Data access for the 1,000 Plants (1KP) project

GigaScience

Volumn 3, Issue 1, 2014, Pages

  Matasci, Naim ^a,b   Hung, Ling Hong ^c   Yan, Zhixiang ^d   Carpenter, Eric J ^e   Wickett, Norman J ^f,g   Mirarab, Siavash ^h   Nguyen, Nam ^h   Warnow, Tandy ^h   Ayyampalayam, Saravanaraj ⁱ   Barker, Michael ^b   Burleigh, J G ^j   Gitzendanner, Matthew A ^j   Wafula, Eric ^k   Der, Joshua P ^k   dePamphilis, Claude W ^k   Roure, Béatrice ^l   Philippe, Hervé ^l,m   Ruhfel, Brad R ^j,n   Miles, Nicholas W ^o   Graham, Sean W ^p   Mathews, Sarah ^q   Surek, Barbara ^r   Melkonian, Michael ^r   Soltis, Douglas E ^j,o   Soltis, Pamela S ^j,o   Rothfels, Carl ^p,s   Pokorny, Lisa ^s,t   Shaw, Jonathan A ^s   DeGironimo, Lisa ^u   Stevenson, Dennis W ^u   Villarreal, Juan C ^v   Chen, Tao ^w   Kutchan, Toni M ^x   Rolf, Megan ^x   Baucom, Regina S ^y   Deyholos, Michael K ^e   Samudrala, Ram ^c   Tian, Zhijian ^d   Wu, Xiaolei ^d   Sun, Xiao ^d   Zhang, Yong ^d   Wang, Jun ^d   Leebens Mack, Jim ⁱ   Wong, Gane Ka Shu ^d,e   more..

^a Thomas W Keating Bioresearch Building   (United States)

^b University of Arizona   (United States)

^c UNIVERSITY OF WASHINGTON   (United States)

^d BGI SHENZHEN   (China)

^e UNIVERSITY OF ALBERTA   (Canada)

^f CHICAGO BOTANIC GARDEN   (United States)

^g NORTHWESTERN UNIVERSITY   (United States)

^h University of Texas at Austin   (United States)

ⁱ UNIVERSITY OF GEORGIA   (United States)

^j UNIVERSITY OF FLORIDA   (United States)

^k PENNSYLVANIA STATE UNIVERSITY   (United States)

^l Universite de Montreal   (Canada)

^m Station d'Ecologie Expérimentale du Centre National de la Recherche Scientifique   (France)

ⁿ EASTERN KENTUCKY UNIVERSITY   (United States)

^o UNIVERSITY OF FLORIDA   (United States)

^p UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^q HARVARD UNIVERSITY   (United States)

^r UNIVERSITY OF COLOGNE   (Germany)

^s DUKE UNIVERSITY   (United States)

^t CSIC   (Spain)

^u NEW YORK BOTANICAL GARDEN   (United States)

^v UNIVERSITY OF MUNICH   (Germany)

^w INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

^x DONALD DANFORTH PLANT SCIENCE CENTER   (United States)

^y UNIVERSITY OF MICHIGAN   (United States)

more..

Author keywords

Biodiversity; Interactions; Pathways; Phylogenomics; Transcriptomes; Viridiplantae

Indexed keywords

TRANSCRIPTOME;

ACCESS TO INFORMATION; CLADISTICS; COMPUTER ANALYSIS; COMPUTER INTERFACE; DATA ANALYSIS; GENETIC DATABASE; INFORMATION RETRIEVAL; INFORMATION SCIENCE; INFORMATION STORAGE; INTERNET; NONHUMAN; ONLINE ANALYSIS; ONLINE SYSTEM; PHYLOGENOMICS; PLANT; PLANT GENOME; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; REVIEW; SEARCH ENGINE; VIRIDIPLANTAE; WEB BROWSER;

EID: 84909590553     PISSN: None     EISSN: 2047217X     Source Type: Journal    
DOI: 10.1186/2047-217X-3-17     Document Type: Review

References (22)

