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Reiser L, Berardini TZ, Li D, Muller R, Strait EM, Li Q, Mezheritsky Y, Vetushko A, Huala E. Sustainable funding for biocuration: The Arabidopsis Information Resource (TAIR) as a case study of a subscription-based funding model. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw018. [PMID: 26989150 PMCID: PMC4795935 DOI: 10.1093/database/baw018] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 02/03/2016] [Indexed: 11/13/2022]
Abstract
Databases and data repositories provide essential functions for the research community by integrating, curating, archiving and otherwise packaging data to facilitate discovery and reuse. Despite their importance, funding for maintenance of these resources is increasingly hard to obtain. Fueled by a desire to find long term, sustainable solutions to database funding, staff from the Arabidopsis Information Resource (TAIR), founded the nonprofit organization, Phoenix Bioinformatics, using TAIR as a test case for user-based funding. Subscription-based funding has been proposed as an alternative to grant funding but its application has been very limited within the nonprofit sector. Our testing of this model indicates that it is a viable option, at least for some databases, and that it is possible to strike a balance that maximizes access while still incentivizing subscriptions. One year after transitioning to subscription support, TAIR is self-sustaining and Phoenix is poised to expand and support additional resources that wish to incorporate user-based funding strategies. Database URL: www.arabidopsis.org.
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Affiliation(s)
- Leonore Reiser
- Phoenix Bioinformatics, The Arabidopsis Information Resource, 643 Bair Island Rd. Suite 403, Redwood City, CA 94063, USA
| | - Tanya Z Berardini
- Phoenix Bioinformatics, The Arabidopsis Information Resource, 643 Bair Island Rd. Suite 403, Redwood City, CA 94063, USA
| | - Donghui Li
- Phoenix Bioinformatics, The Arabidopsis Information Resource, 643 Bair Island Rd. Suite 403, Redwood City, CA 94063, USA
| | - Robert Muller
- Phoenix Bioinformatics, The Arabidopsis Information Resource, 643 Bair Island Rd. Suite 403, Redwood City, CA 94063, USA
| | - Emily M Strait
- Phoenix Bioinformatics, The Arabidopsis Information Resource, 643 Bair Island Rd. Suite 403, Redwood City, CA 94063, USA
| | - Qian Li
- Phoenix Bioinformatics, The Arabidopsis Information Resource, 643 Bair Island Rd. Suite 403, Redwood City, CA 94063, USA
| | - Yarik Mezheritsky
- Phoenix Bioinformatics, The Arabidopsis Information Resource, 643 Bair Island Rd. Suite 403, Redwood City, CA 94063, USA
| | - Andrey Vetushko
- Phoenix Bioinformatics, The Arabidopsis Information Resource, 643 Bair Island Rd. Suite 403, Redwood City, CA 94063, USA
| | - Eva Huala
- Phoenix Bioinformatics, The Arabidopsis Information Resource, 643 Bair Island Rd. Suite 403, Redwood City, CA 94063, USA
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11
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Goff SA, Vaughn M, McKay S, Lyons E, Stapleton AE, Gessler D, Matasci N, Wang L, Hanlon M, Lenards A, Muir A, Merchant N, Lowry S, Mock S, Helmke M, Kubach A, Narro M, Hopkins N, Micklos D, Hilgert U, Gonzales M, Jordan C, Skidmore E, Dooley R, Cazes J, McLay R, Lu Z, Pasternak S, Koesterke L, Piel WH, Grene R, Noutsos C, Gendler K, Feng X, Tang C, Lent M, Kim SJ, Kvilekval K, Manjunath BS, Tannen V, Stamatakis A, Sanderson M, Welch SM, Cranston KA, Soltis P, Soltis D, O'Meara B, Ane C, Brutnell T, Kleibenstein DJ, White JW, Leebens-Mack J, Donoghue MJ, Spalding EP, Vision TJ, Myers CR, Lowenthal D, Enquist BJ, Boyle B, Akoglu A, Andrews G, Ram S, Ware D, Stein L, Stanzione D. The iPlant Collaborative: Cyberinfrastructure for Plant Biology. FRONTIERS IN PLANT SCIENCE 2011; 2:34. [PMID: 22645531 PMCID: PMC3355756 DOI: 10.3389/fpls.2011.00034] [Citation(s) in RCA: 255] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2011] [Accepted: 07/11/2011] [Indexed: 05/17/2023]
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.
