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BioVeL: A virtual l...
BioVeL: A virtual laboratory for data analysis and modelling in biodiversity science and ecology
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- Hardisty, Alex R. (author)
- Cardiff Univ, Sch Comp Sci & Informat, Queens Bldg,5 Parade, Cardiff CF24 3AA, S Glam, Wales, United Kingdom
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- Bacall, Finn (author)
- Univ Manchester, Sch Comp Sci, Kilburn Bldg,Oxford Rd, Manchester M13 9PL, Lancs, England, United Kingdom
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- Beard, Niall (author)
- Univ Manchester, Sch Comp Sci, Kilburn Bldg,Oxford Rd, Manchester M13 9PL, Lancs, England, United Kingdom
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show more...
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- Balcázar-Vargas, Maria Paula (author)
- Univ Amsterdam, IBED, POB 94248, NL-1090 Amsterdam, Netherlands
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- Balech, Bachir (author)
- Natl Res Council CNR, Inst Biomembranes & Bioenerget IBBE, Via Amendola 165-A, I-70126 Bari, Italy
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- Barcza, Zoltán (author)
- Eotvos Lorand Univ, Dept Meteorol, Pazmany Setany 1-A, H-1117 Budapest, Hungary
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- Bourlat, Sarah (author)
- Gothenburg University,Göteborgs universitet,Institutionen för marina vetenskaper,Department of marine sciences,Univ Gothenburg, Dept Marine Sci, Box 463, S-40530 Gothenburg, Sweden
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- Giovanni, Renato (author)
- Ctr Referencia Informacao Ambiental, Ave Dr Romeu Tortima 388, BR-13084791 Campinas, SP, Brazil
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- Jong, Yde (author)
- Univ Amsterdam, IBED, POB 94248, NL-1090 Amsterdam, Netherlands / Univ Eastern Finland, SIB Labs, Joensuu Sci Pk,POB 111, Joensuu 80101, Finland
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- Leo, Francesca (author)
- Natl Res Council CNR, Inst Biomembranes & Bioenerget IBBE, Via Amendola 165-A, I-70126 Bari, Italy
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- Dobor, Laura (author)
- Eotvos Lorand Univ, Dept Meteorol, Pazmany Setany 1-A, H-1117 Budapest, Hungary
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- Donvito, Giacinto (author)
- Ist Nazl Fis Nucl, Inst Nucl Phys, Via E Orabona 4, I-70125 Bari, Italy
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- Fellows, Donal (author)
- Univ Manchester, Sch Comp Sci, Kilburn Bldg,Oxford Rd, Manchester M13 9PL, Lancs, England
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- Guerra, Antonio Fernandez (author)
- Max Planck Inst Marine Microbiol, Celsiusstr 1, D-28359 Bremen, Germany / Jacobs Univ Bremen GmbH, Campus Ring 1, D-28359 Bremen, Germany
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- Ferreira, Nuno (author)
- Stichting EGI Eu, Sci Pk 140, NL-1098 Amsterdam, Netherlands
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- Fetyukova, Yuliya (author)
- Univ Eastern Finland, SIB Labs, Joensuu Sci Pk,POB 111, Joensuu 80101, Finland
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- Fosso, Bruno (author)
- Natl Res Council CNR, Inst Biomembranes & Bioenerget IBBE, Via Amendola 165-A, I-70126 Bari, Italy
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- Giddy, Jonathan (author)
- Cardiff Univ, Sch Comp Sci & Informat, Queens Bldg,5 Parade, Cardiff CF24 3AA, S Glam, Wales
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- Goble, Carole (author)
- Univ Manchester, Sch Comp Sci, Kilburn Bldg,Oxford Rd, Manchester M13 9PL, Lancs, England
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- Güntsch, Anton (author)
- Free Univ Berlin, Bot Garden & Bot Museum Berlin, Konigin Luise Str 6-8, D-14195 Berlin, Germany
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- Haines, Robert (author)
- Univ Manchester, IT Serv, Kilburn Bldg,Oxford Rd, Manchester M13 9PL, Lancs, England, United Kingdom
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- Ernst, Vera Hernández (author)
- Fraunhofer Inst Intelligent Anal & Informat Syst, D-53757 St Augustin, Germany
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- Hettling, Hannes (author)
- Nat Biodivers Ctr, Postbus 9517, NL-2300 Leiden, Netherlands
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- Hidy, Dóra (author)
- Szent Istvan Univ, MTASZIE Plant Ecol Res Grp, Pater Ku 1, H-2103 Godollo, Hungary
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- Horváth, Ferenc (author)
- Hungarian Acad Sci, Ctr Ecol Res, Inst Ecol & Bot, Alkotmany U 2-4, H-2163 Vacratot, Hungary
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- Ittzés, Dóra (author)
- Hungarian Acad Sci, Ctr Ecol Res, Inst Ecol & Bot, Alkotmany U 2-4, H-2163 Vacratot, Hungary
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- Ittzés, Péter (author)
