BIC Publications, Posters, Presentations, New Database Deposition
January 2010 – July 2010

NEW DATABASE DEPOSITIONS

BIRCH Release 2.7, May 2010
BIRCH Release 2.6 March 2010
DrugBank www.drugbank.ca
HMDB – version 2.5 www.hmdb.ca
SMPDB www.smpdb.ca
T3DB www.t3db.org
PRESENTATIONS

Frolkis, A., Ziegler, K., Wishart, D.S. (2010). “Protein Interaction Databases: How Accurate Are They?” poster presented at the 12th Annual Pacific Symposium in Biocomputing (PSB), Hawaii, Jan. 4-8, 2010.
Sensen, C.W. (2010). Invited Talk, “Using Nucleic Acids in Blood as Markers for Infectious Diseases, Epigentics of Health and Disease in Lethbridge, 2010.
Sensen, C.W. (2010). Invited Talk, “A Computational Environment for the Characterization of Epigenetic Phenomena, Genome Alberta Genomics Workshop, 2010.
Wilkinson, M.D. et al. (2010). Invited Speaker, “Semantic Data Modeling for Personalized Clinical Research”, BioIT World Conference and Expo 2010. April 20-22, 2010, Boston,USA.
Wilkinson, M.D. et al. (2010). Invited Speaker, “The SADI Semantic Web Service Framework”, BioHackathon 3 Plenary Session, 2010. February 7, 2010, Tokyo, Japan
Wilkinson, M.D. et al. (2010). Invited Speaker, “The Semantic Web – This Time… it’s Personal!”,Stanford Medical Informatics Symposium. May 14, 2010, Palo Alto, CA, USA.
Wilkinson, M.D. et al. (2010). Plenary Speaker, “From BioMoby to SADI, the evolution of Semantic Web Services”, Bio Open Source Conference (BOSC) 2010 at ISMB, July 9-10, 2010, Boston, MA.
Wishart, D.S. (2010). “Applications of Metabolomics to Drug Research and Development” presented at the Centre for Drug Research and Development, Vancouver, BC, June 10, 2010.
Wishart, D.S. (2010). “Metabolite Identification and Quantification: New Approaches to an Old Problem” presented at the Metabolomics and More Symposium, Munich, Germany, March 11, 2010.
Wishart, D.S. (2010). “Metabolomics: The Capstone to Systems Biology” presented at the Systems Biology 2010 Conference – From Gene to Metabolite Networks, Melbourne, Australia, May 17, 2010.
Wishart, D.S. (2010). “Personal Genomics: The Answer Isn’t Always in the Genes” presented at the Pacific Symposium in Biocomputing (PSB) 2010. Kohala Coast, Hawaii, Jan. 5, 2010.
Zhou, J., Liang, Y., Berjanskii, M., Sobsey, C., Lin, G., Wishart, D.S. (2010). “New Methods for the Assessment of Protein Structure Quality: Applications to Prion Structures Deposited in the PDB” poster presented at the PrP2010 Conference, Ottawa, Ontario, March 8-10, 2010.
Zhou, J., Sobsey, C., Berjanksii, M., Liang, J., Lin, G., Wishart, D.S. (2010). “New Methods for the Assessment of Protein Structure Quality” poster presented at the 12th Annual Pacific Symposium in Biocomputing (PSB), Hawaii, Jan. 4-8, 2010.

PUBLICATIONS

Berjanskii, M., Liang, Y., Zhou, J., Tang, P., Stothard, P., Zhou, Y., Cruz, J., Macdonell, C., Lin, G., Lu, P., Wishart, D.S. (2010) PROSESS: a protein structure evaluation suite and server. Nucleic Acids Res. 38:W633-640.
Biohackathon Consortium (2010): Standardization and interoperability for bioinformatics web services and workflows. Journal of Biomedical Semantics (in press)
Frolkis, A., Knox, C., Lim, E., Jewison, T., Law, V., Hau, D.D., Liu, P., Gautam, B., Ly, S., Guo, A.C., Xia, J., Liang, Y., Shrivastava, S. and Wishart, D.S. (2010) SMPDB: The Small Molecule Pathway Database. Nucleic Acids Res. 38(Database issue):D480-487.
Gordon P.M.K., Barker K., Sensen C.W. (2010). Can Biologists Effectively Build Workflows, Without Programming? Database Integration for the Life Sciences 2010 [in press]
Gordon P.M.K., Barker K., Sensen C.W. (2010). Programming-by-example meets the Semantic Web – Using Ontologies and Web Services to close the Semantic Web. IEEE VL/HCC conference 2010 [in press]
Lim, E., Pon, A., Djoumbou, Y., Knox, C., Shrivastava, S., Guo, A.C., Neuveu, V. and Wishart, D.S. (2010) T3DB: A Comprehensively Annotated Database of Common Toxins and Their Targets. Nucleic Acids Res. 38(Database issue):D781-786.
Neveu, V., Perez-Jiménez, J., Vos, F., Crespy, V., du Chaffaut, L., Mennen, L., Knox, C., Eisner, R., Cruz, J., Wishart, D., Scalbert, A. (2010) Phenol-Explorer: an online comprehensive database on polyphenol contents in foods. Database (Oxford). 2010;2010:bap024.
Ramos-Padrón, E., Bordenave, S., Lin, S., Bhaskar, I.M., Dong, X., Sensen, C., Fournier, J., Voordouw, G., Gieg, L.M. (2010). Carbon and Sulfur Cycling by Microbial Communities in a Gypsum-Treated Oil Sands Tailing Pond. Environmental Science & Technology. [in press]
Schmidt E.J., Parsons T.E., Jamniczky H.A., Gitelman J., Trpkov C., Boughner J., Logan C.C., Sensen C.W., Hallgrímsson B. (2010) Micro-computed tomography-based phenotypic approaches in embryology: Sources and effects of procedural artifacts on assessments of embryonic craniofacial growth and development. BMC Developmental Biology 10:18
Vandervalk, B., McCarthy, E.L., Wilkinson, M. (2010). SHARE & the Semantic Web – This Time it’s Personal! Proceedings of OWLED – OWL Experiences and Directions 2010 (in press)
Wilkinson et al. (2010) “From BioMoby to SADI, the evolution of semantic web services”. (accepted to conference, awaiting news of selection for journal publication)
Wilkinson, et al. (2010): The BioMoby and SADI Taverna Plugins for semantically-guided analytical workflow design. Proceedings of ISoLA (accepted to conference proceedings, awaiting news of selection for journal publication
Wishart, D.S. (2010) Computational Approaches to Metabolomics. Methods Mol. Biol. 593:283-313.
Wishart, D.S. (2010) DrugBank: A General Resource for Pharmaceutical and Pharmacological Research. Mol. Cell. Pharmacol. 2:25-38.
Xia, J., Wishart, D.S. (2010) MSEA: a web-based tool to identify biologically meaningful patterns in quantitative metabolomic data. Nucleic Acids Res. 38:W71-77.
Xiao M., Soh J., Meruvia-Pastor O., Schmidt E., Hallgrímsson B., Sensen C.W. (2010). Building Generic Anatomical Models Using Virtual Model Cutting and Iterative Registration. BMC Medical Imaging 10:5
Xiao M., Soh J., Taschuk M.L., Turinsky A., Parsons T.E., Hallgrímsson B., Sensen C.W. (2010). Visualization of Biological Shape Transformations by 3D Model Morphing. ACM International Conference on Bioinformatics and Computational Biology 2010, Niagara Falls, New York, U.S.A. [in press]
Zuccolo J., Bau J., Childs S., Goss G., Sensen C.W., Deans J. (2010). Phylogenetic Analysis of the MS4A and TMEM176 Gene Families. PLoS One 5:e9369
January 2009 – December 2009

