VECTORBASE: BIOLOGICAL
CYBERINFRASTRUCTURE FOR RESEARCH ON
INVERTEBRATE VECTORS OF HUMAN
PATHOGENS
VectorBase Development Virtual Organization
Arensburger, P., Atkinson, P., Besansky, N.J., Bruggner, R.V., Butler, R., Campbell, K.S., Christophides, G.K., Christley,
S., Dialynas, E., Emmert, D., Hammond, M., Hill, C.A., Kennedy, R.C., Konopinski, N., Lanzaro, G., Lawson, D., Lee,
Y., Lobo, N.F., MacCallum, R.M., Madey, G., Megy, K., Meyer, J., Russo, S., Redmond, S., Taylor, C., Severson, D.W.,
Stinson, E.O., Topalis, P., Zdobonov, E., Birney, E., Gelbart, W.M., Kafatos, F.C., Louis, C. and Collins, F.H.
UC Riverside, Notre Dame, Harvard, Imperial College London, Institute of Molecular Biology & Biotechnology -
Crete, European Bioinformatics Institute (EMBL-EBI), UC Davis, Purdue University, UC Los Angeles, Swiss
Institute of Bioinformatics
Presented by Greg Madey
Computer Science & Engineering
University of Notre Dame
IWPLS'09 - International Workshop on Portals for Life Science e-Science Institute
Edinburgh, Scotland, UK
September 2009

• Team Science
• Bandwidth
• Multidisciplinary Research Teams • Cheap storage
• Distributed Teams & Resources
• Lot’s of data: sensor-nets, high throughput sequencing, data capture technologies
• Big Science (cost => must share resources) • Fast chips
• Because we can - enablers =>
• Middleware / Collaboration tools
• Open source / open access
Benefits: Accelerating Research Productivity

• Shared Data
• Computational Tools
• Collaboration Tools
• Distributed
Development &
Curation Team
• Community
Contributions
• World Wide User
Base

• Sponsored by the U.S. National
Institute of Allergy and Infectious
Diseases (NIAID)
• A Bioinformatics Resource Center to collect, store, display, annotate, query, analyze, and update genomics and related data related to the NIAID Category A-C priority pathogens and emerging or re-emerging infectious diseases transmitted by vectors.
!

Malaria

Yellow and Dengue fever

Lymphatic filariasis (Elephantiasis), West Nile Virus

Lyme disease

Typhus

Glossina morsitans morsitans (tsetse fly)
African sleeping sickness (trypanosomiasis)

Chagas' disease

• Lutzomyia longipalpis (sand fly) => Leishmaniasis
• Phlebotomus papatasi => Leishmaniasis
• Simulium damnosum (black fly) => Onchocerciasis (river blindness)
• Xenopsylla cheopis (oriental rat fly) => Bubonic plague (black death) and murine typhus
• Additional mosquitos, ticks and mites

• Genomics
• Expression Data
• Proteomics
• Metabolic Pathways
• Epidemiology
• Population Genetics
• Genotype/Phenotype
Association Data
• Resistance Data
• Epigenomics
• EST Data Sets
• Controlled vocabularies/
Ontologies
• Images
• Documents
• Publications/Citations
• Resource Links
• News/Jobs/Announcements

BIOINFORMATICS
TOOLS
Analysis
Search
Data Browsers
Integration & Pipelines

•
Project Management Wiki • Skype
• Mail Lists (over 25) with web archives
• Help Wiki
• Developers documentation wiki
• Telephone conference calls
(up to 25 callers)
• Chat / Instance messaging
• Bulletin boards (forums)
• Opinion polls/meeting scheduling (Doodle)
• Bug tracker (Bugzilla)
• Trouble ticket system (RT)
• Streaming video - tutorials

Web Archived

!
Ensembl browser – Blue fields in the above figure (outlined in red) display data retrieved from remote DAS servers; see also the popup window with additional details.

ClustalW aand HMMER also available
!

!
The BioMart ‘data mining’ tool is deployed at VectorBase.org to enable easy export of gene information

Unique Visits Per 6 Month Interval
30000
22500
15000
7500
0
1st Half 2006 2nd Half 2006 1st Half 2007 2nd Half 2007 1st Half 2008 2nd Half 2008 1st Half 2009
Six Month Interval
Growth in Unique Visits (by IP Address) to the
VectorBase BRC Web Site per 6-Month Interval

• VectorBase Portal focus => Data and data mining (search)
• Virtual Organization of Developers
• Virtual Organization of Users (Community Contributions =>
Gene Models, Publications, Controlled Vocabulary Terms, &
Comments)
• Tools to support distributed development of the portal
• Community building activities

Acknowledgements
VectorBase Team
NIAID (contract HHSN266200400039C)
Notre Dame Eck Institute for Global Health
Questions http://www.vectorbase.org