- Hungarian Acad Sci, Ctr Ecol Res, Inst Ecol & Bot, Alkotmany U 2-4, H-2163 Vacratot, Hungary
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- Jones, Andrew (author)
- Cardiff Univ, Sch Comp Sci & Informat, Queens Bldg,5 Parade, Cardiff CF24 3AA, S Glam, Wales
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- Kottmann, Renzo (author)
- Max Planck Inst Marine Microbiol, Celsiusstr 1, D-28359 Bremen, Germany
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- Kulawik, Robert (author)
- Fraunhofer Inst Intelligent Anal & Informat Syst, D-53757 St Augustin, Germany
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- Leidenberger, Sonja (author)
- Swedish University of Agricultural Sciences,Sveriges lantbruksuniversitet,ARTDATABANKEN,Swedish Species Information Centre,Swedish Univ Agr Sci, Swedish Species Informat Ctr ArtDatabanken, Backlasavagen 10, S-75007 Uppsala, Sweden
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- Lyytikäinen-Saarenmaa, Päivi (author)
- Univ Helsinki, Dept Forest Sci, POB 27, FIN-00014 Helsinki, Finland
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- Mathew, Cherian (author)
- Free Univ Berlin, Bot Garden & Bot Museum Berlin, Konigin Luise Str 6-8, D-14195 Berlin, Germany
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- Morrison, Norman (author)
- Univ Manchester, Sch Comp Sci, Kilburn Bldg,Oxford Rd, Manchester M13 9PL, Lancs, England, United Kingdom
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- Nenadic, Aleksandra (author)
- Univ Manchester, Sch Comp Sci, Kilburn Bldg,Oxford Rd, Manchester M13 9PL, Lancs, England, United Kingdom
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- Hidalga, Abraham Nieva (author)
- Cardiff Univ, Sch Comp Sci & Informat, Queens Bldg,5 Parade, Cardiff CF24 3AA, S Glam, Wales, United Kingdom
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- Obst, Matthias, 1974 (author)
- Gothenburg University,Göteborgs universitet,Institutionen för marina vetenskaper,Department of marine sciences,Univ Gothenburg, Dept Marine Sci, Box 463, S-40530 Gothenburg, Sweden
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- Oostermeijer, Gerard (author)
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, PO Box 94248, 1090 Amsterdam, The Netherlands
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- Paymal, Elisabeth (author)
- FRB, 195 Rue St Jacques, F-75005 Paris, France
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- Pesole, Graziano (author)
- Institute of Biomembranes and Bioenergetics (IBBE), National Research Council (CNR), via Amendola 165/A, 70126 Bari, Italy / Department of Biosciences, Biotechnology and Biop‑ harmaceutics, University of Bari “A. Moro”, via Orabona, 1514, 70126 Bari, Italy
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- Pinto, Salvatore (author)
- Stichting EGI (EGI.eu), Science Park 140, 1098 Amsterdam, The Netherlands
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- Poigné, Axel (author)
- Fraunhofer Inst Intelligent Anal & Informat Syst, D-53757 St Augustin, Germany
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- Fernandez, Francisco Quevedo (author)
- Cardiff Univ, Sch Comp Sci & Informat, Queens Bldg,5 Parade, Cardiff CF24 3AA, S Glam, Wales, United Kingdom
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- Santamaria, Monica (author)
- Natl Res Council CNR, Inst Biomembranes & Bioenerget IBBE, Via Amendola 165-A, I-70126 Bari, Italy
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- Saarenmaa, Hannu (author)
- SIB Labs, Joensuu Sci‑ ence Park, University of Eastern Finland, P.O. Box 111, 80101 Joensuu, Finland
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- Sipos, Gergely (author)
- Stichting EGI Eu, Sci Pk 140, NL-1098 Amsterdam, Netherlands
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- Sylla, Karl Heinz (author)
- Fraunhofer Inst Intelligent Anal & Informat Syst, D-53757 St Augustin, Germany
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- Tähtinen, Marko (author)
- Univ Helsinki, Finnish Museum Nat Hist, POB 17, FIN-00014 Helsinki, Finland
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- Vicario, Saverio (author)
- Natl Res Council CNR, Inst Biomed Technol ITB, Via Amendola 122-D, I-70126 Bari, Italy
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- Vos, Rutger Aldo (author)
- Univ Amsterdam, IBED, POB 94248, NL-1090 Amsterdam, Netherlands / Nat Biodivers Ctr, Postbus 9517, NL-2300 Leiden, Netherlands
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- Williams, Alan R. (author)
- Univ Manchester, Sch Comp Sci, Kilburn Bldg,Oxford Rd, Manchester M13 9PL, Lancs, England, United Kingdom
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- Yilmaz, Pelin (author)
- Max Planck Inst Marine Microbiol, Celsiusstr 1, D-28359 Bremen, Germany
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(creator_code:org_t)
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- 2016-10-20
- 2016
- English.
