iPlant Collaborative

Biology is relying more and more on computers.{{Cite journal | last = Stein | first = Lincoln | title = Towards a cyberinfrastructure for the biological sciences: progress, visions and challenges | journal = Nature Reviews Genetics | volume = 9 | pages = 678–688 | date = September 2008 | doi = 10.1038/nrg2414 | issue=9 | pmid=18714290| s2cid = 339653 }} Plant biology is changing with the rise of new technologies.{{Cite journal | last = Dilworth | first = Machi F |author-link=Machi Dilworth| title = Perspective: Plant biology—A quiet pioneer | journal = Plant Biotechnology | volume = 26 | issue = 2 | pages = 183–187 | year = 2009 | doi = 10.5511/plantbiotechnology.26.183| doi-access = free | bibcode = 2009PBiot..26..183D }} With the advent of bioinformatics, computational biology, DNA sequencing, geographic information systems and others computers can greatly assist researchers who study plant life looking for solutions to challenges in medicine, biofuels, biodiversity, agriculture and problems like drought tolerance, plant breeding, and sustainable farming. Many of these problems cross traditional disciplines and facilitating collaboration between plant scientists of diverse backgrounds and specialties is necessary.{{Citation | last1 = Walsh | first1 = Lorraine | last2 = Khan | first2 = Peter E. | title = Collaborative working in higher education: the social academy | place = New York | publisher = Routledge | year = 2010 | page = 37 | isbn = 978-0-415-99167-4}}{{Cite web |title= Biological Sciences and Cyberinfrastructure for the 21st Century |author= Peter Arzberger |work= Coalition for Academic Scientific Computation presentation |date= March 24, 2010 |url= http://www.casc.org/meetings/10mar/PeterArzberger.pdf |access-date= September 29, 2011 |archive-date= September 23, 2015 |archive-url= https://web.archive.org/web/20150923094502/http://casc.org/meetings/10mar/PeterArzberger.pdf |url-status= dead }}

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.{{Cite web |title= Plant Science Cyberinfrastructure Collaborative (PSCIC) |work= Program Solicitation 06-594 |publisher= National Science Foundation |date=November 30, 2006 |url= https://www.nsf.gov/funding/pgm_summ.jsp?pims_id=13704 |access-date= September 21, 2011 }} 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.{{cite news |title= National Science Foundation Awards $50 Million for Collaborative Plant Biology Project to Tackle Greater Science Questions |work= News release |date= January 30, 2008 |publisher= National Science Foundation |url= https://www.nsf.gov/news/news_summ.jsp?cntn_id=111048 |access-date= September 21, 2011 }}

Richard Jorgensen led the team through the proposal stage and was the principal investigator (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.{{Cite web |title= Stephen Goff, Ph.D. |work= Staff biography page from iPlant web site |url= http://www.iplantcollaborative.org/connect/staff-collaborators/stephen-goff-phd |access-date= September 21, 2011 |archive-url= https://web.archive.org/web/20111128135054/http://www.iplantcollaborative.org/connect/staff-collaborators/stephen-goff-phd |archive-date= November 28, 2011 |url-status= dead }}{{Cite web |title=Dan Stanzione, Ph.D. |work= Staff biography page from Texas Advanced Computing Center web site |url= http://www.tacc.utexas.edu/staff/dan-stanzione |access-date= September 21, 2011 }} 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.{{Cite web |title=Leadership |work=Leadership page from iPlant website |url=http://www.iplantcollaborative.org/about-iplant/the-organization/leadership |access-date=May 27, 2014 |archive-date=May 28, 2014 |archive-url=https://web.archive.org/web/20140528050257/http://www.iplantcollaborative.org/about-iplant/the-organization/leadership |url-status=dead }}

