, analysis results ● make VM snapshots: executable binary file, replica of a running VM ● distribute a VM snapshot with pre-installed software and data analysis results ● collaborators can replicate, re-run, add to your analysis results ● a snapshot can be shared directly on the Amazon cloud, downloaded on a private cloud or run on desktop using virtualization software
- 34. Cloud BioLinux: whole system snapshot exchange storage cost: 0.10$ / GB / month
- 35. Cloud BioLinux: whole system snapshot exchange authorize access to the VM: public or for certain users other researchers can access the VM with all the software, data, analysis results directly on the cloud
- 36. Cloud BioLinux for Software Developers ● Issue 1: for researchers with sensitive data a public cloud might not be an option ● Problem 1: moving VMs across clouds is not trivial, need low level operations ● Issue 2: bioinformatic specializations (ex. sequencing, phylogeny, protein structure) ● Problem 2: one VM with many tools to fit all becomes over-sized ● Cloud BioLinux VM deployment framework
- 37. Cloud BioLinux for Software Developers ● framework to customize software installed in cloud VM / image ● based on python Fabric automated deployment tool ● software components listed in simple text configuration files ● edit the files to mix and match software according to your needs ● use source code repository to share configuration files for customized VMs ● start with a bare-bones VM on Amazon EC2 or Eucalyptus private cloud ● Fabric scripts automatically install specified software based on configuration files Free, available from: https://github.com/chapmanb/cloudbiolinux
- 38. software domains in Cloud BioLinux: Genome sequencing, de novo assembly, annotation, phylogeny, molecular structures, gene expression analysis high-level configuration describing software groups for each group individual bioinformatics tools
- 40. Acknowledgments & Credits Brad Chapman - development of the Fabric scripts, website Tim Booth, Mesude Bicak, Dawn Field – BioLinux 6.0 development Enis Afgan – Cloudman and Cloud BioLinux integration Members of the Cloud Biolinux community: http://groups.google.com/group/cloudbiolinux And again our contacts: kkrampis@jcvi.org Thank you ! http://www.cloudbiolinux.org http://www.slideshare.com/agbiotec