The iPlant Collaborative: Cyberinfrastructure for Plant Biology

Abstract

The iPlant Collaborative (iPlant) is a United States National Science Foundation (NSF) funded project that aims to create an innovative, comprehensive, and foundational cyberinfrastructure in support of plant biology research (PSCIC, 2006). iPlant is developing cyberinfrastructure that uniquely enables scientists throughout the diverse fields that comprise plant biology to address Grand Challenges in new ways, to stimulate and facilitate cross-disciplinary research, to promote biology and computer science research interactions, and to train the next generation of scientists on the use of cyberinfrastructure in research and education. Meeting humanity's projected demands for agricultural and forest products and the expectation that natural ecosystems be managed sustainably will require synergies from the application of information technologies. The iPlant cyberinfrastructure design is based on an unprecedented period of research community input, and leverages developments in high-performance computing, data storage, and cyberinfrastructure for the physical sciences. iPlant is an open-source project with application programming interfaces that allow the community to extend the infrastructure to meet its needs. iPlant is sponsoring community-driven workshops addressing specific scientific questions via analysis tool integration and hypothesis testing. These workshops teach researchers how to add bioinformatics tools and/or datasets into the iPlant cyberinfrastructure enabling plant scientists to perform complex analyses on large datasets without the need to master the command-line or high-performance computational services.

Keywords: bioinformatics; computational biology; cyberinfrastructure; plant biology.

Figure 1

Overview of access options for iPlant's major cyberinfrastructure components. iPlant's CI consists of several major systems, each of which provides a set of computational resources for different types of users. The basic level of services provides access to data and data analysis algorithms. For large datasets, there are two general paradigms for computing: high-throughput computing (HTC) and high-performance computing (HPC). The major difference is that HTC provides rapid access to many different data types requiring discreet computation while HPC provides access to many interlinked compute nodes for tightly coupled parallel computation. Data resides in iPlant's Data Store, a cloud-based distributed system for storing and sharing large quantities of data that are automatically replicated between iPlant's major sites. iPlant resources can be accessed directly or through APIs. iPlant's Discovery Environment is a web-based system and provides functionality to manage data, add new algorithms and tools, and run analyses on appropriate computational resources. Atmosphere is iPlant's on-demand cloud computing resource that allows users to launch virtual machines, install complex software of their choice, connect to iPlant's Data Store and other compute resources, and share cloud resources with collaborators. Together, iPlant's CI proves a wealth of interconnected computational and data management resources to users with different needs and diverse levels of computational expertise.

Figure 2

An illustration of the multilayered iPlant cyberinfrastructure platform. The three primary building blocks of the iPlant CI are depicted with overlying community access options. Individual blocks are comprised of distinct software and hardware components that collectively provide the integration and communication capabilities with the adjacent blocks. This architecture facilitates the rapid development of applications and user interfaces on a robust underlying foundation, and provides unified secure access to scalable storage and the computational grid infrastructure.

Figure 3

The DNA Subway. The DNA Subway is an Educational DE, a simplified workflow for gene annotation and comparison. The subway lines are the Red Line (predicts and annotates genes in contigs less than 150kb), the Yellow Line (identifies homologs in other sequenced genomes), and the Blue Line (supports phylogenetics analysis and DNA barcode analysis). Additional “lines” are under development as new tools are integrated into the iPlant CI that can be consumed by a web-based DE.