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Costal Marine Biolabs - Ventura, California 2011

Barcoding talk to students of CMBL

Sujeevan Ratnasingham

on 11 March 2013

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Transcript of Costal Marine Biolabs - Ventura, California 2011

DNA Barcoding & The Barcode of Life Data System Sujeevan Ratnasingham Bioinformatics (bī-ō-in-fr-ma-tiks) the collection, classification, storage, and analysis of biochemical and biological information using computers especially as applied in molecular genetics and genomics Collect Interpret Apply Animal Cell Plant Cell Mitochondria Chloroplast Barcodes for Animals & Plants Astraptes fulgerator Astraptes fulgerator Adult Walch 1775 Data Collection & Integration About me.. Inaugural Meeting - 2007 International Barcode Of Life (iBOL) International Involvement Launch - 2010 Global Coverage - Local Effort 1.3M Specimens Barcoded from 100K Species Enright A.J., Van Dongen S., Ouzounis C.A. An efficient algorithm for large-scale detection of protein families, Nucleic Acids Research 30(7):1575-1584 (2002).

Stijn van Dongen. Graph clustering via a discrete uncoupling process. Siam Journal on Matrix Analysis and Applications 30-1, p121-141, 2008.

Ratnasingham and Hebert, 2011 in prep. Cataloging Life Through DNA(beta) 250 Years of Registering Life Application of BINs Thank You Registering Life Through DNA Registering Life Through DNA Registering Life Through DNA(beta) Carr et al. 2010 in prep. Acknowledgements:
Paul D.N. Hebert
Daniel Janzen
Scott Miller
Colleagues at BIO
Collaborators at CBOL Team Members:
Megan Milton
Taika von Konigslow
Lily Abraham
James Robertson
Catherine Wei
Dana Rea
Danny Roes
Many others Long Tail of Biodiversity Frequency of Human Contact Species Bioinformatics Chasm (Specimens & Sequences)
Mobilization of large interdisciplinary teams
Varied workflows – data standards
Data privacy
Integration of Sequencing Facilities Informatics Challenges Use Activity 17,000 - Identification Service
5,800 - NJ Tree Builder
623 - Other Analytics (Top 5 tools) as of Feb 2011 Community Resource Analytical Requests “More and more often these days, a research project’s success is measured not just by the publications if produces, but also be the data it makes available to the wider community. Pioneering archives such as GenBank have demonstrated just how powerful such legacy data sets can be for generating new discoveries – especially when data are combined from many laboratories and analyzed in ways that the original researchers could not have anticipated.” “Data’s Shameful Neglect” in Nature. Vol. 461, Issue 7621, 10 September 2009, p. 148. Data Release Data Dissemination & Services Identification Engine*
Taxon Pages
Specimen Pages
Primer Registry
Electropherogram Repository
Web Service API Data Partners Sept 2010: 1.3M - Specimen records
999K - DNA barcodes
2.1M - Trace electropherograms
750K - Specimen images
900K - Occurrence records
230 - Countries

2.4K - Collections (personal/lab and formal collections) Data Storage Workbench Data Management Data Analysis Project based
Combine records as necessary
Password protected
Live reporting
Compute cluster supported Commonly Shared Data
Data Sharing Framework
Granular Permissions

Structured Campaigns Campaign Management Collaboration Framework Developing Collaborative Linkages Study of Biodiversity Species Directory 2005 500K Species
5M Specimens
26 Nations Barcoding Workflow (Walch 1775) {Two Barred Flasher} Climate Change Land Use & Development Biodiversity Data
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