NEW DATABASE DEPOSITION

BIRCH Release 2.5, September 2009
BIRCH Release 2.45, April 2009
BIRCH Release 2.4, February 2009
PRESENTATIONS

Eisner, R., Greiner, R., Knox, C., Cruz, J., Wishart, D.S. (2009). “Annotating Drugs and Metabolites with their Chemical Class” poster presented at the 17th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Stockholm, Sweden, June 27-July 2, 2009.
Eisner, R., Xia, J., Stretch, C., Eastman, T., Greiner, R., Baracos, V., Wishart, D.S., Hau, D. (2009). “Diagnostic markers of cancer-associated skeletal muscle wasting using 1H-NMR profiling of urinary metabolites and machine learning approaches” poster presented at Metabolomics Society’s 5th Annual international Conference, Edmonton, Canada, Aug 30 – Sept 2, 2009.
Guo, A.C., Shrivastava, S., Knox, C., Mandal, R., Gautam, B., Wishart, D.S. (2009). “The E. coli Metabolome” poster presented at Metabolomics Society’s 5th Annual International Conference, Edmonton, Canada, Aug 30 – Sept 2, 2009.
Lim, E., Frolkis, A., Gautam, B., Liu, P., Guo, A.C., Knox, C., Jewison, T., Shrivastava, S., Law, V., Xia, J.G., Wishart, D.S., Ly, S. (2009). “Small Molecule Pathway Database: illustrating human metabolism at subcellular and organ level” poster presented at Metabolomics Society’s 5th Annual International Conference, Edmonton, Canada, Aug 30 – Sept 2, 2009.
Meruvia-Pastor O., Soh J., Schmidt E., Boughner J.C., Xiao M., Jamnizcky H.A., Hallgrímsson B., Sensen C.W. (2009). Cell Distribution for Morphometrics Analysis Using Incremental Cell Search on Histology Samples of Mice Embryos. iCORE Summit 2009 in Banff
Neveu, V., Vos, F., Perez, J., Cruz, J., Eisner, R., Knox, C., Wishart, D.S., Scalbert, A. (2009). “Phenol-Explorer: a comprehensive database on the content of dietary polyphenols in foods” poster presented at Metabolomics Society’s 5th Annual International Conference, Edmonton, Canada, Aug 30 – Sept 2, 2009.
Pon, A., Lim, E., Djoumbou, Y., Knox, C., Shrivastava, S., Guo, A.C., Wishart, D.S. (2009). “T3DB: The Toxin and Toxin Target Database” poster presented at Metabolomics Society’s 5th Annual International Conference, Edmonton, Canada, Aug 30 – Sept 2, 2009
Sensen, C.W. (2009). A Computational Environment for the Characterization of Epigenetic Phenomena. Genome Alberta Genomics Workshop [invited talk]
Sensen, C.W. (2009). Characterization of DNA Sequences from Circulating Nucleic Acid Sequences in CWD-infected Elk. Prionet Canada Video-conferencing Regional PrP Seminar Series [invited talk]
Sensen, C.W. (2009). Creating CAVEman. Sanofi Aventis Biotalent Challenge Calgary Awards Ceremony [invited talk]
Sensen, C.W. (2009). From 2D Bioinformatics to 4D Systems Biology. CeBiTec Kolloquium in Bielefeld, Germany. [invited talk]
Sensen, C.W. (2009). From Mycoplasma capricolum to 1000 complete microbial genomes: Building genome analysis and annotation tools for 15 years. Prokagenomics in Göttingen, Germany [invited talk]
Sensen, C.W. (2009). Studien zur Wirt-Pathogen Interaktion. Computer and Systems Biology Kolloquium at the HZI Braunschweig, Germany [invidted talk]
Sensen, C. W. (2009). Towards a Life Testing System for Chronic Wasting Disease and BSE. From Baden to Banff [invited talk]
Sensen, C. W. (2009). TSE-specific Sequences can be Identified in Circulating Nucleic Acids from Experimentally Infected Live Elk and Cattle. APRI Live Animal Testing & the Clinical and Biological Perspective of Atypical BSE Workshop in Edmonton [invited talk]
Sensen, C.W. (2009). Using Nucleic Acids in Blood as Markers for Infectious Diseases. Epigenetics of Health and Disease in Lethbridge [invited talk]
Sinelnikov, I., Dong, E., Huang, P., Young, N., Knox, C., Eisner, R., Guo, A.C., Bouatra, S., Xia J., Psychogios, N., Greiner, R., Wishart, D.S. (2009). “HMDB (version 2.5): Human Metabolome Database” poster presented at Metabolomics Society’s 5th Annual International Conference, Edmonton, Canada, Aug 30 – Sept 2, 2009.