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,{{Cite web |title= ELIXIR: Data for Life |work= Official web site |publisher=EMBL-European Bioinformatics Institute |location= Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom |url= http://www.elixir-europe.org/ |access-date= September 28, 2011 }} and the Bamboo Technology Project that started in September 2010.{{Cite web |title= About Bamboo |work= Project Bamboo website |url= http://www.projectbamboo.org/about/ |access-date= September 27, 2011 |archive-url= https://web.archive.org/web/20111009074754/http://www.projectbamboo.org/about/ |archive-date= October 9, 2011 |url-status= usurped }}{{Cite journal | last1 = Brown | first1 = Susan | last2 = Thatcher | first2 = Sherry |title= Factors Influencing Adoption And Non-Adoption Of Cyberinfrastructure By The Research Community |url = http://aisel.aisnet.org/pacis2011/31 |journal= Pacific Asia Conference on Information Systems Proceedings | year = 2011 |isbn= 978-1-86435-644-1 }} 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."{{Cite journal | last1= Goff | first1= Stephen A. | title = The iPlant Collaborative: Cyberinfrastructure for Plant Biology | journal = Frontiers in Plant Science | volume = 2 | pages= 34 | year = 2011 | issn = 1664-462X | doi = 10.3389/fpls.2011.00034|display-authors=etal | pmid=22645531 | pmc=3355756| doi-access= free | bibcode= 2011FrPS....2...34G }}{{Cite web |title= The iPlant Collaborative: A Cyberinfrastructure-Centered Community of Plant and Computing Scientists |author= Steve Goff |work= New PhytologistSymposium presentation |date= September 18, 2008 |url= http://www.newphytologist.org/physiological/goff.pdf |access-date= September 29, 2011 |archive-url= https://web.archive.org/web/20120422175116/http://www.newphytologist.org/physiological/goff.pdf |archive-date= April 22, 2012 |url-status= dead }}

The project works as a collaboration. It seeks input from the wider plant science community on what to build.{{Cite journal |title= Cyberinfrastructure: Feed me data |quote= The iPlant programme was designed to give plant scientists a new information infrastructure. But first they had to decide what they wanted... |author= Heidi Ledford |journal= Nature |volume= 459 |issue= 7250 |pages= 1047–1049 |date= June 24, 2009 |doi= 10.1038/4591047a |pmid=19553968|doi-access= free }}

Based on that input, it has enabled easier use of large data sets,{{Cite book |doi= 10.1109/CLUSTERWKSP.2010.5613093 | isbn= 978-1-4244-8395-2 | chapter= Comprehensive data infrastructure for plant bioinformatics | title= 2010 IEEE International Conference on Cluster Computing Workshops and Posters (CLUSTER WORKSHOPS) | pages= 1–5 | year= 2010 | last1= Jordan | first1= Chris | last2= Stanzione | first2= Dan | last3= Ware | first3= Doreen | last4= Lu | first4= Jerry | last5= Noutsos | first5= Christos | s2cid= 2278398 | chapter-url= http://repository.cshl.edu/15442/1/Comprehensive_Data_Infrastructure_for_Plant_Bioinformatics.pdf }} created a community-driven research environment to share existing data collections within a research area and between research areas{{Cite journal| first1= Reagan W. | last1= Moore | title = Policy-Based Distributed Data Management Systems | publisher = Georgia Institute of Technology | date = May 19, 2009 | journal= 4th International Conference on Open Repositories | url = http://smartech.gatech.edu/handle/1853/28455 | access-date = September 28, 2011 |display-authors=etal}} and shares data with provenance tracking.{{Cite book| last1= Ram | first1= Sudha |author2= Jun Liu |chapter = Provenance Management in BioSciences | year = 2010 | title = Advances in Conceptual Modeling – Applications and Challenges | volume= 6413 |series = Advances in Conceptual Modeling‚ Applications and Challenges | pages = 54–64 | publisher = Springer Berlin / Heidelberg |doi = 10.1007/978-3-642-16385-2_8| isbn= 978-3-642-16384-5 }}{{Cite book |doi = 10.1109/HICSS.2010.263|chapter = Managing Knowledge in a Changing Scientific Landscape: The Impact of Cyberinfrastructure|title = 2010 43rd Hawaii International Conference on System Sciences|pages = 1–10|year = 2010|last1 = Brown|first1 = Susan A.|last2 = Thatcher|first2 = Sherry|last3 = Dang|first3 = Yan|isbn = 978-1-4244-5509-6|s2cid = 1132763}}