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Affiliation(s)
- Stephen A. Goff
- BIO5 Institute, University of ArizonaTucson, AZ, USA
- *Correspondence: Stephen A. Goff, iPlant Collaborative, BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA. e-mail:
| | - Matthew Vaughn
- Texas Advanced Computer Center, University of TexasAustin, TX, USA
| | - Sheldon McKay
- BIO5 Institute, University of ArizonaTucson, AZ, USA
| | - Eric Lyons
- BIO5 Institute, University of ArizonaTucson, AZ, USA
| | - Ann E. Stapleton
- Department of Biology, University of North CarolinaWilmington, NC, USA
- Department of Marine Sciences, University of North CarolinaWilmington, NC, USA
| | | | - Naim Matasci
- BIO5 Institute, University of ArizonaTucson, AZ, USA
| | - Liya Wang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Matthew Hanlon
- Texas Advanced Computer Center, University of TexasAustin, TX, USA
| | | | - Andy Muir
- BIO5 Institute, University of ArizonaTucson, AZ, USA
| | | | - Sonya Lowry
- BIO5 Institute, University of ArizonaTucson, AZ, USA
| | - Stephen Mock
- Texas Advanced Computer Center, University of TexasAustin, TX, USA
| | | | - Adam Kubach
- Texas Advanced Computer Center, University of TexasAustin, TX, USA
| | - Martha Narro
- BIO5 Institute, University of ArizonaTucson, AZ, USA
| | | | - David Micklos
- DNA Learning Center, Cold Spring Harbor Laboratory, Cold Spring HarborNY, USA
| | - Uwe Hilgert
- DNA Learning Center, Cold Spring Harbor Laboratory, Cold Spring HarborNY, USA
| | - Michael Gonzales
- Texas Advanced Computer Center, University of TexasAustin, TX, USA
| | - Chris Jordan
- Texas Advanced Computer Center, University of TexasAustin, TX, USA
| | | | - Rion Dooley
- Texas Advanced Computer Center, University of TexasAustin, TX, USA
| | - John Cazes
- Texas Advanced Computer Center, University of TexasAustin, TX, USA
| | - Robert McLay
- Texas Advanced Computer Center, University of TexasAustin, TX, USA
| | - Zhenyuan Lu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | - Lars Koesterke
- Texas Advanced Computer Center, University of TexasAustin, TX, USA
| | | | - Ruth Grene
- Department of Plant Pathology, Physiology and Weed Science, Virginia Tech UniversityBlacksburg, VA, USA
| | | | - Karla Gendler
- Texas Advanced Computer Center, University of TexasAustin, TX, USA
| | - Xin Feng
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Ontario Center for Cancer ResearchToronto, ON, Canada
| | - Chunlao Tang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Monica Lent
- BIO5 Institute, University of ArizonaTucson, AZ, USA
| | - Seung-Jin Kim
- BIO5 Institute, University of ArizonaTucson, AZ, USA
| | - Kristian Kvilekval
- Center for Bio-image Informatics, University of CaliforniaSanta Barbara, CA, USA
| | - B. S. Manjunath
- Center for Bio-image Informatics, University of CaliforniaSanta Barbara, CA, USA
- Electrical and Computer Engineering, University of CaliforniaSanta Barbara, CA, USA
| | - Val Tannen
- Department of Computer and Information Science, University of PennsylvaniaPhiladelphia, PA, USA
| | - Alexandros Stamatakis
- Scientific Computing Group, Heidelberg Institute for Theoretical StudiesHeidelberg, Germany
| | - Michael Sanderson
- Department of Ecology and Evolutionary Biology, University of ArizonaTucson, AZ, USA
| | - Stephen M. Welch
- Department of Agronomy, Kansas State UniversityManhattan, KS, USA
| | | | - Pamela Soltis
- Florida Museum of Natural History, University of FloridaGainesville, FL, USA
| | - Doug Soltis
- Department of Biology, University of FloridaGainesville, FL, USA
| | - Brian O'Meara
- Department of Ecology and Evolutionary Biology, University of TennesseeKnoxville, TN, USA
| | - Cecile Ane
- Department of Statistics, University of WisconsinMadison, WI, USA
- Department of Botany, University of WisconsinMadison, WI, USA
| | - Tom Brutnell
- Boyce Thompson Institute for Plant Research, Cornell UniversityIthaca, NY, USA
| | | | - Jeffery W. White
- Arid-Land Agricultural Research Center, United States Department of Agriculture-Agricultural Research ServiceMaricopa, AZ, USA
| | | | - Michael J. Donoghue
- Department of Ecology and Evolutionary Biology, Yale UniversityNew Haven, CT, USA
| | | | - Todd J. Vision
- Department of Biology, University of North CarolinaChapel Hill, NC, USA
| | | | - David Lowenthal
- Department of Computer Science, University of ArizonaTucson, AZ, USA
| | - Brian J. Enquist
- Department of Ecology and Evolutionary Biology, University of ArizonaTucson, AZ, USA
| | - Brad Boyle
- Department of Ecology and Evolutionary Biology, University of ArizonaTucson, AZ, USA
| | - Ali Akoglu
- Department of Electrical and Computer Engineering, University of ArizonaTucson, AZ, USA
| | - Greg Andrews
- Department of Computer Science, University of ArizonaTucson, AZ, USA
| | - Sudha Ram
- Eller School of Business, University of ArizonaTucson, AZ, USA
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Lincoln Stein
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Ontario Center for Cancer ResearchToronto, ON, Canada
| | - Dan Stanzione
- Texas Advanced Computer Center, University of TexasAustin, TX, USA
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