CyVerse Austria-A Local, Collaborative Cyberinfrastructure

被引:4
作者
Lang, Konrad [1 ]
Stryeck, Sarah [1 ]
Bodruzic, David [2 ]
Stepponat, Manfred [3 ]
Trajanoski, Slave [4 ]
Winkler, Ursula [2 ]
Lindstaedt, Stefanie [1 ,5 ]
机构
[1] Graz Univ Technol, Inst Interact Syst & Data Sci, A-8010 Graz, Austria
[2] Karl Franzens Univ Graz, Server & Storage Syst, A-8010 Graz, Austria
[3] Graz Univ Technol, Cent Informat Technol, A-8010 Graz, Austria
[4] Med Univ Graz, Core Facil Computat Bioanalyt, A-8010 Graz, Austria
[5] Know Ctr GmbH, A-8010 Graz, Austria
关键词
computational infrastructure; Docker; bioinformatics; life sciences; HPC; computing; container; singularity;
D O I
10.3390/mca25020038
中图分类号
O1 [数学];
学科分类号
0701 ; 070101 ;
摘要
Life sciences (LS) are advanced in research data management, since LS have established disciplinary tools for data archiving as well as metadata standards for data reuse. However, there is a lack of tools supporting the active research process in terms of data management and data analytics. This leads to tedious and demanding work to ensure that research data before and after publication are FAIR (findable, accessible, interoperable and reusable) and that analyses are reproducible. The initiative CyVerse US from the University of Arizona, US, supports all processes from data generation, management, sharing and collaboration to analytics. Within the presented project, we deployed an independent instance of CyVerse in Graz, Austria (CAT) in frame of the BioTechMed association. CAT helped to enhance and simplify collaborations between the three main universities in Graz. Presuming steps were (i) creating a distributed computational and data management architecture (iRODS-based), (ii) identifying and incorporating relevant data from researchers in LS and (iii) identifying and hosting relevant tools, including analytics software to ensure reproducible analytics using Docker technology for the researchers taking part in the initiative. This initiative supports research-related processes, including data management and analytics for LS researchers. It also holds the potential to serve other disciplines and provides potential for Austrian universities to integrate their infrastructure in the European Open Science Cloud.
引用
收藏
页数:15
相关论文
共 11 条
  • [1] Bloom K., P 2013 COMM SUMM STU
  • [2] The FAIR guiding principles for data stewardship: fair enough?
    Boeckhout, Martin
    Zielhuis, Gerhard A.
    Bredenoord, Annelien L.
    [J]. EUROPEAN JOURNAL OF HUMAN GENETICS, 2018, 26 (07) : 931 - 936
  • [3] Devisetty Upendra Kumar, 2016, F1000Res, V5, P1442
  • [4] The iPlant collaborative: cyberinfrastructure for plant biology
    Goff, Stephen A.
    Vaughn, Matthew
    McKay, Sheldon
    Lyons, Eric
    Stapleton, Ann E.
    Gessler, Damian
    Matasci, Naim
    Wang, Liya
    Hanlon, Matthew
    Lenards, Andrew
    Muir, Andy
    Merchant, Nirav
    Lowry, Sonya
    Mock, Stephen
    Helmke, Matthew
    Kubach, Adam
    Narro, Martha
    Hopkins, Nicole
    Micklos, David
    Hilgert, Uwe
    Gonzales, Michael
    Jordan, Chris
    Skidmore, Edwin
    Dooley, Rion
    Cazes, John
    McLay, Robert
    Lu, Zhenyuan
    Pasternak, Shiran
    Koesterke, Lars
    Piel, William H.
    Grene, Ruth
    Noutsos, Christos
    Gendler, Karla
    Feng, Xin
    Tang, Chunlao
    Lent, Monica
    Kim, Seung-Jin
    Kvilekval, Kristian
    Manjunath, B. S.
    Tannen, Val
    Stamatakis, Alexandros
    Sanderson, Michael
    Welch, Stephen M.
    Cranston, Karen A.
    Soltis, Pamela
    Soltis, Doug
    O'Meara, Brian
    Ane, Cecile
    Brutnell, Tom
    Kleibenstein, Daniel J.
    [J]. FRONTIERS IN PLANT SCIENCE, 2011, 2
  • [5] Hollowell C., 2017, Journal of Physics: Conference Series, V898, DOI 10.1088/1742-6596/898/8/082014
  • [6] Lenhardt WC, 2016, HIGH PERF EXTR COMP, P1, DOI DOI 10.1109/HPEC.2016.7761597
  • [7] Toward collaborative open data science in metabolomics using Jupyter Notebooks and cloud computing
    Mendez, Kevin M.
    Pritchard, Leighton
    Reinke, Stacey N.
    Broadhurst, David I.
    [J]. METABOLOMICS, 2019, 15 (10)
  • [8] The iPlant Collaborative: Cyberinfrastructure for Enabling Data to Discovery for the Life Sciences
    Merchant, Nirav
    Lyons, Eric
    Goff, Stephen
    Vaughn, Matthew
    Ware, Doreen
    Micklos, David
    Antin, Parker
    [J]. PLOS BIOLOGY, 2016, 14 (01):
  • [9] Randles Bernadette M., 2017, 2017 ACM/IEEE Joint Conference on Digital Libraries (JCDL), P1
  • [10] Stewart CraigA., 2010, Proceedings of the 38th Annual ACM SIGUCCS Fall Conference: Navigation and Discovery, SIGUCCS'10, P37, DOI [DOI 10.1145/1878335.1878347, 10.1145/1878335.1878347]