The iPlant Collaborative, renamed Cyverse in 2017, is a
virtual organization
A virtual organization is a temporary or permanent collection of geographically dispersed individuals, groups, organizational units, or entire organizations that depend on electronic linking in order to complete the production process (working defi ...
created by a
cooperative agreement
A cooperative (also known as co-operative, co-op, or coop) is "an autonomous association of persons united voluntarily to meet their common economic, social and cultural needs and aspirations through a jointly owned and democratically-contro ...
funded by the US
National Science Foundation
The National Science Foundation (NSF) is an independent agency of the United States government that supports fundamental research and education in all the non-medical fields of science and engineering. Its medical counterpart is the National I ...
(NSF) to create
cyberinfrastructure United States federal research funders use the term cyberinfrastructure to describe research environments that support advanced data acquisition, data storage, data management, data integration, data mining, data visualization and other computing a ...
for the plant sciences (
botany
Botany, also called , plant biology or phytology, is the science of plant life and a branch of biology. A botanist, plant scientist or phytologist is a scientist who specialises in this field. The term "botany" comes from the Ancient Greek w ...
).
The NSF compared cyberinfrastructure to physical
infrastructure
Infrastructure is the set of facilities and systems that serve a country, city, or other area, and encompasses the services and facilities necessary for its economy, households and firms to function. Infrastructure is composed of public and priv ...
, "... the
distributed computer,
information and communication technologies
Information and communications technology (ICT) is an extensional term for information technology (IT) that stresses the role of unified communications and the integration of telecommunications (telephone lines and wireless signals) and computers, ...
combined with the personnel and integrating components that provide a long-term platform to empower the modern scientific research endeavor".
In September 2013 it was announced that the National Science Foundation had renewed iPlant's funding for a second 5-year term with an expansion of scope to all non-human life science research.
The project develops computing systems and software that combine computing resources, like those of
TeraGrid, and
bioinformatics
Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combi ...
and
computational biology
Computational biology refers to the use of data analysis, mathematical modeling and computational simulations to understand biological systems and relationships. An intersection of computer science, biology, and big data, the field also has fo ...
software. Its goal is easier collaboration among researchers with improved data access and processing efficiency. Primarily centered in the United States, it collaborates internationally.
History
Biology is relying more and more on computers. Plant biology is changing with the rise of new technologies. With the advent of
bioinformatics
Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combi ...
,
computational biology
Computational biology refers to the use of data analysis, mathematical modeling and computational simulations to understand biological systems and relationships. An intersection of computer science, biology, and big data, the field also has fo ...
,
DNA sequencing
DNA sequencing is the process of determining the nucleic acid sequence – the order of nucleotides in DNA. It includes any method or technology that is used to determine the order of the four bases: adenine, guanine, cytosine, and thymine. Th ...
,
geographic information systems
A geographic information system (GIS) is a type of database containing geographic data (that is, descriptions of phenomena for which location is relevant), combined with software tools for managing, analyzing, and visualizing those data. In a br ...
and others computers can greatly assist researchers who study plant life looking for solutions to challenges in
medicine
Medicine is the science and practice of caring for a patient, managing the diagnosis, prognosis, prevention, treatment, palliation of their injury or disease, and promoting their health. Medicine encompasses a variety of health care pract ...
,
biofuels
Biofuel is a fuel that is produced over a short time span from biomass, rather than by the very slow natural processes involved in the formation of fossil fuels, such as oil. According to the United States Energy Information Administration (E ...
,
biodiversity
Biodiversity or biological diversity is the variety and variability of life on Earth. Biodiversity is a measure of variation at the genetic (''genetic variability''), species (''species diversity''), and ecosystem (''ecosystem diversity'') l ...
,
agriculture
Agriculture or farming is the practice of cultivating plants and livestock. Agriculture was the key development in the rise of sedentary human civilization, whereby farming of domesticated species created food surpluses that enabled people to ...
and problems like
drought tolerance,
plant breeding
Plant breeding is the science of changing the traits of plants in order to produce desired characteristics. It has been used to improve the quality of nutrition in products for humans and animals. The goals of plant breeding are to produce cro ...
, and
sustainable farming
Sustainable agriculture is farming in sustainable ways meeting society's present food and textile needs, without compromising the ability for current or future generations to meet their needs. It can be based on an understanding of ecosystem se ...
.
[ Many of these problems cross traditional disciplines and facilitating collaboration between plant scientists of diverse backgrounds and specialties is necessary.][
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.] A proposal was accepted (adopting the convention of using the word "Collaborative" as a noun) and iPlant was officially created on February 1, 2008.
Funding was estimated as $10 million per year over five years.
Richard Jorgensen
Richard A. Jorgensen (born 1951) is an American molecular genetics, molecular geneticist and an early pioneer in the study of post transcriptional gene silencing.
