BOLD Systems

Adelaide Barcode Conference, November 2011

Overview

The Barcode of Life Data Systems (BOLD) was established in 2005 with a mandate to provide informatics tools and databases in support of researchers building libraries of DNA barcodes - short standardized DNA sequences used to identify organisms. Over the past few years, BOLD has grown to become a powerful online workbench and the central informatics hub for the generation and publication of DNA barcodes. Visit the BOLD Systems site for more details.

During the conference BOLD v3.0 beta will be released. This site can be found at v3.boldsystems.org.

4th International Barcode of Life Conference

The University of Adelaide will host the first-ever Southern Hemisphere barcode conference, co-organized by CBOL and co-hosted by several biodiversity institutions and initiatives in Australia. The goals of the conference are: highlighting the great progress barcoding has made since the Mexico City Conference in November 2009; learning about barcoding activities in Australia and the region; and bringing barcoders together to exchange ideas and plan new activities. The conference takes place from November 30th to December 3rd, 2011 with two days of pre-conference activities on November 28th and 29th. View the conference site for more information.

Staff from BOLD will be attending the conference to conduct a pre-conference workshop on Informatics, provide support via a conference booth, and present new research and initiatives for DNA barcoding during the conference sessions. The launch of the newest version of BOLD (BOLD v3.0 beta) will also take place at the conference. Below are further details on the activities and events that we will be involved in.

Adelaide

Workshop

The pre-conference workshop on Informatics will be held on Monday, November 28th in Napier Hall.

The workshop will have an overview of BOLD v3.0 beta features and example uses. The morning session will cover introductory level topics to help new users get started on BOLD, showcase new features and functionality available in BOLD v3.0 beta, and demonstrate workflows for standard uses. Experienced users should take advantage of the refresher and gain knowledge of new functionality. The afternoon sessions will consist of domain specific presentations followed by mirror partners and other informatics tools and workflows.

Attendance to the first session requires an understanding of sequence analysis and some experience generating barcode data. The second session requires experience using BOLD to manage barcode projects. For the third session, having some technical knowledge of databases would be beneficial.

The following is the agenda for the workshop. Click on the titles to access to the slideshare video and audio for the talks.

