Scientific publications

Towards a better understanding of Apis mellifera and Varroa destructor microbiomes: introducing ‘phyloh’ as a novel phylogenetic diversity
analysis tool

A. Sandionigi, S. Vicario, E. M. Prosdocimi, A. Galimberti, E. Ferri, A. Bruno, B. Balech, V. Mezzasalma and M. Casiraghi
Molecular Ecology Resources First published online: 19 NOV 2014, doi: 10.1111/1755-0998.12341

Semantics in Support of Biodiversity Knowledge Discovery: An Introduction to the Biological Collections Ontology and Related Ontologies

Walls RL, Deck J, Guralnick R, et al including Morrison N. (2014)
PloS ONE 9(3) doi:10.1371/journal.pone.0089606

Enriched biodiversity data as a resource and service

Rutger Vos et al including Hannes Hettling (2014)
Biodiversity Data Journal 2: e1125 (16 Jun 2014), doi:10.3897/BDJ.2.e1125

SCRAM-CK: A collaborative requirements engineering process for designing a web based e-science toolkit

Nieva de la Hidalga A, Hardisty A, and Jones AC. (2014)
Requirements Engineering, First appeared online, 25th September 2014 doi: 10.1007/s00766-014-0212-0

DigiWeb-a workflow environment for quality assurance of transcription in digitization of natural history collections

Mononen T, Tegelberg R, Sääskilahti M, et al. (2014)
Biodiversity Informatics 9(1).

The influence of invasive jellyfish blooms on the aquatic microbiome in a coastal lagoon (Varano, SE Italy) detected by an Illumina-based deep sequencing strategy

Manzari C. Fosso B, Marzano M, et al.
Biological Invasions 2014 1-18 doi:10.1007/s10530-014-0810-2

A semi-automated workflow for biodiversity data retrieval, cleaning, and quality control

Cherian Mathew, Anton Güntsch, Matthias Obst, Saverio Vicario, Robert Haines, Alan R. Williams, Yde de Jong, Carole Goble
Biodiversity Data Journal, doi: 10.3897/BDJ.2.e4221

The Pacific Oyster (Crassostrea gigas) invasion in Scandinavian coastal waters in a changing climate: impact on local ecosystem services

Laugen AT, Hollander J, Obst M, et al. (2015)
Book chapter in: Canning-Clode, J (Ed.). Biological Invasions in Aquatic and Terrestrial Systems: Biogeography, Ecological Impacts, Predictions and Management. In press, publication expected September 2015: 

Mapping present and future predicted distribution patterns for a meso-grazer guild in the Baltic Sea

Leidenberger S, De Giovanni R, Kulawik R, Williams A, Bourlat S.J. (2014)
Journal of Biogeography. DOI: 10.1111/jbi.12395.

Supporting environmental modelling with Taverna workflows, web services and desktop grid technology

Horváth, F., Ittzés, P., Ittzés, D., Barcza, Z., Dobor, L., Hidy, D., Marosi, A., Hardisty, A.
Ames, D.P., Quinn, N.W.T., Rizzoli, A.E. (Eds.)
Proceedings of the 7th International Congress on Environmental Modelling and Software, June 15-19, San Diego, California, USA. 2014

The environment ontology: contextualising biological and biomedical entities

Buttigieg PL Morrison N Smith B Mungall CJ Lewis SE et al and the ENVO Consortium (2013)
Journal of Biomedical Semantics 4:43 doi:10.1186/2041-1480-4-43

On specifying and sharing scientific workflow optimization results using research objects

Holl S, Garijo D, Belhajjame K, et al. (2013)
Proceedings of the 8th ACM Workshop on Workflows in Support of Large-Scale Science doi: 10.1145/2534248.2534251

Future carbon cycle in mountain spruce forests of Central Europe: Modelling framework and ecological inferences

Hlásny T, Barcza Z, Barka I, et al. (2014)
Forest Ecology and Management 328:55-68 doi: 10.1016/j.foreco.2014.04.038

Horizon 2020: A call to forge biodiversity links

Hardisty A. (2013)
Nature 502(7470):171 doi:10.1038/502171d

Integrating Taverna Player into Scratchpads

Haines R, Rycroft S, Smith V, Goble C. (2014)
15th Annual Bioinformatics Open Source Conference (BOSC 2014) 11-12 July 2014, Boston MA (USA)

Common motifs in scientific workflows: An empirical analysis

Garijo D, Alper P, Belhajjame K, et al. (2014)
Future Generation Computer Systems 36: 338-351

Bridging the gap between climate models and impact studies: The FORESEE Database

Dobor L, Barcza Z, Hlásny T, et al. (2015)
Geoscience Data Journal First appeared online 5 Feb 2015 doi: 10.1002/gdj3.22

Automating Data Curation in Scientific Dataflows Using Labels

Alper P, Belhajjame K, Goble C. (2013)

WORKS 2013: 8th Workshop On Workflows in Support of Large-Scale Science 17 Nov 2013, Denver CO (USA) doi: 10.1145/2534248.2534249

Application of Niche Modeling and Earth Observation for the risk assessment and monitoring of invasive species in the Baltic Sea

Stelzer K, Heyer K, Bourlat SJ, Obst M
Report to the European Space Agency, May 2013

A decadal view of biodiversity informatics: challenges and priorities

Hardisty, A., Roberts, D., and the bioinformatics community
BMC Ecology
2013, 13:16, May 2013

The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud

Wolstencroft K, Haines R, Fellows D, Williams A, Withers D, Owen S, Soiland-Reyes S, Dunlop I, Nenadic A, Fisher P, Bhagat J, Belhajjame K, Bacall F, Hardisty A, Nieva de la Hidalga A, Balcazar Vargas MP, Sufi S and Goble C
Nucleic Acids Research, April 2013

The BioVeL Project: Robust phylogenetic workflows running on the GRID

Vicario, Balech, Donvito, Notarangelo, Pesole
EMBnet.journal, vol 18 Supp. B., November 2012

BioVeL: Biodiversity Virtual e-Laboratory

Vicario, Hardisty, Haitas
EMBnet.journal, vol 17 No. 2, December 2011




19 February 2015

At the final review of the project by the EC, one of the reviewers said: “Incredible work done with a community that is not unified. Remarkable work. It opens for new development in a near future. Hope for success. Good project. Happy that you have been financed three plus years ago.”

Read all about the project and its results in the Project Final Report or read the Executive Summary only.