Facilitating access to customized computational infrastructure for plant sciences: Atmosphere cloudfront Seung-­‐jin Kim, Nirav Merchant, and Edwin Skidmore iPlant Collaborative University of Arizona, Tucson, Arizona, USA http://www.iplantcollaborative.org {seungjin,nirav}@email.arizona.edu, edwin@iplantcollaborative.org Cloud based infrastructure is seeing increased adoption as popular computational biology applications and algorithms are leveraging unique capabilities offered by cloud style infrastructure [1][2]. With multiple open source options for deploying in-­‐house cloud infrastructure, many research facilities are implementing local or private clouds. This wide spread adoption of cloud as a IaaS (Infrastructure as a Service) model has significant benefits, but comes with significant limitations in self service capabilities from the end user perspective. While many commercial offerings such as Amazon and Rackspace offer dashboard style web application for provisioning and management, they are primarily designed for users conversant with the management capabilities of IaaS. In order to facilitate the use of cloud style infrastructure for research needs in plant sciences, the iPlant Collaborative has deployed project Atmosphere a integrative cloud services platform with the primary goal of providing ease of access to preconfigured, frequently used analysis routines, algorithms and datasets in an available-­‐on-­‐demand environment which is designed to accommodate computationally and data intense bioinformatics tasks. It enables end user provisioned and managed, on-­‐demand virtual machine access within iPlant’s compute infrastructure. This allows plant scientists to utilize this capability in a PaaS (Platform as a Service) model, allowing them to focus on the broader application and data analysis tasks, while the underlying computational infrastructure and the application dependencies are configured and optimized for the task at hand. Key features include 1. A powerful Web 2.0 style client for ease of management and administration 2. An API Service that allows integration with existing infrastructure components 3. Virtual Machine Images preconfigured for popular plant sciences domain specific tasks 4. Access to iPlant Cyberinfrastucture (cloud style storage, selected plant sciences datasets) 5.
Integrated gateway access to grid and high performance computing (HPC) resources Currently iPlant offers limited access to a preview release version of Atmosphere. This release includes: 1. Management of ssh credentials 2. Access to virtual machine image collection 3. Launching new virtual machines with various predefined CPU and memory configurations. 4. Integrated IP number management for virtual instances 5. Listing of current active virtual instances and their metrics and descriptions and meta data 6. Terminating existing virtual machine instances
For the preview release, Atmosphere utilizes the open-­‐source Eucalyptus cloud platform. However, Atmosphere’s API abstracts the virtualization layer and is compatible with other virtualization resources such as Amazon EC2, Xen(XM) and Libvirt. Figure 1: Atmosphere’s architecture Atmosphere is comprised of the following three services: • Cloudauth: API Authorization server that issues/validates API tokens • Cloudservice: API Abstract layer that controls database and virtualization platform API (Euca2ools) • Cloudfront: Rich web application framework based on Atmosphere’s cloudservice api Cloudfront is a rich web application that manages and controls virtual machine instances Figure 2: Atmosphere shows running instances Cloudfront requests API authorization call to Cloudauth service. Once Cloudfront receives a validated api token, it communicates with Cloudservice. Cloudservice is an abstract API layer that controls Atmosphere database and its virtualization platform (currently eucalyptus) (see Figure 1). Figure 3: Atmosphere’s ssh key manage interface Cloudfront’s rich web interface provides users with easy web experience to launch and manage iPlant’s virtual resources. Figure 3 shows how users can manage their ssh-­‐key for virtual instances as well as their user properties (right side panel). It provides desktop-­‐like user experience over the web. Developers with minimal exposure to web 2.0 style application development can adopt Atmosphere’s interface with ease for launching and managing their virtual machines. Advanced users also can access Atmosphere’s resources using Atmosphere’s API request call. Atmosphere’s cloudservice provides HTTP/RPC/RESTFul-­‐like API that can be easily integrated with existing infrastructural components For the demonstration session, we will step through typical usage scenarios related to computational and data analytical tasks for plant biologists. The live demonstration will highlight how end users can quickly identify and launch suitable instances, querying Atmosphere metadata catalog through Cloudfront, allowing users to integrate these deployed resources with their analysis workflows. We also will discuss the underlying API, which also powers the flexible and extensible web front end. *The iPlant Collaborative is funded by a grant from the National Science Foundation Plant Cyberinfrastructure Program (#EF-­‐0735191). 1: Langmead B, Hansen KD, Leek JT. Cloud-­‐scale RNA-­‐sequencing differential expression analysis with Myrna. Genome Biol. 2010;11(8):R83. Epub 2010 Aug 11. 2: Dudley JT, Pouliot Y, Chen R, Morgan AA, Butte AJ. Translational bioinformatics in the cloud: an affordable alternative. Genome Med. 2010 Aug 6;2(8):51. * NOTE: High speed internet required for demo Overall Concept of Atmosphere Poster example