The project develops computing systems and software that combine computing resources, like those ofTeraGrid, andbioinformatics andcomputational biology software. Its goal is easier collaboration among researchers with improved data access and processing efficiency. Primarily centered in the United States, it collaborates internationally.
In 2006, the NSF solicited proposals to create "a new type of organization – a cyberinfrastructure collaborative for plant science" with a program titled "Plant Science Cyberinfrastructure Collaborative" (PSCIC) with Christopher Greer as program director.[9] A proposal was accepted (adopting the convention of using the word "Collaborative" as a noun) and iPlant was officially created on February 1, 2008.[1][9]Funding was estimated as $10 million per year over five years.[10]
Richard Jorgensen led the team through the proposal stage and was theprincipal investigator (PI) from 2008 to 2009.[10] Gregory Andrews, Vicki Chandler, Sudha Ram and Lincoln Stein served as Co-Principal Investigators (Co-PIs) from 2008 to 2009. In late 2009, Stephen Goff was named PI and Daniel Stanzione was added as a Co-PI.[1][11][12] As of May 2014, Co-PI Stanzione was replaced by 4 new Co-PIs: Doreen Ware at Cold Spring Harbor, Nirav Merchant and Eric Lyons at the University of Arizona, and Matthew Vaughn at the Texas Advanced Computing Center.[13]
The iPlant project supports what has been callede-Science, which is a use of information systems technology that is being adopted by the research community in efforts such as theNational Center for Ecological Analysis and Synthesis (NCEAS), ELIXIR,[14] and the Bamboo Technology Project that started in September 2010.[15][16] iPlant is "designed to create the foundation to support the computational needs of the research community and facilitate progress toward solutions of major problems in plant biology."[6][17]
The project works as acollaboration. It seeks input from the wider plant science community on what to build.[18]Based on that input, it has enabled easier use of large data sets,[19] created a community-driven research environment to share existing data collections within a research area and between research areas[20] and shares data withprovenance tracking.[21][22]One model studied for collaboration wasWikipedia.[23][24]
Several more recent National Science Foundation awards mentioned iPlant explicitly in their descriptions, as either a design pattern to follow or a collaborator with whom the recipient will work.[25]
The NSF requires that funding subcontracts stay within the United States, but international collaboration started in 2009 with theTechnical University Munich[27] andUniversity of Toronto in 2010.[29][30]East Main Evaluation & Consulting provides external oversight, advice, and assistance.[31]
The iPlant project makes its cyberinfrastructure available several different ways and offers services to make it the accessible to its primary audience. The design was meant to grow in response to needs of the research community it serves.[6]
The Discovery Environment integrates community-recommended software tools into a system that can handleterabytes of data using high-performance supercomputers to perform these tasks much more quickly. It has an interface designed to hide the complexity needed to do this from the end user. The goal was to make the cyberinfrastructure available to non-technical end users who are not as comfortable using acommand-line interface.[6][32]
A set ofapplication programming interfaces (APIs) for developers allow access to iPlant services, including authentication, data management, high performance supercomputing resources from custom, locally produced software.[6][33]
Atmosphere is acloud computing platform that provides easy access to pre-configured, frequently used analysis routines, relevant algorithms, and data sets, and accommodates computationally and data-intensive bioinformatics tasks.[6]It uses theEucalyptus virtualization platform.[34][35]
The iPlant Semantic Web effort uses an iPlant-created architecture, protocol, and platform called the Simple Semantic Web Architecture and Protocol (SSWAP) forsemantic web linking using a plant science focusedontology.[6][36][37] SSWAP is based on the notion ofRESTful web services with an ontology based onWeb Ontology Language (OWL).[38][39]
The Taxonomic Name Resolution Service (TNRS) is a free utility for correcting and standardizing plant names. This is needed because plant names that are misspelled, out of date (because a newer synonym is preferred), or incomplete make it hard to use computers to process large lists.[6][40][41]
My-Plant.org is asocial networking community for plant biologists, educators and others to come together to share information and research, collaborate, and track the latest developments in plant science.[6][42]The My-Plant network uses the terminologyclades to group users in a manner similar tophylogenetics of plants themselves.[42]It was implemented usingDrupal as itscontent management system.[42]
^Stein, Lincoln (September 2008). "Towards a cyberinfrastructure for the biological sciences: progress, visions and challenges".Nature Reviews Genetics.9 (9):678–688.doi:10.1038/nrg2414.PMID18714290.S2CID339653.
^Walsh, Lorraine; Khan, Peter E. (2010),Collaborative working in higher education: the social academy, New York: Routledge, p. 37,ISBN978-0-415-99167-4
^"Stephen Goff, Ph.D."Staff biography page from iPlant web site. Archived fromthe original on November 28, 2011. RetrievedSeptember 21, 2011.
^"Dan Stanzione, Ph.D."Staff biography page from Texas Advanced Computing Center web site. RetrievedSeptember 21, 2011.
^"Leadership".Leadership page from iPlant website. Archived fromthe original on May 28, 2014. RetrievedMay 27, 2014.
^"ELIXIR: Data for Life".Official web site. Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom: EMBL-European Bioinformatics Institute. RetrievedSeptember 28, 2011.
^"About Bamboo".Project Bamboo website. Archived from the original on October 9, 2011. RetrievedSeptember 27, 2011.
^Heidi Ledford (June 24, 2009)."Cyberinfrastructure: Feed me data".Nature.459 (7250):1047–1049.doi:10.1038/4591047a.PMID19553968.The iPlant programme was designed to give plant scientists a new information infrastructure. But first they had to decide what they wanted...
^Moore, Reagan W.; et al. (May 19, 2009)."Policy-Based Distributed Data Management Systems".4th International Conference on Open Repositories. Georgia Institute of Technology. RetrievedSeptember 28, 2011.
^Ram, Sudha; Jun Liu (2010). "Provenance Management in BioSciences".Advances in Conceptual Modeling – Applications and Challenges. Advances in Conceptual Modeling‚ Applications and Challenges. Vol. 6413. Springer Berlin / Heidelberg. pp. 54–64.doi:10.1007/978-3-642-16385-2_8.ISBN978-3-642-16384-5.
^Brown, Susan A.; Thatcher, Sherry; Dang, Yan (2010). "Managing Knowledge in a Changing Scientific Landscape: The Impact of Cyberinfrastructure".2010 43rd Hawaii International Conference on System Sciences. pp. 1–10.doi:10.1109/HICSS.2010.263.ISBN978-1-4244-5509-6.S2CID1132763.
^Jun Liu; Sudha Ram (December 2009). "Who Does What: Collaboration Patterns in the Wikipedia and Their Impact on Data Quality".19th Workshop on Information Technologies and Systems:175–180.SSRN1565682.
^"Award Search—Awardee Information".NSF website search. National Science Foundation. RetrievedSeptember 28, 2011. See abstracts for awards #0849861, #0923975, #0940841, #0953184, #1027542, #1031416, #1032105, #1126481, #1126998.
^Dooley, Rion (July 19, 2011)."An API To Feed the World".TeraGrid 2011: Extreme Digital Discovery. Salt Lake City, Utah. Archived fromthe original(PDF) on September 19, 2012. RetrievedSeptember 28, 2011.
"My-Plant.org".Phylogenetically Based Social Network for the Plant Sciences. iPlant Collaborative. Archived fromthe original on October 13, 2011. RetrievedSeptember 28, 2011.