Time	Title of Talk	Presenter(s)
Session 1: Introductory Level Topics
9:00 AM	Workshop Overview	Sujeevan Ratnasingham (BOLD)
9:00 AM	BOLD 3.0: an introduction An introduction to the the BOLD platform and a brief overview of the latest version of the online software. BOLD has become the primary data collection platform for the DNA barcoding community, providing the necessary databasing and analytical tools to build barcode libraries that meet community standards. The latest version of the system, v3.0 beta, provides significant advances in data management and curation. It supports more complex data collection and publication workflows allowing for community curation and rapid release of barcode data.	Sujeevan Ratnasingham (BOLD)
9:20 AM	Managing Barcode Data Library Generation This presentation will lay out steps for packaging and submitting data to BOLD and provide a walk through of data management and validation features. Attendees will gain an understanding of key BOLD features and how they assist in the building of barcode libraries. Key points that will be covered are: formatting specimen data, building BOLD compliant trace and image packages, uploaded sequences, organizing and sharing data.	Megan Milton and Mallory Van Wyngaarden (BOLD)
9:40 AM	Barcode Data Life-cycle BOLD is more than a storage facility. Uploaded barcode sequences are useful right away, but they can become even more valuable later. This presentation explains how to track the progress of your sequences, maintain and improve data quality in your projects, and use shared and public data to help you plan your next research project.	Dr. Julie Stahlhut (BIO)
10:00 AM	Data Sharing/Collaboration and Publication using BOLD This presentation will describe the use of BOLD in collaborative projects and publication of barcode data. Specifically, it will show how a project manager can give access to the project to his/her collaborators, depict the different roles and levels of access to data that collaborators can have, emphasize the usefulness of interacting through BOLD in barcoding collaborative projects, and explain the functions of BOLD related to the publication of the data. The project to barcode the birds of Southern South America will be used as an example.	Dr. Dario Lijtmaer (MACN)
10:10 AM	Plant Barcoding Data Workflow The steps involved in handling sequence data for plants are similar to those for other major lineages, but there are some key steps that are critical for users generating plant data. The processes involved in editing raw sequence data (primer trimming, data alignment, handling gaps, and detecting pseudo genes) will be reviewed. BOLD v3.0 beta features such as batch BLAST, and use of the Taxon ID tree as tools to detect contaminants or misidentified samples will be discussed.	Dr. Aron Fazekas (BIO)
10:30 AM	Coffee Break
11:00 AM	Data Standards: making every barcode count! With respect to species recognition at the molecular level, DNA Barcoding differs from prior art because of the emphasis placed on the evidence used to construct reference sequence libraries as a basis for the identification of unknowns. Previous approaches relied primarily on couplets of <species name_DNA sequence> as the basis of a lookup table, but both of these elements are assertions and without reference to underlying evidence, are of limited utility. Barcoding addresses this issue by extending the lookup table to include information about the primary evidence upon which these assertions rest (voucher specimen+electropherogram 'trace' file). This, in combination with the selection of standard barcoding loci and the reporting of other key meta-data elements provide a sound basis for molecular diagnostic applications. This talk will summarize current community-based standards and their ongoing evolution.	Dr. Robert Hanner (BIO)
11:20 AM	Bioinformatics Applications The BOLD workbench and the barcode library it contains are an excellent resource, not only for biodiversity science, but also for studying genomics, proteiomics, and molecular evolution among many other fields. This talk will provide a brief overview of some of the varied applications of barcode data as well as instruction in how to use BOLD to facilitate such research. BOLD v3.0 beta offers several different workflows for analyzing and extracting sequence data in ready to use formats.	Dr. Justin Schonfeld (BOLD)
11:40 AM	Campaigns on BOLD Over the past years, researchers with shared interests have started campaigns to collate and share information on the collection and registration of DNA barcodes from specific taxonomic groups or geographical regions. This talk will use the example of a developing campaign to demonstrate the utility of BOLD's workbench structure to organize a campaign project. Furthermore, we will show how BOLD's external connectivity tools can be used to disseminate information and organize campaign efforts.	Dr. Robert Hanner and Dr. Dirk Steinke (BIO)
12:00 AM	Live Demos and Q&A period
12:30 PM	Lunch Break
Session 2: Domain Specific Studies
2:00 PM	Sessions Introduction	Sujeevan Ratnasingham (BOLD)
2:05 PM	Ecological Studies I will review several of the key ways that BOLD is revolutionizing ecological research. Foremost among these is that BOLD assigns individuals to genetic clusters or BINs (Barcode Index Numbers), which can be used as an interim species-level taxonomic system for the purposes of many types of ecological analysis. This allows species-level ecological questions to be addressed immediately without morphological identification of specimens, long recognized as a major impediment of ecological research (especially for the study of hyper-diverse groups of invertebrates and larval life stages). Randomized BIN accumulation curves are available within BOLD itself, while other types of analyses (such as statistics to estimate total diversity or composition overlap among sites) can be performed in external software based on the BINs. I highlight the usage of BOLD for ecological research using examples of real datasets from arctic Canada.	Dr. Sarah Adamowicz (BIO)
2:20 PM	Regulatory Datasets This contribution will demonstrate the evolution from a standard experimental dataset to a project that contains records applicable to regulatory decisions based on adequately authenticated standards and/or scientific publication. This talk showcases analytical features as well as management tools available on BOLD that aid in the assembly of records that meet the various standards needed for publication of DNA barcode data and regulatory decisions bases on those.	Dr. Dirk Steinke (BIO)
Session 3: Mirrors and Data Partners
2:40 PM	EU BOLD Mirror & Fungal Barcoding The EU BOLD mirror is using the BioloMICS software to manage and analyse data. BioloMICS is a tool allowing specialized and scientific biological databases to be created dynamically. Any data can be recorded, analysed and published. A broad base of users such as taxonomists, ecologists, human, animal or plant pathologists, molecular biologists, pharmacists or industrial researchers are using it on a diversity of organisms (viruses, bacteria, fungi, plants, insects to animals). No prior knowledge of either databasing or programming is required. A number of tools for data retrieval and analysis are also included in the system, including a LIMS system for the management of sequences. Please visit the BioloMICS webpage for more information.	Dr. Vincent Robert (CBS)
3:10 PM	BOLD Mirror Setup Global Mirror System of DNA Barcode Data (GMS-DBD, www.boldmirror.net). GMS-DBD is designed and currently served as a system for the presentation and analysis of DNA barcode data, but not for the management of barcoding projects. It has three main functions including data synchronization, data presentation, and statistics and analysis. Data synchronization module features to obtain data from BOLD and to distribute data to mirror sites.	Dr. Di Liu (CAS)
3:30 PM	Coffee Break
4:00 PM	Submitting to GenBank Submission of Barcode sequence data to INSDC (DDBJ/ENA/GenBank) is one of the requirements of the Barcode data standard. An overview of submission requirements, tools and validations suites that have been built for Barcode submitters will be presented to assist users in creating submissions for GenBank. Please visit the BarSTool site for more information.	Dr. Ilene Mizrachi (NCBI)
4:10 PM	EMBL: European Molecular Biology Laboratory The EMBL Nucleotide Sequence Database (also known as EMBL-Bank) constitutes Europe's primary nucleotide sequence resource. Main sources for DNA and RNA sequences are direct submissions from individual researchers, genome sequencing projects and patent applications.	Dr. Guy Cockrane
4:20 PM	Barcode of Life Data Portal The Barcode of Life Data Portal (BDP) provides an online collection of tools for barcode data analysis. Please visit the site at bol.uvm.edu	Dr. David Schindel and Mike Trizna (CBOL)
4:40 PM	Managing your Barcoding Data with Geneious and the Biocode LIMS The Biocode Laboratory Information Management System is a free plugin to the Geneious sequence analysis tool. The plugin manages your lab workflow, from extraction through to sequence analysis and database submission. Learn how to use the Biocode LIMS to speed up your data processing by quickly tracking down errors, automating your analysis pipeline, and automatically generating submissions to barcode databases.	Steven Stones-Havas (Geneious)
5:00 PM	Question and Answer Period
5:30 PM	Adjourn