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In: BMC Ecology. - : Springer Science and Business Media LLC. - 1472-6785. ; 16
- Related links:
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https://bmcecol.biom...
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https://doi.org/10.1...
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https://gup.ub.gu.se...
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https://doi.org/10.1...
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https://res.slu.se/i...
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https://urn.kb.se/re...
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Abstract
Subject headings
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- © 2016 The Author(s).Background: Making forecasts about biodiversity and giving support to policy relies increasingly on large collections of data held electronically, and on substantial computational capability and capacity to analyse, model, simulate and predict using such data. However, the physically distributed nature of data resources and of expertise in advanced analytical tools creates many challenges for the modern scientist. Across the wider biological sciences, presenting such capabilities on the Internet (as "Web services") and using scientific workflow systems to compose them for particular tasks is a practical way to carry out robust "in silico" science. However, use of this approach in biodiversity science and ecology has thus far been quite limited. Results: BioVeL is a virtual laboratory for data analysis and modelling in biodiversity science and ecology, freely accessible via the Internet. BioVeL includes functions for accessing and analysing data through curated Web services; for performing complex in silico analysis through exposure of R programs, workflows, and batch processing functions; for on-line collaboration through sharing of workflows and workflow runs; for experiment documentation through reproducibility and repeatability; and for computational support via seamless connections to supporting computing infrastructures. We developed and improved more than 60 Web services with significant potential in many different kinds of data analysis and modelling tasks. We composed reusable workflows using these Web services, also incorporating R programs. Deploying these tools into an easy-to-use and accessible 'virtual laboratory', free via the Internet, we applied the workflows in several diverse case studies. We opened the virtual laboratory for public use and through a programme of external engagement we actively encouraged scientists and third party application and tool developers to try out the services and contribute to the activity. Conclusions: Our work shows we can deliver an operational, scalable and flexible Internet-based virtual laboratory to meet new demands for data processing and analysis in biodiversity science and ecology. In particular, we have successfully integrated existing and popular tools and practices from different scientific disciplines to be used in biodiversity and ecological research.
Subject headings
- NATURVETENSKAP -- Biologi -- Ekologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Ecology (hsv//eng)
- NATURVETENSKAP -- Biologi -- Bioinformatik och systembiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Bioinformatics and Systems Biology (hsv//eng)
- NATURVETENSKAP -- Biologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences (hsv//eng)
- NATURVETENSKAP -- Data- och informationsvetenskap (hsv//swe)
- NATURAL SCIENCES -- Computer and Information Sciences (hsv//eng)
- NATURVETENSKAP -- Geovetenskap och miljövetenskap -- Miljövetenskap (hsv//swe)
- NATURAL SCIENCES -- Earth and Related Environmental Sciences -- Environmental Sciences (hsv//eng)
Keyword
- Analysis
- Automation
- Biodiversity science
- Biodiversity virtual e-laboratory
- Computing software
- Data processing
- Ecology
- Informatics
- Virtual laboratory
- Workflows
- Biodiversity science
Publication and Content Type
- ref (subject category)
- art (subject category)
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To the university's database
- By the author/editor
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Hardisty, Alex R ...
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Bacall, Finn
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Beard, Niall
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Balcázar-Vargas, ...
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Balech, Bachir
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Barcza, Zoltán
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show more...
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Bourlat, Sarah
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Giovanni, Renato
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Jong, Yde
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Leo, Francesca
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Dobor, Laura
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Donvito, Giacint ...
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Fellows, Donal
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Guerra, Antonio ...
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Ferreira, Nuno
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Fetyukova, Yuliy ...
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Fosso, Bruno
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Giddy, Jonathan
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Goble, Carole
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Güntsch, Anton
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Haines, Robert
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Ernst, Vera Hern ...
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Hettling, Hannes
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Hidy, Dóra
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Horváth, Ferenc
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Ittzés, Dóra
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Ittzés, Péter
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Jones, Andrew
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Kottmann, Renzo
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Kulawik, Robert
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Leidenberger, So ...
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Lyytikäinen-Saar ...
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Mathew, Cherian
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Morrison, Norman
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Nenadic, Aleksan ...
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Hidalga, Abraham ...
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Obst, Matthias, ...
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Oostermeijer, Ge ...
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Paymal, Elisabet ...
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Pesole, Graziano
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Pinto, Salvatore
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Poigné, Axel
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Fernandez, Franc ...
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Santamaria, Moni ...
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Saarenmaa, Hannu
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Sipos, Gergely
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Sylla, Karl Hein ...
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Tähtinen, Marko
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Vicario, Saverio
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Vos, Rutger Aldo
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Williams, Alan R ...
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Yilmaz, Pelin
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- About the subject
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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and Ecology
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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and Bioinformatics a ...
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Computer and Inf ...
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Earth and Relate ...
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and Environmental Sc ...
- Articles in the publication
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BMC Ecology
- By the university
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University of Gothenburg
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Swedish University of Agricultural Sciences
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University of Skövde