1. Customized cloud platform for computing on your terms !

2. What is cloud computing ?

3. Atmosphere: motivation
Standalone GUI-based applications are frequently required for analysis
GUI apps not easily 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)
Availability of Next Gen map-reduce based algorithms (currently we have limited support)

4. Challenges of existing platforms
Amazon Web Services (AWS)
Flexible and scalable
High level of expertise required for configurations
Fairly challenging for biologists to master all steps
Limited lifecycle management (cost, time)

5. Steps to get started !

6. What is Atmosphere ? Self-service cloud infrastructure
Designed to make underlying cloud infrastructure easy to use by novice user
Built on open source Eucalyptus
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
VNC is virtual networking computing developed

7. 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

8. The iPlant Collaborative
Project Atmosphere™: Custom Cloud Computing
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
Run servers, CloudBurst desktop use cases. Big data and the desktop are co-local again!
>60 hosted applications in Atmosphere today, including users from USDA, Forest Service, database providers, etc.
(30 more for postdocs and grad students for training classes)

9. Atmosphere: Collaboration
iPlant Data Store

10. Lifecycle

11. How to Connect

12. Different Ways to Log in to VMs

13. Hands on exercise Launching a instance (one per team)
Connecting to it (vnc and ssh) using the web browser and vnc client software
Bringing data from iDS to Atmosphere (use idrop or icommands)
Launching a application
Installing a new application (optional)
Saving data back to iDS
Collaborating with other users (sharing your session)
Terminating the instance when you are done

14. Exercise (cont.)
Atmosphere manual is at:
To get started point your browser to
Login with your iPlant credentials
Please do not launch an instance until your instructor has directed you to do so. It is ideal if 4 or 5 users form a team and launch a single instance to limit the load on the system
Once launched, check for availability of your instance (usually 10 to 15 min) or you can check the web interface
Once you instance is ready you use the IP address and connect to it, and invite others to connect to it and collaborate with them with a shared screen
For todays session we will use the “NGS Viewers” application
You can go to and get started ..no software install rquired

15. Uses of Atmosphere Workshops: Graduate course work:
Frontiers and Techniques in Plant Sciences CSHL 2011
Genotyping by Sequencing Cornell Computational Biology
Graduate course work:
BCB 660 Prof. Volker Brendel and Amy Toth Fall 2011, Iowa State University
Popular community contributed images:
PhytoMorph (Nate Miller, U. Wisconsin)
Twig2Genome (Haibao Tang, JCVI)
Julin Maloof, UC Davis*