One model studied for collaboration was Wikipedia.{{Cite web |title= Who does what on Wikipedia? |author= Thomas Veneklasen |work= e! Science News |date=March 11, 2010 |url= http://esciencenews.com/articles/2010/03/11/who.does.what.wikipedia |access-date= September 29, 2011 }}{{Cite journal |title= Who Does What: Collaboration Patterns in the Wikipedia and Their Impact on Data Quality |author1= Jun Liu

|author2= Sudha Ram |date= December 2009 |journal= 19th Workshop on Information Technologies and Systems |pages= 175–180 |ssrn= 1565682 }}

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.{{Cite web |title= Award Search—Awardee Information |work= NSF website search |publisher= National Science Foundation |url= https://www.nsf.gov/awardsearch/piSearch.do?SearchType=piSearch&page=1&QueryText=iplant |access-date= September 28, 2011 }} See abstracts for awards #0849861, #0923975, #0940841, #0953184, #1027542, #1031416, #1032105, #1126481, #1126998.

The primary institution for the iPlant project is the University of Arizona, located within the BIO5 Institute in Tucson.{{Cite news |title= UA-Led Research Team Awarded $50 Million to Solve Plant Biology's Grand Challenges |work= News release |date= January 30, 2008 |publisher= University of Arizona |url= http://bio5.arizona.edu/node/1142 |access-date= September 23, 2011 |archive-date= April 2, 2012 |archive-url= https://web.archive.org/web/20120402212136/http://bio5.arizona.edu/node/1142 |url-status= dead }} Since its inception in 2008, personnel worked at other institutions including Cold Spring Harbor Laboratory, University of North Carolina, Wilmington, and the University of Texas at Austin in the Texas Advanced Computing Center.{{Cite news |title= iPlant Moving Forward on Grand Challenge Collaborations |date= April 9, 2009 |work= iPlant Leaflet |volume= 09-2 |url= http://www.iplantcollaborative.org/learn/news/leaflet/apr-09-2009 |access-date= September 25, 2011 |archive-date= April 2, 2012 |archive-url= https://web.archive.org/web/20120402121640/http://www.iplantcollaborative.org/learn/news/leaflet/apr-09-2009 |url-status= dead }}

Purdue University and Arizona State University were part of the original project group.

Other collaborating institutions that received support from iPlant for their work on a Grand Challenge in phylogenetics starting in March 2009 included Yale University, University of Florida, and the University of Pennsylvania.

A trait evolution group was led at the University of Tennessee.{{Cite web |title= Trait Evolution |work= iPlant web site |url= http://www.iplantcollaborative.org/challenge/iplant-tree-life/trait-evolution |access-date= September 25, 2011 |archive-date= November 28, 2011 |archive-url= https://web.archive.org/web/20111128131435/http://www.iplantcollaborative.org/challenge/iplant-tree-life/trait-evolution |url-status= dead }}

A visualization workshop employing iPlant was run by Virginia Tech in 2011.{{Cite news |title= Integration and Visualization Workshop |date= June 8, 2011 |work= iPlant Leaflet |volume= 11-2 |url= http://www.iplantcollaborative.org/learn/news/leaflet/jun-08-2011 |access-date= September 25, 2011 |archive-date= April 2, 2012 |archive-url= https://web.archive.org/web/20120402121656/http://www.iplantcollaborative.org/learn/news/leaflet/jun-08-2011 |url-status= dead }}

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 in 2010.{{Cite news |title= Computing for Life: Scientists depend on advanced computing to better understand evolution, drug discovery and genetics |date= May 31, 2010 |publisher= University of Texas at Austin |url= http://www.utexas.edu/features/2010/05/31/computing_life/ |access-date= September 25, 2011 |archive-url= https://web.archive.org/web/20111002012404/http://www.utexas.edu/features/2010/05/31/computing_life/ |archive-date= October 2, 2011 |url-status= dead }}

East Main Evaluation & Consulting provides external oversight, advice, and assistance.{{Cite web |title= Current Projects |work= EMEC website |url= http://www.emeconline.com/current-projects/universities-and-colleges/ |access-date= February 21, 2013 |archive-date= January 8, 2016 |archive-url= https://web.archive.org/web/20160108090744/http://www.emeconline.com/current-projects/universities-and-colleges/ |url-status= dead }}