Biography
From 1965 through 1969 he attended Loyola Academy in Wilmette, Illinois, ...
led the team through the proposal stage and was the principal investigator
In many countries, the term principal investigator (PI) refers to the holder of an independent grant and the lead researcher for the grant project, usually in the sciences, such as a laboratory study or a clinical trial. The phrase is also often us ...
(PI) from 2008 to 2009. 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. 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.
The iPlant project supports what has been called e-Science, which is a use of information systems technology that is being adopted by the research community in efforts such as the National Center for Ecological Analysis and Synthesis (NCEAS), ELIXIR, and the Bamboo Technology Project that started in September 2010. 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."
The project works as a collaboration
Collaboration (from Latin ''com-'' "with" + ''laborare'' "to labor", "to work") is the process of two or more people, entities or organizations working together to complete a task or achieve a goal. Collaboration is similar to cooperation. Most ...
. It seeks input from the wider plant science community on what to build.
Based on that input, it has enabled easier use of large data sets, created a community-driven research environment to share existing data collections within a research area and between research areas and shares data with provenance
Provenance (from the French ''provenir'', 'to come from/forth') is the chronology of the ownership, custody or location of a historical object. The term was originally mostly used in relation to works of art but is now used in similar senses i ...
tracking.
One model studied for collaboration was Wikipedia
Wikipedia is a multilingual free online encyclopedia written and maintained by a community of volunteers, known as Wikipedians, through open collaboration and using a wiki-based editing system. Wikipedia is the largest and most-read refer ...
.
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.
Institutions
The primary institution for the iPlant project is the University of Arizona
The University of Arizona (Arizona, U of A, UArizona, or UA) is a public land-grant research university in Tucson, Arizona. Founded in 1885 by the 13th Arizona Territorial Legislature, it was the first university in the Arizona Territory.
T ...
, located within the BIO5 Institute in Tucson. Since its inception in 2008, personnel worked at other institutions including Cold Spring Harbor Laboratory, University of North Carolina, Wilmington
The University of North Carolina Wilmington (UNCW or UNC Wilmington) is a public research university in Wilmington, North Carolina. It is part of the University of North Carolina System and enrolls 17,499 undergraduate and graduate students eac ...
, and the University of Texas at Austin
The University of Texas at Austin (UT Austin, UT, or Texas) is a public research university in Austin, Texas. It was founded in 1883 and is the oldest institution in the University of Texas System. With 40,916 undergraduate students, 11,075 ...
in the Texas Advanced Computing Center.
Purdue University
Purdue University is a public land-grant research university in West Lafayette, Indiana, and the flagship campus of the Purdue University system. The university was founded in 1869 after Lafayette businessman John Purdue donated land and money ...
and Arizona State University
Arizona State University (Arizona State or ASU) is a public research university in the Phoenix metropolitan area. Founded in 1885 by the 13th Arizona Territorial Legislature, ASU is one of the largest public universities by enrollment in the ...
were part of the original project group.
Other collaborating institutions that received support from iPlant for their work on a Grand Challenge Grand Challenges are difficult but important problems set by various institutions or professions to encourage solutions or advocate for the application of government or philanthropic funds especially in the most highly developed economies Gould, M. ...
in phylogenetics
In biology, phylogenetics (; from Greek language, Greek wikt:φυλή, φυλή/wikt:φῦλον, φῦλον [] "tribe, clan, race", and wikt:γενετικός, γενετικός [] "origin, source, birth") is the study of the evolutionary his ...
starting in March 2009 included Yale University, University of Florida
The University of Florida (Florida or UF) is a public land-grant research university in Gainesville, Florida. It is a senior member of the State University System of Florida, traces its origins to 1853, and has operated continuously on its ...
, and the University of Pennsylvania
The University of Pennsylvania (also known as Penn or UPenn) is a private research university in Philadelphia. It is the fourth-oldest institution of higher education in the United States and is ranked among the highest-regarded universitie ...
.
A trait evolution group was led at the University of Tennessee
The University of Tennessee (officially The University of Tennessee, Knoxville; or UT Knoxville; UTK; or UT) is a public land-grant research university in Knoxville, Tennessee. Founded in 1794, two years before Tennessee became the 16th state, ...
.
A visualization workshop employing iPlant was run by Virginia Tech
Virginia Tech (formally the Virginia Polytechnic Institute and State University and informally VT, or VPI) is a Public university, public Land-grant college, land-grant research university with its main campus in Blacksburg, Virginia. It also ...
in 2011.
The NSF requires that funding subcontracts stay within the United States, but international collaboration started in 2009 with the Technical University Munich and University of Toronto
The University of Toronto (UToronto or U of T) is a public research university in Toronto, Ontario, Canada, located on the grounds that surround Queen's Park. It was founded by royal charter in 1827 as King's College, the first institution ...
in 2010.
East Main Evaluation & Consulting provides external oversight, advice, and assistance.
Services
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.
