Publications and Press

To cite the BioMoby project, please cite THIS paper:

The BioMoby Consortium (2008)
Interoperability with Moby 1.0 — It’s better than sharing your toothbrush!
Briefings in Bioinformatics, 9 (3), pp. 220-231.

Peer Reviewed & Books

(Connotea link – BioMoby)

Néron B, Ménager H, Maufrais C, Joly N, Maupetit J, Letort S, Carrere S, Tuffery P, Letondal C. (2009).
Mobyle: a new full web bioinformatics framework.
Bioinformatics. 2009 Nov 15;25(22):3005-11.

Vandervalk B.P., McCarthy E.L., Wilkinson M.D. (2009).
Moby and Moby 2: Creatures of the Deep (Web)
Briefings in Bioinformatics 10 (2), 114 (16 Jan 2009)

Michael DiBernardo, Rachel Pottinger, Mark Wilkinson (2008).
Semi-automatic web service composition for the life sciences using the BioMoby semantic web framework

Journal of Biomedical Informatics 41 (5), 837 (2008)

The BioMoby Consortium (2008).
Interoperability with Moby 1.0–It’s better than sharing your toothbrush!
Briefings in Bioinformatics 9 (3), pp. 220-231.

Gordon P.M.K., Kawas E., Wilkinson M.D., Sensen C.W. (2007).
Using a novel data transformation technique to provide the EMBOSS software suite as Semantic Web Services.
To appear in Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (San Jose, California), November 2-4, 2007

Kerhornou A, Guigó R. (2007).
BioMoby web services to support clustering of co-regulated genes based on similarity of promoter configurations.
Bioinformatics (Oxford, England) 23 (14), 1831-3 (15 Jul 2007).

Gordon P.M.K., Sensen C.W. (2007).
Seahawk: Moving Beyond HTML in Web-based Bioinformatics Analysis
BMC Bioinformatics 8:208.

Gordon P.M.K., Trinh Q., Sensen C.W. (2007).
Semantic Web Service Provision: a Realistic Framework for Bioinformatics Programmers.
Bioinformatics 23(9):1178-1180.

Young C. Song , Edward Kawas , Ben M. Good , Mark D. Wilkinson and Scott J. Tebbutt (2007).
DataBiNS: a BioMoby-based data-mining workflow for biological pathways and non-synonymous SNPs.
Bioinformatics 23(6):780-782; doi:10.1093/bioinformatics/btl648

Kawas, Edward, Senger, Martin, Wilkinson, Mark (2006).
BioMoby extensions to the Taverna workflow management and enactment software
BMC Bioinformatics 2006, Nov 30;7:523

Wilkinson M (2006).
Gbrowse Moby: A Web-based browser for BioMOBY Services.
Source Code for Biology and Medicine 2006, 1:4 (24 October 2006)

Sébastien Carrere and Jérôme Gouzy (2006).
REMORA: a pilot in the ocean of BioMoby web-services.
Bioinformatics (Oxford, England) 22 (7), 900-1 (01 Apr 2006)

Ismael Navas-Delgado et al. (2006).
Intelligent client for integrating bioinformatics services.>/a>
Bioinformatics (Oxford, England) 22 (1), 106-11 (01 Jan 2006)

P.B.T. Neerincx, J.A.M. Leunissen (2005).
Evolution of web services in bioinformatics.
Briefings in Bioinformatics, Jun;6(2):178-88.

Andrei L Turinsky et al. (2005).
Bioinformatics visualization and integration with open standards: the Bluejay genomic browser.
In silico biology. 5 (2), 187-98 (2005).

Schoof H, Spannagl M, Yang L, Ernst R, Gundlach H, Haase D, Haberer G, Mayer KF. (2005).
Munich information center for protein sequences plant genome resources: a framework for integrative and comparative analyses 1(W).
Plant Physiol. 2005 Jul;138(3):1301-9.

Wilkinson M, Schoof H, Ernst R, Haase D (2005).
BioMOBY successfully integrates disributed heterogenous bioinformatics web services.
The PlaNet exemplar case. Plant Physol 138, p1-13.

Schiltz G, Gessler D, Stein L (2004).
Semantic MOBY.
Position paper for the 2004 W3C Workshop on Semantic Web for Life Sciences.

Lord P, Bechhofer S, Wilkinson MD, Schiltz G, Gessler D, Hull D, Goble C, Stein L (2004).
Applying semantic web services to Bioinformatics: Experiences gained, lessons learnt
in ISWC 2004. Springer-Verlag Berlin Heidelberg, p350-364.

Wilkinson MD (2004).
BioMOBY – the MOBY-S Platform for Interoperable Data Service Provision
in Computational Genomics Theory and Application. Richard P. Grant (ed) Horizon Bioscience, Wymondham, U.K.

Wilkinson MD, Gessler D, Farmer A, Stein L (2003).
The BioMOBY Project Explores Open-Source, Simple, Extensible Protocols for Enabling Biological Database Interoperability
Proc Virt Conf Genom and Bioinf (3):16-26. (ISSN 1547-383X)

Wilkinson, MD, Links, M. (2002).
BioMOBY: an open-source biological web services proposal.
Briefings In Bioinformatics 3:4. 331-341.

Other press and manuscripts

Coding a bridge across the data divide. The Scientist 18(24), pp 25-27. Dec 20, 2004.

MOBY project serves up database interoperability for the open-source crowd.
Bioinform 6:24. p8, June 17, 2002.

BioMOBY: the IT initiative founded in the Saskatchewan Woods. Biotechnology Focus 5:7, p22. Sept., 2002.

Bioinformatics:  bringing it all together.
Nature 419, p751. Oct. 17, 2002.