Soh J., Meruvia-Pastor O., Xiao M., Tang P., Lim E., Wishart D., Sensen C.W. (2009). Visual Integration of Pharmacokinetics Data in the CAVEman System. iCORE Summit 2009 in Banff
Wilkinson, M.D. et al. (2009). Demo Presentation Track, “SHARE – The Semantic Health and Research Environment”, Asian Semantic Web Conference, 2009. , Dec 5-9. 2009, Shanghai, China.
Wilkinson, M.D. et al. (2009). Invited Delegate, Phylionformatics working Group VoCamp, Montpelier, France. November 12-16, 2009.
Wilkinson, M.D. et al. (2009). Invited Speaker. National Centre for Biomedical Ontology (NCBO) Virtual Seminar Series. “Web 2.0 + Web 3.0 = Web 5.0?” June, 2009.
Wilkinson, M.D. et al. (2009). Invited Speaker, TWDG Conference “Wild Ideas” Track, Montpellier, France, November 2009
Wilkinson, M.D. et al. (2009). Keynote Speaker. Advanced Technologies Keynote – “Web 2.0 + Web 3.0 = Web 5.0?”. Conference on Semantics in HealthCare and Life Sciences (C-SHALS) 2009, Cambridge, MA, USA. Feb 25-27, 2009
Wilkinson, M.D. et al. (2009). Plenary Session. 2nd Canadian Semantic Web Conference, “Open Semantic Annotation”. May 25, 2009. Kelowna, BC, Canada.
Wilkinson, M.D. et al. (2009). Plenary Speaker, “SADI: ‘Cause you can’t always GET what you want”, Semantic Web Services in Practice, 2009. Dec. 4-12, Singapore.
Wilkinson, M.D. et al. (2009). Workshop Leader and invited participant, “Cool URIs and Semantic Web Services”, 2009 BioHackathon, OIST, Okinawa, Japan, March 14-21, 2009.
Wishart, D.S. (2009). “Cord Blood Banking and Informatics” presented at the Alberta Cord Blood Bank Symposium, Edmonton, AB, June 17, 2009.
Wishart, D.S. (2009). “Food, Nutrition and the Human Metabolome” presented at the The 4th International Conference on Polyphenols & Health (ICPH 2009), Harrogate, UK, Dec. 11, 2009.
Wishart, D.S. (2009). “Informatics and Metabolomics” presented at the ELIXIR/EBI International Metabolomics Workshop, Hinxton, UK, Jan. 27, 2009.
Wishart, D.S. (2009). “The Human Biofluid Metabolome(s): Different Answers from Different Technologies”, presented at the NuGO & SysDiet Metabolomics Workshop, Copenhagen, DK, Feb. 23, 2009.
Wishart, D.S. (2009). “Pathways and Statistics in Metabolomics” workshop/tutorial presented at the 5th International Metabolomics Society Meeting, Edmonton, AB, Aug. 30, 2009.
Wishart, D.S. (2009). “The Human Metabolome Project: Potential Applications to Structural and Functional Genomics”, presented at Columbia University, NY, April 27, 2009.
Wishart, D.S. (2009). “Tools, Issues and Opinions on Structure Validation” presented at the wwPDB NMR Structure Validation Task Force Workshop, Paris, France, Sept. 21, 2009.
Wishart, D.S., Knox, C., Cruz, J., Guo, A., Gautam, B., Eisner, R., Young N. (2009). “New Resources for Disease Bioinformatics”, poster presented at the 11th Annual Pacific Symposium in Biocomputing (PSB), Hawaii, Jan. 3-7, 2009.
Wishart, D.S. & Psychogios, N. (2009). “The Human Metabolome Database: A General Metabolomics Resource” presented at the 11th International Congress of Inborn Errors of Metabolism, San Diego, USA, Aug. 30, 2009.
Xia, J., Young, N., Wishart, D.S. (2009). “MetaboAnalyst” poster presented at the First Annual Australasian Metabolomics Conference, Auckland, New Zealand, July 3-5, 2009.
Xiao M., Soh J., Meruvia-Pastor O., Schmidt E., Hallgrímsson B., Sensen C.W. (2009). Building Generic Anatomical Models Using Virtual Cutting and Iterative Registration. iCORE Summit 2009 in Banff
Young, N., Xia, J, Psychogios, N., Wishart, D.S. (2009). “MetaboAnalyst-A Web Service For Metabolomic Data Analysis” poster presented at Metabolomics Society’s 5th Annual International Conference, Edmonton, Canada, Aug 30 – Sept 2, 2009.

