1. Customized cloud platform for computing on your terms !

2. What is cloud computing ? http://geekandpoke.typepad.com/geekandpoke/2009/03/let-the-clouds-make-your-life-easier.html The practice of using a network of remote servers hosted on the Internet to store, manage, and process data

3. What is Atmosphere? On-demand computing resource built on a cloud infrastructure Virtual Machine pre-configured with: – Software – Memory requirements – Processing power Fully integrated into iPlant authentication and storage and HPC capabilities Enables users to build custom images/appliances and share with community Cross-platform desktop access to GUI applications in the cloud (using VNC) Provide easy web based access to resources

4. Atmosphere: motivation Standalone GUI-based applications are frequently required for analysis but not easy to transform into web apps Need to handle complex software dependencies (e.g specific bioperl version and R modules) Users needing full control of their software stack (occasional sudo access) Need to share desktop/applications for collaborative analysis (remote collaborators)

5. Who is this tutorial designed for ? Users wanting to launch configured images in atmosphere (like app store) Developers for application distribution Prototyping/Testing new software/modules Tailored software training setups (custom workshops/laboratory courses etc) Extend compute capabilities of existing applications i.e. utilize iPlant API

6. API-compatible implementation of Amazon EC2/S3 interfaces Virtualize the execution environment for applications and services Up to 12 core / 48 GB instances Access to Cloud Storage + EBS >60 hosted applications in Atmosphere today, including users from USDA, Forest Service, database providers, etc. The iPlant Collaborative Project Atmosphere™: Custom Cloud Computing

7. Atmosphere: Collaboration iPlant Data Store

8. Lifecycle

9. How to Connect

10. Different Ways to Log in to VMs

11. Run the Integrative Genome Viewer

12. Accessing Your Virtual Machine VNC client Command line tools (e.g. SSH) www.realvnc.com

13. Atmosphere Exercise Objectives Launch an Atmosphere VM, “NGS Viewers” Connect using VNC Viewer Move data using iDrop Share instance with selected users Launch IGV “Integrative Genomics Viewer” View RNA-seq alignments to Arabidopsis reference genome TERMINATE YOUR INSTANCE WHEN DONE

14. Additional On-line Instruction Atmosphere Manual: https://pods.iplantcollaborative.org/wiki/displ ay/atmman/Table+of+Contents https://pods.iplantcollaborative.org/wiki/displ ay/atmman/Table+of+Contents iDrop: https://pods.iplantcollaborative.org/wiki/displ ay/start/Using+iDrop https://pods.iplantcollaborative.org/wiki/displ ay/start/Using+iDrop IGV: http://www.broadinstitute.org/igv/UserGuide http://www.broadinstitute.org/igv/UserGuide RealVNC: https://www.realvnc.com/https://www.realvnc.com/

15. Atmosphere Exercise Preparation Work in teams of 4 – One person in team will launch Atmosphere & share with other team members Download and Install VNC Viewer – https://pods.iplantcollaborative.org/wiki/display/atmman/Using+VNC +to+Connect+to+an+Atmosphere+VM https://pods.iplantcollaborative.org/wiki/display/atmman/Using+VNC +to+Connect+to+an+Atmosphere+VM Import required data files to your home directory – http://data.iplantcollaborative.org/quickshare/ca5fe5d6defaec8e/WT _rep1.fastq.tophat.bam http://data.iplantcollaborative.org/quickshare/ca5fe5d6defaec8e/WT _rep1.fastq.tophat.bam – http://data.iplantcollaborative.org/quickshare/b4bd99ee1ec54b6a/W T_rep1.fastq.tophat.bam.bai http://data.iplantcollaborative.org/quickshare/b4bd99ee1ec54b6a/W T_rep1.fastq.tophat.bam.bai

16. Import Needed Data using DE Step 1: click icon “Import from URL” Step 2: Paste URL’s & click “Upload”

17. Log In to Atmosphere (One member of team) https://atmo-beta.iplantcollaborative.org/login/

18. Launch Atmosphere Select “NGS Viewers” Takes 10-15 min: you will receive e-mail notification with needed IP address

19. Launch Atmosphere Confirmation message Can take 10-15 min to complete request You will receive e-mail notification with needed IP address

20. View Status in Dashboard Status “pending” will change to “running” You will also get an e-mail notification with IP address IP Address needed to log into VNC

21. Launching VNC Paste your DNS (IP address) Add “:1” to end Enter iPlant Username & Password

23. Moving Data with iDrop Right click on iDrop icon and select “Open” *Do not click icon multiple times!

24. Log In to iDrop Atmosphere: Moving Data w/ iDrop

25. Navigate to files in your iRods Data Store Navigate to your Atmosphere Home Directory Drag Files to copy: WT_rep1_fastq.tophat.bam WT_rep1_fastq.tophat.bam.bai

26. Sharing Your Atmosphere Instance Step 1 Open “VNC Server (User-Mode) or click icon

27. Sharing Your Atmosphere Instance Step 2 Click “Configure”

28. Sharing Your Atmosphere Instance Step 3 1.Click “Add User” 2.Enter iPlant User Name you wish to share with 3.Click “Add User” AGAIN! 4.“OK” Give Users the IP Address needed to Log In Shared Users can launch VNC, login, and share the desktop

29. Launch Integrative Genomics Viewer IGV is desktop application for customized Genome Browsing Many pre-installed genomes (or can load your own genome) Upload and view your own annotations & experimental data Many file formats accepted (e.g. BAM, GFF, BED)

30. Load Arabidopsis v10 Genome

31. Load Expression Data From File Load From File: ”WT_rep1.fastq.tophat.bam” WT_rep1.fastq.tophat.bam.bai must be in same directory but is not loaded directly

33. IGV View RNA-seq Alignment Tracks Need to zoom in and navigate around to find aligned regions Good Example Chr1:4,560,423-4,568,773 Or enter gene of interest Tracks show stacked alignment and bar-graph

34. Terminate Your Instance! Final Step…

35. https://pods.iplantcollaborative.org/wiki/display/atmman/Getting+H elp+and+Asking+Questions# https://forums.iplantcollaborative.org/ support@iplantcollaborative.org Thank you!