customized cloud platform for computing on your terms !

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Customized cloud platform for computing on your terms !

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Page 1: Customized cloud platform for computing on your terms !

Customized cloud platform for computing on your terms !

Page 2: Customized cloud platform for computing on your terms !

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

Page 3: Customized cloud platform for computing on your terms !

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

Page 4: Customized cloud platform for computing on your terms !

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)

Page 5: Customized cloud platform for computing on your terms !

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

Page 6: Customized cloud platform for computing on your terms !

• 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 CollaborativeProject Atmosphere™: Custom Cloud Computing

Page 7: Customized cloud platform for computing on your terms !

Atmosphere: Collaboration

iPlant Data Store

Page 8: Customized cloud platform for computing on your terms !

Lifecycle

Page 9: Customized cloud platform for computing on your terms !

How to Connect

Page 10: Customized cloud platform for computing on your terms !

Different Ways to Log in to VMs

Page 11: Customized cloud platform for computing on your terms !

Run the Integrative Genome Viewer

Page 12: Customized cloud platform for computing on your terms !

Accessing Your Virtual Machine• VNC client• Command line tools (e.g. SSH)

www.realvnc.com

Page 13: Customized cloud platform for computing on your terms !

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

Page 16: Customized cloud platform for computing on your terms !

Import Needed Data using DE

Step 1: click icon “Import from URL”Step 2: Paste URL’s & click “Upload”

Page 17: Customized cloud platform for computing on your terms !

Log In to Atmosphere(One member of team)

https://atmo-beta.iplantcollaborative.org/login/

Page 18: Customized cloud platform for computing on your terms !

Launch AtmosphereSelect “NGS Viewers” Takes 10-15 min: you will receive e-mail

notification with needed IP address

Page 19: Customized cloud platform for computing on your terms !

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

Page 20: Customized cloud platform for computing on your terms !

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

Page 21: Customized cloud platform for computing on your terms !

Launching VNC

Paste your DNS (IP address)Add “:1” to end

Enter iPlant Username & Password

Page 22: Customized cloud platform for computing on your terms !
Page 23: Customized cloud platform for computing on your terms !

Moving Data with iDrop

Right click on iDrop icon and select “Open”

*Do not click icon multiple times!

Page 24: Customized cloud platform for computing on your terms !

Log In to iDropAtmosphere: Moving Data w/ iDrop

Page 25: Customized cloud platform for computing on your terms !

Atmosphere: Moving Data w/ iDrop

• 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

Page 26: Customized cloud platform for computing on your terms !

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

Page 27: Customized cloud platform for computing on your terms !

Sharing Your Atmosphere Instance Step 2

Click “Configure”

Page 28: Customized cloud platform for computing on your terms !

Sharing Your Atmosphere Instance Step 3

1. Click “Add User”2. Enter iPlant User Name you

wish to share with3. 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

Page 29: Customized cloud platform for computing on your terms !

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)

Page 30: Customized cloud platform for computing on your terms !

Load Arabidopsis v10 Genome

Page 31: Customized cloud platform for computing on your terms !

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

Page 32: Customized cloud platform for computing on your terms !
Page 33: Customized cloud platform for computing on your terms !

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

Page 34: Customized cloud platform for computing on your terms !

Terminate Your Instance!Final Step…