PUBLICATIONS

Antranikian G., Ruepp A., Gordon P.M.K., Ballschmiter A., Zibat A., Sensen C.W., Frishman D., Liebl W., Klenk H.-P. (2009) Rapid access to genes of biotechnologically useful enzymes by partial genome sequencing: the thermoalkaliphile Anaerobranca gottschalkii. Journal of Molecular Microbiology and Biotechnology 16:81-90
Berjanskii, M., Tang, P., Liang, J., Cruz, J.A., Zhou, J., Zhou, Y., Bassett, E., MacDonell, C., Lu, P., Lin, G., Wishart, D.S. (2009) GeNMR: A Web Server for Rapid NMR-Based Protein Structure Determination. Nucleic Acids Res. 37(Web Server Issue):W670-677.
Birney E., Hudson T.J., Green E.D., Gunter C., Eddy S., Rogers J., Harris J.R., Ehrlich S.D., Apweiler R., Austin C.P., Berglund L., Bobrow M., Bountra C., Brookes A.J., Cambon-Thomsen A., Carter N.P., Chisholm R.L., Contreras J.L., Cooke R.M., Crosby W.L., Dewar K., Durbin R., Dyke S.O., Ecker J.R., El Emam K., Feuk L., Gabriel S.B., Gallacher J., Gelbart W.M., Granell A., Guarner F., Hubbard T., Jackson S.A., Jennings J.L., Joly Y., Jones S.M., Kaye J., Kennedy K., Knoppers B.M., Kyrpides N.C., Lowrance W.W., Luo J., MacKay J.J., Martin-Rivera L., McCombie W.R., McPherson J.D., Miller L., Miller W., Moerman D., Mooser V., Morton C.C., Ostell J.M., Ouellette B.F., Parkhill J., Raina P.S., Rawlings C., Scherer S.E., Scherer S.W., Schofield P.N., Sensen C.W., Stodden V.C., Sussman M.R., Tanaka T., Thornton J., Tsunoda T., Valle D., Vuorio E.I., Walker N.M., Wallace S., Weinstock G., Whitman W.B., Worley K.C., Wu C., Yu J. (2009). Toronto International Data Release Workshop Prepublication data sharing. Nature 461:168-170
Forsythe, I.J. and Wishart, D.S. (2009) “Exploring Human Metabolites using the Human Metabolome Database” in Curr. Protoc. Bioinformatics. Chapter 14: Unit 14.8.
Good, B., Lu, P., Kawas, E., Wilkinson, M. (2009). Open semantic annotation: an experiment with BioMoby Web services. Proceedings of the Second Canadian Semantic Web Working Symposium.
Gordon, P.M.K., Schuetz, E., Beck, J., Urnovitz, H.B., Graham, C., Clark, R., Dudas, S., Czub, S., Sensen, M., Brenig, B., Groschup, M.H., Church, R.B., Sensen, C.W. (2009). Disease-specific motifs can be identified in circulating nucleic acids from live elk and cattle infected with transmissible spongiform encephalopathies. Nucleic Acids Research, 37(2): 550-556.
Hallgrímsson B., Boughner J., Turinsky A., Parsons T.E., Logan C., Sensen C.W. (2009). Geometric Morphometrics and the Study of Development. In Sensen, C.W., Hallgrímsson, B. [Eds.] Advanced Imaging in Biology and Medicine – Technology, Software Environments, Applications. Springer Verlag, Heidelberg pp. 319-338
Meruvia-Pastor O., Soh J., Xiao M., Schmidt E., Logan C., Boughner J.C., Jones N., Osborn D., Santiago J., Gittleman J., Hallgrímsson B., Sensen C.W. (2009) Fast Interactive Integration of Cross-Sectional Image Datasets and Surface Data for Morphometric Analysis. Stud Health Technol Inform 142:183-188
Sensen, C.W., Hallgrímsson, B. [Eds.] (2009). Advanced Imaging in Biology and Medicine – Technology, Software Environments, Applications. Springer Verlag, Heidelberg, 445 pages. ISBN 978-3-540-68992-8
Sensen C.W., Soh J. (2009). CAVEman, an Object-Oriented Model of the Human Body. In Sensen, C.W., Hallgrímsson, B. [Eds.] Advanced Imaging in Biology and Medicine – Technology, Software Environments, Applications. Springer Verlag, Heidelberg pp. 289-300
Soh J., Gordon P.M.K., Sensen C.W. (2009). Genomic Data Visualization – The Bluejay System. In Sensen, C.W., Hallgrímsson, B. [Eds.] Advanced Imaging in Biology and Medicine – Technology, Software Environments, Applications. Springer Verlag, Heidelberg pp. 395-400
Soh J., Turinsky A.L., Trinh Q.M., Chang J., Sabhaney A., Dong X., Gordon P.M.K., Janzen R.P.W., Hau D., Wishart D.S., Sensen C.W. (2009). Spatiotemporal Integration of Molecular and Anatomical Data in Virtual Reality using Semantic Mapping. Int. J. Nanomedicine 4:79-89
Vandervalk, B., McCarthy, L., Wilkinson, M. (2009). Moby and Moby 2: Creatures of the Deep (Web). Invited review; Briefings in Bioinformatics special edition on Semantic Web in Healthcare and Life Science 2009.
Vandervalk, B., McCarthy, E.L., Wilkinson, M. (2009). Optimization of Distributed SPARQL Queries Using Edmonds’ Algorithm and Prim’s Algorithm. IEEE Proceedings of the Conference of Computational Science and Engineering, Vancouver, BC, August, 2009.
Vandervalk, B., McCarthy, E.L., Wilkinson, M. (2009). SHARE: A Semantic Web Query Engine for Bioinformatics. Proceedings of the Asian Semantic Web
Conference 2009, (in press).
Wilkinson, M.D., Vandervalk, B., McCarthy, L. (2009). SADI Semantic Web Services – Because you can’t always GET what you want! Proceedings of the IEEE International Workshop on Semantic Web Services in Practice, Singapore,
2009 (in press)
Wishart, D.S. (2009) Computational Strategies for Metabolite Identification in Metabolomics. BioAnalysis 1:1579-1596.
Wishart, D.S., Knox, C., Guo, A.C., Eisner, R., Young, N., Gautam, B., Hau, D.D., Psychogios, N., Dong, E., Bouatra, S., Mandal, R., Sinelnikov, I., Xia, J., Jia, L., Cruz, J.A., Lim, E., Sobsey, C.A., Shrivastava, S., Huang, P., Liu, P., Fang, L., Peng, J., Fradette, R., Cheng, D., Tzur, D., Clements, M., Lewis, A., De Souza, A., Zuniga, A., Dawe, M., Xiong, Y., Clive, D., Greiner, R., Nazyrova, A., Shaykhutdinov, R., Li, L., Vogel, H.J. and Forsythe, I. (2009) HMDB: a Knowledgebase for the Human Metabolome. Nucleic Acids Res. 37(Database issue):D603-610.
Xia, J., Psychogios, N., Young, N. and Wishart, D.S. (2009) MetaboAnalyst: A Web Server for Metabolomic Data Analysis and Interpretation. Nucleic Acids Res. 37(Web Server Issue):W652-660
January 2008 – December 2008