The Discovery Environment
The Discovery Environment integrates community-recommended software tools into a system that can handle terabyte
The byte is a units of information, unit of digital information that most commonly consists of eight bits. Historically, the byte was the number of bits used to encode a single character (computing), character of text in a computer and for this ...
s 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 a command-line interface
A command-line interpreter or command-line processor uses a command-line interface (CLI) to receive commands from a user in the form of lines of text. This provides a means of setting parameters for the environment, invoking executables and pro ...
.[
]
iPlant Foundational APIs
A set of application programming interface
An application programming interface (API) is a way for two or more computer programs to communicate with each other. It is a type of software interface, offering a service to other pieces of software. A document or standard that describes how t ...
s (APIs) for developers allow access to iPlant services, including authentication, data management, high performance supercomputing resources from custom, locally produced software.[
]
Atmosphere
Atmosphere is a cloud computing
Cloud computing is the on-demand availability of computer system resources, especially data storage ( cloud storage) and computing power, without direct active management by the user. Large clouds often have functions distributed over mul ...
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.[
It uses the ]Eucalyptus
''Eucalyptus'' () is a genus of over seven hundred species of flowering trees, shrubs or mallees in the myrtle family, Myrtaceae. Along with several other genera in the tribe Eucalypteae, including '' Corymbia'', they are commonly known as euca ...
virtualization platform.
iPlant Semantic Web
The iPlant Semantic Web effort uses an iPlant-created architecture, protocol, and platform called the Simple Semantic Web Architecture and Protocol (SSWAP
The iPlant Collaborative, renamed Cyverse in 2017, is a virtual organization created by a cooperative agreement funded by the US National Science Foundation (NSF) to create cyberinfrastructure for the plant sciences (botany). The NSF compared c ...
) for semantic web linking using a plant science focused ontology
In metaphysics, ontology is the philosophical study of being, as well as related concepts such as existence, becoming, and reality.
Ontology addresses questions like how entities are grouped into categories and which of these entities exis ...
.[ SSWAP is based on the notion of RESTful web services with an ontology based on Web Ontology Language (OWL).]
Taxonomic Name Resolution Service
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.[
]
My-Plant
My-Plant.org is a social networking
A social network is a social structure made up of a set of social actors (such as individuals or organizations), sets of dyadic ties, and other social interactions between actors. The social network perspective provides a set of methods for an ...
community for plant biologists, educators and others to come together to share information and research, collaborate, and track the latest developments in plant science.
The My-Plant network uses the terminology ''clade
A clade (), also known as a monophyletic group or natural group, is a group of organisms that are monophyletic – that is, composed of a common ancestor and all its lineal descendants – on a phylogenetic tree. Rather than the English term, ...
s'' to group users in a manner similar to phylogenetics
In biology, phylogenetics (; from Greek language, Greek wikt:φυλή, φυλή/wikt:φῦλον, φῦλον [] "tribe, clan, race", and wikt:γενετικός, γενετικός [] "origin, source, birth") is the study of the evolutionary his ...
of plants themselves.
It was implemented using Drupal
Drupal () is a free and open-source web content management system (CMS) written in PHP and distributed under the GNU General Public License. Drupal provides an open-source back-end framework for at least 14% of the top 10,000 websites worldwide ...
as its content management system
A content management system (CMS) is computer software used to manage the creation and modification of digital content (content management).''Managing Enterprise Content: A Unified Content Strategy''. Ann Rockley, Pamela Kostur, Steve Manning. New ...
.
DNA Subway
The DNA Subway website uses a graphical user interface
The GUI ( "UI" by itself is still usually pronounced . or ), graphical user interface, is a form of user interface that allows users to interact with electronic devices through graphical icons and audio indicator such as primary notation, inste ...
(GUI) to generate DNA sequence annotations, explore plant genome
In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding ge ...
s for members of gene and transposon families, and conduct phylogenetic
In biology, phylogenetics (; from Greek φυλή/ φῦλον [] "tribe, clan, race", and wikt:γενετικός, γενετικός [] "origin, source, birth") is the study of the evolutionary history and relationships among or within groups o ...
analyses. It makes high-level DNA analysis available to faculty and students by simplifying annotation and comparative genomics
Comparative genomics is a field of biological research in which the genomic features of different organisms are compared. The genomic features may include the DNA sequence, genes, gene order, regulatory sequences, and other genomic structural lan ...
workflows.[
It was developed for iPlant by the ]Dolan DNA Learning Center
The DNA Learning Center (DNALC) is a genetics learning center affiliated with the Cold Spring Harbor Laboratory, in Cold Spring Harbor, New York. It is the world's first science center devoted entirely to genetics education and offers online educ ...
.
References
External links
*
**
**
** {{Cite web , title= Fast Track to Gene Annotation and Genome Analysis - DNA Subway , work= Tool web site , publisher= iPlant Collaborative , url= http://www.dnasubway.org , access-date= September 21, 2011
E-Science
Organizations established in 2008