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 integrates community-recommended software tools into a system that can handle terabytes 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.{{Cite web |title= The iPlant Discovery Environment |work= Discovery Environment manual 0.4 |author= Matthew Helmke |date= August 19, 2011 |url= http://pods.iplantcollaborative.org/wiki/display/DEman0p4/About+the+Discovery+Environment |access-date= September 28, 2011 }}{{Dead link|date=December 2024 |bot=InternetArchiveBot |fix-attempted=yes }}

A set of application programming interfaces (APIs) for developers allow access to iPlant services, including authentication, data management, high performance supercomputing resources from custom, locally produced software.{{Cite journal |first= Rion |last= Dooley |title= An API To Feed the World |url= http://www.teragrid.org/c/document_library/get_file?uuid=6004ae82-248f-4c53-8427-5570815eda25&groupId=334534 |archive-url= https://archive.today/20120919035959/http://www.teragrid.org/c/document_library/get_file?uuid=6004ae82-248f-4c53-8427-5570815eda25&groupId=334534 |url-status= dead |archive-date= September 19, 2012 |format= PDF |journal= TeraGrid 2011: Extreme Digital Discovery |date= July 19, 2011 |location= Salt Lake City, Utah |access-date= September 28, 2011 }}

Atmosphere is a cloud 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.

It uses the Eucalyptus virtualization platform.{{Cite journal |first= Kim |last= Seung-jin |title= Facilitating access to customized computational infrastructure for plant sciences: Atmosphere cloudfront |url= http://salsahpc.indiana.edu/CloudCom2010/Edemo/Facilitating%20access%20to%20customized%20computational%20infrastructure%20for%20plant%20sciences%20Atmosphere%20cloudfront.pdf |journal= 2nd IEEE International Conference on Cloud Computing Technology and Science |date= November 1, 2010 |location= Indianapolis, Indiana |access-date= September 28, 2011 |display-authors= etal |archive-date= April 2, 2012 |archive-url= https://web.archive.org/web/20120402161155/http://salsahpc.indiana.edu/CloudCom2010/Edemo/Facilitating%20access%20to%20customized%20computational%20infrastructure%20for%20plant%20sciences%20Atmosphere%20cloudfront.pdf |url-status= dead }}{{Cite web |title= Enabling Plant Sciences Research with the iPlant Discovery Environment and Condor |author1=Juan Antonio Raygoza Garay |author2=Sonya Lowry |author3=John Wregglesworth |date= May 3, 2011 |work= Condor Week presentation |publisher= University of Wisconsin Computer Science Department |url= http://www.cs.wisc.edu/condor/CondorWeek2011/presentations/garay-iplant.pdf |access-date= September 28, 2011 }}

The iPlant Semantic Web effort uses an iPlant-created architecture, protocol, and platform called the Simple Semantic Web Architecture and Protocol (SSWAP) for semantic web linking using a plant science focused ontology.{{Cite journal | last1= Gessler | first1= D. D. | title = SSWAP: A Simple Semantic Web Architecture and Protocol for semantic web services | journal = BMC Bioinformatics | volume = 10 | issue = 309 | date = September 23, 2009 | pmid=19775460 | doi=10.1186/1471-2105-10-309 | pmc=2761904 | pages=309|display-authors=etal | doi-access= free }}{{Cite journal | last1= Nelson | first1= R. T. | title = Applications and methods utilizing the Simple Semantic Web Architecture and Protocol (SSWAP) for bioinformatics resource discovery and disparate data and service integration | journal = BioData Mining |volume = 3 | issue = 1 | date = June 4, 2010 |pmid= 20525377 | doi=10.1186/1756-0381-3-3 | pmc=2894815 | pages=3|display-authors=etal | doi-access= free }} SSWAP is based on the notion of RESTful web services with an ontology based on Web Ontology Language (OWL).{{cite book|last1=Pautasso|first1=Cesare|last2=Wilde|first2=Erik|last3=Alarcon|first3=Rosa|title=REST: Advanced Research Topics and Practical Applications|publisher=Springer Science & Business Media|isbn=9781461492993|pages=76–77|url=https://books.google.com/books?id=jhS4BAAAQBAJ&q=%22SSWAP%22&pg=PA76|access-date=27 June 2016|language=en|date=2013-12-04}}{{cite book|last1=Barros|first1=Alistair|last2=Oberle|first2=Daniel|title=Handbook of Service Description: USDL and Its Methods|publisher=Springer Science & Business Media|isbn=9781461418641|page=169|url=https://books.google.com/books?id=BRBLAAAAQBAJ&q=sswap&pg=PA169|access-date=27 June 2016|language=en|date=2012-03-02}}