NEW DATABASE DEPOSITION
MOSES::MOBY released to CPAN
OBY 1.0 Client and Server libraries released to CPAN
LSID Libraries released to CPAN
PRESENTATIONS
Open-Bio Hackathon – BioMoby developers meeting and presentation, Tokyo, Japan
BioMoby and Web Service Interoperability – presentation to the Semantic Astronomy Workshop, CalTech, USA.
Moby, Legacy Apps and the Semantic Web, 2008-02-11 Presentation by Paul Gordon:Tokyo, Japan
Creating Bioinformatics Semantic Web Services from existing Web Services: a Real-World Application of SAWSDL: PMK Gordon and CW Sensen. Submitted to IEEE Conference on Web Services
PUBLICATIONS
“Semi-automatic web Services compositino in the life sciences using the BioMoby framework” Journal of BioMedical Informatics
“Interoperability with BioMoby 1.0 – it’s better than sharing your toothbrush!” Briefings in Bioinformatics
Borowski K, Soh J, Sensen CW (2008) Visual comparison of multiple gene expression datasets in a genomic context. International Symposium on Integrative Bioinformatics, Leucorea, Lutherstadt Wittenberg, Germany, August 2008. [submitted]
Cheng D, Knox C, Young N, Stothard P, Damaraju S, Wishart DS. PolySearch: a web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W399-405. Epub 2008 May 16.
Gordon P.M.K., Schuetz E., Beck J., Urnovitz H.B., Graham C., Clark R., Dudas S., Czub S., Sensen M., Brenig B., Groschup M.H., Church R.B., Sensen C.W. (2008) Disease-Specific Motifs can be identified in Circulating Nucleic Acids from live Elk and Cattle infected with Transmissible Spongiform Encephalopathies. [submitted to Nucleic Acids Research]
Gordon P.M.K., Sensen C.W. (2008) Creating Bioinformatics Semantic Web Services from Existing Web Services: A real-world application of SAWSDL. In: Proceedings of the IEEE International Conference on Web Services (Beijing, China), September 23-26, 2008, pp. 608-614.
Gordon P.M.K., Soliman M.A., Bose P., Trinh Q., Sensen C.W. and Riabowol K. (2008) Interspecies data mining to predict novel ING-protein interactions in human BMC Genomics 9:426.
Montgomerie S, Cruz JA, Shrivastava S, Arndt D, Berjanskii M, Wishart DS. PROTEUS2: a web server for comprehensive protein structure prediction and structure-based annotation. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W202-9. Epub 2008 May 15.
Shi Y, Zhou J, Arndt D, Wishart DS, Lin G. Protein contact order prediction from primary sequences. BMC Bioinformatics. 2008 May 30;9:255.
Soh J., Gordon P.M.K., Taschuk M.L., Dong A., Ah-Seng A.C., Turinsky A.L., Sensen C.W. (2008) Bluejay 1.0: genome browsing and comparison with rich customization provision and dynamic resource linking BMC Bioinformatics 9:450.
Wishart DS. Identifying putative drug targets and potential drug leads: starting points for virtual screening and docking. Methods Mol Biol. 2008;443:333-51.
Wishart DS, Arndt D, Berjanskii M, Tang P, Zhou J, Lin G. CS23D: a web server for rapid protein structure generation using NMR chemical shifts and sequence data. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W496-502. Epub 2008 May 30.
OTHER
BIRCH Release 2.35, February, 2008
July 2007 – December 2007
NEW DATABASE DEPOSITION
Total new Help Desk registrants from July 2007 – Sept 2007 = 9
Total new researchers in the directory from July 2007 – Sept 2007 = 1
Total new software packages in the repository from July 2007 – Sept 2007 = 0
Total newsletters distributed from July 2007- Sept 2007 = 1
Total software downloads from July 2007- Sept 2007 = 13,066
Total web hits at the Help Desk website from July 2007 – Sept 2007 = 291,708
Total new researchers in the directory from Oct-Dec 2007 = 2
Total new software packages in the repository from Oct-Dec 2007 = 3
Total newsletters distributed from Oct-Dec 2007 = 2
Total software downloads from Oct-Dec 2007 = 9596
Total web hits at the Help Desk website from Oct-Dec 2007 = 228,797
MOSES::MOBY – Code release to CPAN
PRESENTATIONS
MOBY presentation at the National Heart Lung and Blood Institute in Bethesda, MD on June 12, 2006.
Wilkinson M. (2006) The Institute for Genome Research (TIGR) BioMoby Applications and Training Workshop. April 2006 [workshop leader]
Wilkinson M. (2007) MOBY-DIC. Model Organism Database Interface Conference. Vancovuer, BC, June 2-3, 2007 [host and organizer]
Wilkinson M. (2007) MOBY-DIC. Model Organism Database Interface Conference. Vancovuer, BC, June 2-3, 2007 [host and organizer]
Wilkinson M. (2007) The Institute for Genome Research (TIGR) BioMoby Applications and Training Workshop. May 2007 [workshop leader]
Wishart, D. Greiner, R. “Computational Approaches to Metabolomics: An Introduction” presented at Pacific Symposium on Biocomputing, August 2007.
Wishart, D. Greiner, R. “Computational Approaches to Metabolomics: An Introduction” presented at Pacific Symposium on Biocomputing, January 2007.
Wishart, D.S. “How Bioinformatics Helped Reveal the Human Metabolome” presented at InCOB 2007, Hong Kong, Aug 28. 2007
Moby workshop in Wageningen, Netherlands
OMII Presentation- Hinxton UK, Oct 6-10, 2008
OMII Presentation- Hinxton UK, Oct 6-10, 2008
Presentation to the University of Amsterdam, Netherlands
PUBLICATIONS
Knox C, Shrivastava S, Stothard P, Eisner R, Wishart DS. BioSpider: a web server for automating metabolome annotations. Pac Symp Biocomput. 2007:145-56.
Kuo B.Y.-L., Hentrich T, Good B.M., Wilkinson M.D. (2007) Tag clouds for summarizing Web search results. Proceedings of the World Wide Web Conference (WWW 2007), Banff, AB, May 2007, pp. 1203-1024
AssistedWorkflow Assembly for Life-SciencesWeb Service Composition in the BioMoby SemanticWeb Framework, JBI (under review)
“Bridging the gap between social tagging and semantic annotation: E.D. the Entity Describer, JBI (under review)”
Materi, M. Wishart, D.S. “Computational Systems Biology in Cancer: Modeling Methods and Applications” Gene Reg. Systems Biol. 1:91-110 (2007).
Wishart DS, Arndt D, Berjanskii M, Guo AC, Shi Y, Shrivastava S, Zhou J, Zhou Y, Lin G. PPT-DB: the protein property prediction and testing database. Nucleic Acids Res. 2008 Jan; 36 (Database issue): D222-9. Epub 2007 Oct 4.
Wishart DS, Knox C, Guo A, Cheng D, Shrivastava S, Tzur D, Gautam B, Hassanali M. DrugBank: A Knowledgebase for Drugs, Drug Actions and Drug Targets Nucleic Acids Res. 2008 Jan; 36 (Database issue): D901-6. Epub 2007 Nov 29.
Wishart, D.S. “Current Progress in Computational Metabolomics” Brief. Bioinform. 8:275-284. (2007).
Abtranikian G., Ruepp A., Gordon P.M.K., Ballschmiter M., Zibat A., Sensen C.W., Frishman D., Liebl W., Klenk H.-P. (2007) Rapid Access to genes of biotechnologically useful enzymes by partial genome sequencing: the thermoalkaliphile Anaerobranca gottscha
Froels S., Gordon P.M.K., Panlilio M., Duggin I.G., Bell S.D., Sensen C.W., Schleper C. (2007) Response of the hyperthermophilic archaeon Sulfolobus solfataricus to UV damage. Journal of Bacteriology
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 Biom
Soh J.*, Gordon P.M.K.*, Ah-Seng A.C., Turinsky A.L., Taschuk M., Borowski K., Sensen C.W. (2007) Bluejay: a Highly Scalable and Integrative Visual Environment for Genome Exploration. In: Proceedings of the IEEE Congress on services [The 1st IEEE Interna
Gordon P.M.K., Meng C., Cruz J., Wishart D., Halloran P., Sensen C.W. (2007) Simplicity and Parallelism for Emerging Application of Microarrays. Bioinformatics
BioMoby 1.0 Publication – Briefings in Bioinformatics, 2008
BioMoby Workflow Publication, Journal of Biomedical Informatics, 2008
Berjanskii MV, Wishart DS. Application of the random coil index to studying protein flexibility. J Biomol NMR. 2008 Jan;40(1):31-48. Epub 2007 Nov 6. PMID: 17985196
Wishart DS. Improving early drug discovery through ADME modelling: an overview. Drugs R D. 2007;8(6):349-62. Review. PMID: 17963426
OTHER
BIRCH Version 2.3
to June 2007 (as reported in the Interim Review)
Publications Arising Directly from the Innovation Centre

