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iPlant: A Cyberinfrastructure for Plant Biology

Mimi Padmabandu
| Jan 13, 2013
iPlant Collaborative

It’s getting harder to be a plant—there’s wind, rain, drought, pathogens, and now more manmade changes to the environment than ever before. Responses to changing environmental conditions are quickly becoming central to studies of plant adaptation, agriculture, ecological studies, and physiology. Addressing the data complexities of plant science requires concerted efforts from specialists in a diverse array of disciplines, including computational genomics, bioinformatics, physiology, and computer science. Until now, most of the analysis tools available to the plant science research community were specific to individual labs and lacked helpful documentation, intuitive design, and scalability. In an effort to create a rich cyberinfrastructure for the plant science community, a group of researchers, educators, and students created the iPlant Collaborative. In addition to computing resources, data analysis software, and virtual data management systems, iPlant’s cyberinfrastructure provides a collaborative environment that encourages sharing of ideas, data, and tools to drive plant studies forward.

iPlant’s Discovery Environment (DE) allows researchers to access computing applications and data. This environment includes not only tools built by iPlant, but community-contributed tools as well. The DE features a web interface to access computing, data storage, and analysis applications through iPlant, all in one convenient location. Simple integration makes it easy for researchers to contribute new tools into the interface, creating an ever-expanding set of programs for researchers to tailor analyses. The DE currently features data analysis resources supporting a variety of research areas, including clustering and network analysis, QTL mapping, sequence alignments, and phylogenetic comparison. iPlant also features Atmosphere, a cloud infrastructure platform, which allows plant researchers to launch their own virtual working environment and manage their studies.

To make genomic analysis even easier for the non-expert user, DNA Subway provides easy access to data and informatics tools. Designed to look like a subway map, DNA Subway organizes analysis tools into logical workflows and presents them in an intuitive interface, so students and educators can easily navigate through the informatics pipeline by “riding” different lines. The cloud-based iPlant Data Store makes it easy to store and share data between collaborators, iPlant’s tools, and even other web-based systems.

In addition to providing access to data storage and computing power, iPlant also offers services that promote collaboration and targeted communication designed to advance computational thinking in plant biology. With workshops and Grand Challenge Teams, the iPlant Collaborative is leading the way forward in developing innovative cyberinfrastructure to handle “big data” and further understand plant genomics.

If you’re in San Diego for PAG XXI, January 12–16, 2013, drop by the iPlant workshop to learn more about the collaboration.

Image ©2011 iPlant Collaborative, released under the Creative Commons Attribution 3.0 Unported License