File:DNA Subway login screen.png

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.{{Cite journal |first1= Martha L. |last1= Narro |title= The TNRS: a taxonomic name resolution service for plants |url= http://abstracts.aspb.org/pb2011/public/P21/P21011.html |date= August 2011 |journal= Plant Biology |location= Minneapolis |display-authors= etal |access-date= September 14, 2011 |archive-url= https://web.archive.org/web/20110516074847/http://abstracts.aspb.org/pb2011/public/P21/P21011.html |archive-date= May 16, 2011 |url-status= dead }}{{Cite journal |title= Species spellchecker fixes plant glitches: Online tool should weed out misspellings and duplications |author= John Whitfield |journal= Nature |volume= 474 |issue= 7351 |page= 263 |date= June 13, 2011 |doi= 10.1038/474263a |pmid= 21677719 |doi-access= free }}

My-Plant.org is a social 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.{{Cite book |doi = 10.1109/GCE.2010.5676118 | isbn= 978-1-4244-9751-5 | chapter= My-Plant.org: A phylogenetically structured social network | title= 2010 Gateway Computing Environments Workshop (GCE) | pages= 1–8 | year= 2010 | last1= Hanlon | first1= Matthew R. | last2= Mock | first2= Stephen | last3= Nuthulapati | first3= Praveen | last4= Gonzales | first4= Michael B. | last5= Soltis | first5= Pamela | last6= Soltis | first6= Douglas | last7= Majure | first7= Lucas C. | last8= Payton | first8= Adam | last9= Mishler | first9= Brent | last10= Tremblay | first10= Susan | last11= Madsen | first11= Thomas | last12= Olmstead | first12= Richard | last13= McCourt | first13= Richard | last14= Wojciechowski | first14= Martin | last15= Merchant | first15= Nirav | s2cid= 12621375 }}

The My-Plant network uses the terminology clades to group users in a manner similar to phylogenetics of plants themselves.

It was implemented using Drupal as its content management system.

The DNA Subway website uses a graphical user interface (GUI) to generate DNA sequence annotations, explore plant genomes for members of gene and transposon families, and conduct phylogenetic analyses. It makes high-level DNA analysis available to faculty and students by simplifying annotation and comparative genomics workflows.{{Cite journal | first1= Mary | last1= Schaeffer |title= MaizeGDB: curation and outreach go hand-in-hand |publisher=Oxford University Press |journal= Database: The Journal of Biological Databases and Curation | year = 2011 | doi = 10.1093/database/bar022 |pmc=3104940 | pmid=21624896 | volume=2011 |pages=bar022 |display-authors=etal}}

It was developed for iPlant by the Dolan DNA Learning Center.{{Cite web |title= DNA Subway: Fast Track to Gene Annotation and Genome Analysis |work= Dolan DNA Learning Center website |url= http://www.dnalc.org/websites/dnasubway.html |access-date=September 29, 2011 }}{{Cite web |title= DNA Subway Places Students On Fast Track To Plant Genome Analysis and DNA BarCoding |author= Uwe Hilgert |work= Botany 2011: Healing the Planet (workshop) |date= July 9, 2011 |url= http://www.2011.botanyconference.org/Info/Workshops1.php |access-date=September 29, 2011}}

{{Reflist|2}}

• {{Cite web |title= iPlant Collaborative, renamed to CyVerse |work= Official website |url= http://www.cyverse.org/ |access-date=May 22, 2017 }}
• {{Cite web |title= Taxonomic Name Resolution Service |work= Official website |url= http://tnrs.iplantcollaborative.org |access-date=May 22, 2017 }}
• {{Cite web |title= My-Plant.org |work= Phylogenetically Based Social Network for the Plant Sciences |publisher= iPlant Collaborative |url= http://my-plant.org |access-date= September 28, 2011 |archive-url= https://web.archive.org/web/20111013213029/https://my-plant.org/ |archive-date= October 13, 2011 |url-status= dead }}
• {{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}}

Category:E-Science

Category:Organizations established in 2008