Refereed Papers
Berjanskii M.V., Neal S., Wishart D.S. (2006) PREDITOR: a web server for predicting protein torsion angle restraints. Nucleic Acids Research 34(Web Server issue):W63-W69
Berjanskii M.V., Wishart D.S. (2006) NMR: prediction of protein flexibility. Nature Protocols 1(2): 683-688
Berjanskii M.V., Wishart D.S. (2007) The RCI server: rapid and accurate calculation of protein flexibility using chemical shifts. Nucleic Acids Research [in press]
Cruz J.A., Wishart D.S. (2006) Applications of machine learning in cancer prediction and prognosis. Cancer Informatics 2:59-67
Dong A., Turinsky A.L., Ah-Seng A.C., Taschuk M., Gordon P.M.K., Hochauer K., Fröls S., Soh J., Sensen C.W. (2007) Enhancing Bluejay with scalability, genome comparison, and microarray visualization. In: Decker R., Lenz H.-J. [eds.] Advances in Data Analysis (GfKl 2006 Conference Proceedings). Springer, Berlin–Heidelberg, pp. 557-568
Famulski K.S., Einecke G., Reeve J., Ramassar V., Allanach K., Mueller T., Hidalgo L.G., Zhu L.F., Halloran P.F. (2006) Changes in the transcriptome in allograft rejection: IFN-gamma-induced transcripts in mouse kidney allografts. American Journal of Transplantation 6(6):1342-1354
Fristensky B. (2007) BIRCH: A user-oriented, locally-customizable, bioinformatics system. BMC Bioinformatics 8:54
Fröls S., Gordon P.M.K., Panlilio M., Sensen C.W., Schleper C. (2007) Elucidating the transcription cycle of the UV-inducible hyperthermophilic archaeal virus SSV1 by DNA microarrays. Virology 15:48-59
Good B.M., Kawas E.A., Kuo B.Y.-L., Wilkinson M.D. (2006) iHOPerator: user-scripting a personalized bioinformatics Web, starting with the iHOP website. BMC Bioinformatics 7(1):534
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. 2007 IEEE Conference on Bioinformatics and Biomedicine [submitted]
Gordon P.M.K., Meng C., Cruz J.A., Wishart D.S., Halloran P.F., Sensen C.W.(2007) Addressing computational challenges in the clinical diagnostic application of microarrays. Bioinformatics [submitted]
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, Soliman M.A., Bose P., Trinh Q., Sensen C.W., Riabowol K. (2007) Interspecies data mining to predict novel protein-protein interactions in human. Genome Research [submitted]
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
Gordon P.M.K., Weinel C., Carsten J., Kampf U., Kriventseva E., Sensen C.W. (2006) Creating hierarchical models of protein families based on expressed sequence tags: the ‘Sprockets’ analysis pipeline. Analytica Chimica Acta 564(1):123-132
Halloran P.F., Reeve J., Kaplan B. (2006) Lies, damn lies, and statistics: the perils of the P value. American Journal of Transplantation 6(1):10-11
Kawas E., Senger M., Wilkinson M. D. (2006) BioMoby extensions to the Taverna workflow management and enactment software. BMC Bioinformatics 7(1):523
Knox C., Shrivastava S., Stothard P., Eisner R., Wishart D.S. (2007) BioSpider: A Web server for automating metabolome annotations. Pacific Symposium on Biocomputing 12:145-156
Liapounova N.A., Hampl V., Gordon P.M.K., Sensen C.W., Gedamu L., Dacks J.B. (2006) Reconstructing the mosaic glycolytic pathway of the anaerobic eukaryote monocercomonoides. Eukaryotic Cell 5(12):2138-46
Montgomerie S., Sundararaj S., Gallin W.J., Wishart, D.S. (2006) Improving the accuracy of protein secondary structure prediction using structural alignment. BMC Bioinformatics 7(1):301
Murata J., Bienzle D., Brandle J.E., Sensen C.W., De Luca V. (2006) Expressed sequence tags from Madagascar periwinkle (Catharanthus roseus). FEBS Letters 580:4501-4507
Neal S., Berjanskii M., Zhang H., Wishart D.S. (2006) Accurate prediction of protein torsion angles using chemical shifts and sequence homology. Magnetic Resonance in Chemistry 44(S1):158-167
Poulin B., Eisner R., Szafron D., Lu P., Greiner R., Wishart D.S., Fyshe A., Pearcy B., MacDonell C., Anvik J. (2006) Visual explanation of evidence in additive classifiers. Proceedings of the 18th Conference on Innovative Applications of Artificial Intelligence (IAAI-06), Boston, MA, July 2006. pp. 1822-1829
Riley M., Abe T., Arnaud M.B., Berlyn M.K., Blattner F.R., Chaudhuri R.R., Glasner J.D., Horiuchi T., Keseler I.M., Kosuge T., Mori H., Perna N.T., Plunkett G. 3rd, Rudd K.E., Serres M.H., Thomas G.H., Thomson N.R., Wishart D.S., Wanner B.L. (2006) Escherichia coli K-12: a cooperatively developed annotation snapshot—2005. Nucleic Acids Research 34(1):1–9
Soh J., Gordon P.M.K., Ah-Seng A., Turinsky A., Taschuk M., Borowski K., Sensen C.W. (2007) Bluejay: a highly scalable and integrative visual environment for genome exploration. Proceedings of 2007 IEEE Congress on Services (Services 2007), Salt Lake City, UT, July 2007, pp. 92-98.
Song Y.C., Kawas E., Good B.M., Wilkinson M.D., Tebbutt S.J. (2007) DataBiNS: a BioMoby-based data mining workflow for biological pathways and non-synonymous SNPs. Bioinformatics (Advance Access published January 24, 2007)
Stothard P., Wishart D.S. (2006) Automated bacterial genome analysis and annotation. Current Opinion in Microbiology 9(5):505-510
Wang C., Gordon P.M.K., Turinsky A.L., Burgess J., Dalton T., Sensen C.W. (2007) Combining a high-throughput bioinformatics grid and bioinformatics Web Services. In: Dubitzky W., Schuster A., Sloot P.M.A., Schroeder M., Romberg M. [eds.] Distributed, High-Performance and Grid Computing in Computational Biology (GCCB 2006 Conference Proceedings). Springer, Berlin-Heidelberg, pp. 1-10
Wilkinson M. (2006) Gbrowse Moby: A Web-based browser for BioMoby Services. Source Code for Biology and Medicine 1(1):4
Wishart D.S. (2006) Drug-target discovery in silico: using the Web to identify novel molecular targets for drug action. In: Parrington J., Coward K. [eds.] Comparative genomics and Proteomics in Drug Discovery. Taylor and Francis, Abingdon, UK, pp. 145-176
Wishart D.S. (2007) In silico drug exploration and discovery using DrugBank. Current Protocols in Bioinformatics 14.4.1-14.4.32 [in press]
Wishart D.S. (2007) Introduction to cheminformatics. Current Protocols in Bioinformatics 14.1.1-14.1.8 [in press]
Wishart D.S. (2006) Metabolism and metabolic disease resources on the web. In: Scriver, Beaudet, Sly, Valle, Vogelstein, Kinzler, Childs [eds.] Online Molecular and Metabolic Basis of Inherited Disease – OMMBID. John Wiley & Sons, New York, Chapter 3.1
Wishart D.S., Greiner R. (2007) Computational approaches to metabolomics: an introduction. Pacific Symposium on Biocomputing 112-114
Wishart D.S., Knox C., Guo A., Shrivastava S., Hassanali M., Stothard P., Woolsey J. (2006) DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Research 34 (Database issue):D668-D672
Wishart D.S., Tzur D., Knox C., Eisner R., Guo A.C., Young N., Cheng D., Jewell K., Arndt D., Sawhney S., Fung C., Nikolai L., Lewis M., Coutouly M.A., Forsythe I., Tang P., Shrivastava S., Jeroncic K., Stothard P., Amegbey G., Block D., Hau D.D., Wagner J., Miniaci J., Clements M., Gebremedhin M., Guo N., Zhang Y., Duggan G.E., Macinnis G.D., Weljie A.M., Dowlatabadi R., Bamforth F., Clive D., Greiner R., Li L., Marrie T., Sykes B.D., Vogel H.J., Querengesser L. (2007) HMDB: the Human Metabolome Database. Nucleic Acids Research 35(Database issue):D521-D526
Zhang N., Chen R., Young N., Wishart D.S., Winter P., Weiner J.H., Li L. (2007) Comparison of SDS- and methanol-assisted protein solubilization and digestion methods for Escherichia coli membrane proteome analysis by 2-D LC-MS/MS. Proteomics 7(4):484-93
Zulak K.G., Cornish A., Daskalchuk T.E., Deyholos M.K., Goodenowe D.B., Gordon P.M.K., Klassen D., Pelcher L.E., Sensen C.W., Facchini P.J. (2006) Gene transcript and metabolite profiling of cultured opium poppy cells reveals the integrated biochemical machinery of an alkaloid factory. Planta 225:1085-1106