1. 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, et al. The iPlant Collaborative: Cyberinfrastructure for Plant Biology. Front Plant Sci 2011, 2:34. 3355756, 22645531.
2. 1KP BLAST Search Portal [http://www.bioinfodata.org/app/Blast4OneKP/home].
3. Johnson MT, Carpenter EJ, Tian Z, Bruskiewich R, Burris JN, Carrigan CT, Chase MW, Clarke ND, Covshoff S, dePamphilis CW, Edger PP, Goh F, Graham S, Greiner S, Hibberd JM, Jordon-Thaden I, Kutchan TM, Leebens-Mack J, Melkonian M, Miles N, Myburg H, Patterson J, Pires JC, Ralph P, Rolf M, Sage RF, Soltis D, Soltis P, Stevenson D, Stewart CN, et al. Evaluating methods for isolating total RNA and predicting the success of sequencing phylogenetically diverse plant transcriptomes. PLoS One 2012, 7:e50226. 10.1371/journal.pone.0050226, 3504007, 23185583.
4. Xie Y, Wu G, Tang J, Luo R, Patterson J, Liu S, Huang W, He G, Gu S, Li S, Zhou X, Lam TW, Li Y, Xu X, Wong GK, Wang J. SOAPdenovo-Trans: De novo transcriptome assembly with short RNA-Seq reads. Bioinformatics 2014, 30:1660-1666. 10.1093/bioinformatics/btu077, 24532719.
5. Wickett NJ, Mirarab S, Nguyen N, Warnow T, Carpenter E, Matasci N, Ayyampalayam S, Barker M, Burleigh JG, Gitzendanner MA, Ruhfel B, Wafula E, Der JP, Graham SW, Mathews S, Melkonian M, Soltis DE, Soltis PS, Miles NW, Rothfels C, Pokorny L, Shaw AJ, deGironimo L, Stevenson DW, Surek B, Villarreal JC, Roure B, Philippe H, dePamphilis CW, Chen T, et al. A phylotranscriptomics analysis of the origin and early diversification of land plants. Proc Natl Acad Sci U S A IN PRESS.
6. iPlant Data Store for 1KP Pilot [http://mirrors.iplantcollaborative.org/browse/iplant/home/shared/onekp_pilot].
7. iPlant User Registration [http://user.iplantcollaborative.org].
8. iPlant Learning Center [http://www.iplantcollaborative.org/learning-center/all-tutorials].
9. iPlant Discovery Environment [http://de.iplantcollaborative.org].
10. Using the iDrop Desktop [https://pods.iplantcollaborative.org/wiki/display/DS/Using+iDrop+Desktop].
11. Matasci N, McKay SJ. Phylogenetic analysis with the iPlant discovery environment. Curr Protoc Bioinformatics 2013, 6:Unit 6.13.
12. Newick Trees Format [http://evolution.genetics.washington.edu/phylip/newicktree.html].
13. iRODS Data Management Software [http://irods.org].
14. Using iCommands (Unix) [https://pods.iplantcollaborative.org/wiki/display/DS/Using+iCommands].
15. Minie M, Chopra G, Sethi G, Horst J, White G, Roy A, Hatti K, Samudrala R. CANDO and the infinite drug discovery frontier. Drug Discov Today 2014, 19:1353-1363. 10.1016/j.drudis.2014.06.018, 24980786.
16. BioGRID Interactions [http://thebiogrid.org].
17. Kyoto Encylopedia of Genes and Genomes (KEGG) [http://www.genome.jp/kegg].
18. 1KP Protein-Protein Interactions Mapped to Metabolic Pathways [http://protinfo.org/1kp].
19. 1KP Capstone Objective [https://pods.iplantcollaborative.org/wiki/display/iptol/OneKP+Capstone+Wiki].
20. 1KP Papers in Progress [https://pods.iplantcollaborative.org/wiki/display/iptol/OneKP+companion+papers].
21. Sayou C, Monniaux M, Nanao MH, Moyroud E, Brockington SF, Thévenon E, Chahtane H, Warthmann N, Melkonian M, Zhang Y, Wong GK, Weigel D, Parcy F, Dumas R. A promiscuous intermediate underlies the evolution of LEAFY DNA binding specificity. Science 2014, 343:645-648. 10.1126/science.1248229, 24436181.
22. Klapoetke NC, Murata Y, Kim SS, Pulver SR, Birdsey-Benson A, Cho YK, Morimoto TK, Chuong AS, Carpenter EJ, Tian Z, Wang J, Xie Y, Yan Z, Zhang Y, Chow BY, Surek B, Melkonian M, Jayaraman V, Constantine-Paton M, Wong GK, Boyden ES. Independent optical excitation of distinct neural populations. Nat Methods 2014, 11:338-346. 10.1038/nmeth.2836, 3943671, 24509633.