Abstracts/Notes
Fristensky B. (2006) Bioinformatics on Solaris x64. Sun Computational Biology Special Interest Group Newsletter, May 26, 2006

Invited Presentations
Fristensky B. (2006) Advanced Computational Genomics Course (ACGC). Winnipeg, MB, September 8 – 14, 2006
Sensen C.W. (2006) From 2D to 4D bioinformatics. GfKl 2006, Berlin [invited semi-plenary lecture]
Sensen C.W. (2006) From 2D to 4D bioinformatics. Canadian Food Inspection Agency (CFIA), Lethbridge, AB, 2007
Wilkinson M. (2006) Bio Data. Microsoft eScience Workshop, Johns Hopkins University, October 12 – 15, 2006 [session chair]
Wilkinson M. (2007) Brains needed, donations welcome! Alberta Agricultural Genomics and Biotechnology Workshop, March 18-21, 2007
Wilkinson M. (2006) Brains! Need more BRAINS! How would zombies create the life sciences Semantic Web? Fourth Canadian Workshop on Plant Genomics, Ottawa, ON, June 19-22, 2006
Wilkinson M. (2006) Collaborative science platforms. Microsoft Faculty Summit, Microsoft Campus, Redmond, WA, July 16-18, 2006
Wilkinson M. (2006) Hands-on tutorial for BioMoby and Taverna high-throughput analyses. Advancing Practice, Instruction, and Innovation through Informatics; Advances in Oncology and Pathology Informatics Meeting, Vancouver, BC, August 16, 2006 [workshop leader]
Wilkinson M. (2006) Knowledge for the masses, from the masses. Microsoft eScience Workshop, Johns Hopkins University, October 12-15, 2006
Wilkinson M. (2006) Mass-collaborative approaches to the Semantic Web. Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, December 2-5, 2006
Wilkinson M. (2006) MOBY & Ontologies. Canadian Workshop on Plant Genomics, Ottawa, ON, June 20, 2006 [plenary talk]
Wilkinson M. (2007) MOBY-DIC. Model Organism Database Interface Conference. Vancovuer, BC, June 2-3, 2007 [host and organizer]
Wilkinson M. (2006) MOBY presentation. National Heart Lung and Blood Institute, Bethesda, MD, June 12, 2006
Wilkinson M. (2006) MOBY presentation. S-MOBY Developers Meeting, Santa Fe, NM, June 8, 2006
Wilkinson M. (2006) The Institute for Genome Research (TIGR) BioMoby Applications and Training Workshop. April 2006 [workshop leader]
Wilkinson M. (2007) The Institute for Genome Research (TIGR) BioMoby Applications and Training Workshop. May 2007 [workshop leader]
Wishart D.S. (2006) A new strategy for disease diagnosis. U of A Alumni Association Meeting, Edmonton, AB, April 20, 2006
Wishart D.S. (2006) Nanotechnology – a new direction for Alberta. Edmonton Professional Business (ProBus) meeting, Edmonton, AB, October 24, 2006
Wishart D.S. (2006) NMR, structural genomics and metabolomics – what’s the connection. 6th Annual Protein Structure Initiative Bottlenecks Workshop, Bethesda, MD, April 14, 2006
Wishart D.S. (2006) Novel bioinformatics systems. IBM Centre for Advanced Studies (CAS) Board Meeting, Edmonton, AB, November 29, 2006
Wishart D.S. (2006) Perl and Perl programming in Bioinformatics. Advanced Computational Genomics Course (ACGC), Winnipeg, MB, September 10, 2006 [lecture]
Wishart D.S. (2006) Protein structure analysis and protein-protein interactions II. National Human Genome Research Institute (NHGRI), Bethesda, MD, October 15, 2006
Wishart D.S. (2006) Proteomics and informatics: the fundamentals. Advancing Practice through Instruction, Innovation, and Informatics Conference (APIII 2006), Vancouver, BC, August 17, 2006

Posters
Cheng D., Zhang H., Young N., Damaraju S., Wishart D.S. (2006) PolySearch: a web based system integrating pubmed, human genome data and primer design tools for management of pharmacogenomic projects. 6th International Conference of the Canadian Proteomics Initiative, May 10-12, 2006
Cheng D, Zhang H, Young N, Knox C, Stothard P, Damaraju S, Wishart D.S. (2006) PolySearch: a Web based text mining system for extracting relationships between diseases, genes, mutations, drugs and metabolites. Alberta Cancer Board’s Annual Research Meeting, Banff, AB, November 7-9, 2006
Coutouly, M., Maiti, R., Montgomerie, S., Langen, C., Wishart, D.S. (2006) A method to determine protein structures with minimal information. 6th International Conference of the Canadian Proteomics Initiative, Edmonton, AB, May 10-12, 2006
Cruz J., Wishart D.S., Meng C., Soong K., Yeh E. (2006) A laboratory information management system for transcriptomics. 6th International Conference of the Canadian Proteomics Initiative, Edmonton, AB, May 10-12, 2006
Eisner R., Knox C., Cheng D., Greiner R., Wishart D.S. (2007) Text analysis in the Human Metabolome Project. 3rd Annual Meeting of the Metabolomics Society, Manchester UK, June 11-14, 2007
Eisner R., Knox C., Greiner R., Wishart D.S. (2006) Predicting chemical properties of small molecules. Second Annual Metabolomics Symposium: Exploring the Human Metabolome, University of Alberta, October 12, 2006
Fristensky B. (2006) How to build an in-house bioinformatics system tailored to your local user community. Plant and Animal Genome XVI Conference, San Diego, CA, January 18, 2006 [poster and computer demo]
Fung C., Tang P., Wishart D.S. (2006) Systems biology using SimCell. 6th International Conference of the Canadian Proteomics Initiative, Edmonton, AB, May 10-12, 2006
Liu Y., Fyshe A., Lu P., Szafron D., Greiner R., Wishart D.S., Pearcy B., Poulin B., Eisner R., Ngo D., Lamb N. (2007) Proteome Analyst: machine learning for protein annotation. CPI 2007 Meeting, Ottawa ON, June 16-18, 2007
Mongomerie S., Cruz J., Shrivastava S., Arndt D., Berjanskii M., Wishart D.S. (2007) Proteus2: A Web server for comprehensive protein structure prediction and structure-based annotation. CPI 2007 Meeting, Ottawa ON, June 16-18, 2007
Montgomerie S., Sundararaj S., Gallin W.J., Wishart D.S. (2006) Secondary structure prediction at 88% accuracy. 6th International Conference of the Canadian Proteomics Initiative, Edmonton, AB, May 10-12, 2006
Sissons P., Kawas E., Senger M., Wilkinson M.D., Wishart D.S. (2007) BioMoby extensions to the Taverna workflow management and enactment software. CPI 2007 Meeting, Ottawa ON, June 16-18, 2007
Tang P., Arndt D., Cruz J., Yang R., Fung C., Wishart D.S. (2007) Dynamic cellular automata: an alternative approach to cellular simulation. CPI 2007 Meeting, Ottawa ON, June 16-18, 2007
Wopereis S., Van Ommen B., Gibney M., Gibney S., German B., Knox C., Cheng D., Wishart D.S., Querengesser L. (2006) Development of the public wiki nutritional metabolomics biology database: NuGOwiki. 3rd Annual Metabolomics Conference, Boston, MA, June 2006
Xia J., Magor K., Wishart D.S. (2006) EST analysis step-by-step. 6th International Conference of the Canadian Proteomics Initiative, Edmonton, AB, May 10-12, 2006
Young N., Jewell K., Block D., Knox C., Tang P., Greiner R., Wishart D.S. (2006) MetaboLIMS: a general laboratory information management system for metabolomics. 3rd Annual Scientific Conference for the Metabolomics Society, Boston, MA, June 2006
Zhou J., Shi Y., Lin G., Wishart D.S. (2007) A contact order prediction method. CPI 2007 Meeting, Ottawa ON, June 16-18, 2007
Publications Arising from Collaboration or through Service

Refereed Paper
Good B.M., Wilkinson M.D. (2006) The life sciences Semantic Web is full of creeps! Briefings in Bioinformatics 7(3):275-286
Abstracts/Notes
Good B.M., Wilkinson M.D. (2007) Ontology engineering using volunteer labor, Proceedings of the World Wide Web Conference (WWW 2007), Banff, AB, May 2007
Kuo B.Y.-L., Hentrich T, Good B.M., Wilkinson M.D. (2007) Tag clouds for summarizing Web search results. Proceedings of the World Wide Web Conference (WWW 2007), Banff, AB, May 2007, pp. 1203-1024
Invited Presentation
Wilkinson M. (2006) The semantic web in cardiovascular sciences. The National Heart Lung and Blood Institute Cardiovascular Ontologies Working Group Meeting, Bethesda, MD, June 11-12, 2006