Booth

Two adjacent booths in Bonython Hall have been reserved for BOLD during the conference (November 30 - December 3). They will be occupied by staff during conference hours and breaks. Information pamphlets and in-person tutorials will be available at the booth.


	Bonython Hall		Floor Plan

Clinics

We will also offer two clinics, providing hands-on training for those interested. To sign up for the clinics, please email info@boldsystems.org.

	Date	Time	Location	Topics
	Friday, December 2	1pm-2pm	Napier Hall, room 210	Uploading Specimen Data, Images and Sequences; Analyzing Data with BOLD v3.0 beta
	Saturday, December 3	1pm-2pm	Napier Hall, room 210	TBA

Communication

The following BOLD staff will be attending the conference. Please feel free to find us at our booth in Bonython Hall.

Sujeevan Ratnasingham Director of Informatics Sujeevan is the lead architect of BOLD, and the creator of the system. He oversees the development of new functionality on BOLD and is heavily involved in requirements gathering activities. He's also involved with the establishment of data standards and data exchange protocols for barcode data.	Megan Milton Data and Communication Lead Megan handles communications and broadcasts for the BOLD team, as well as coordinating the efforts of the data managers. She joined the BOLD team in 2006 as a data manager, and has lead the data management team for the past 3 years. Her major projects with BOLD have included the online and print documentation for use of functions and tools (The BOLD Handbook) and coordinating BOLD workshops and training initiatives. Follow Megan on Twitter!
Catherine Wei Programming Lead Catherine joined the BOLD team in 2010 as a programmer and was recently appointed as the lead, coordinating efforts of the programming team. Catherine's background in bioinformatics and proteomics allowed her to quickly get involved with analytics development at BOLD. Her most recent contribution includes development on BOLD version 3.0 beta.	Justin Schonfeld Analytics Lead and Postdoctoral Fellow Justin joined the Biodiversity Institute of Ontario in 2008 as a research fellow studying novel applications for barcode data. Recently, he was appointed as the lead of the BOLD analytics team and charged with integrating newly developed analytical methods for ecology, genetics, and biodiversity into the BOLD workbench. Current research focuses on the taxonomically broad analysis of variation in amino acids, indels, and genetic codes made possible by DNA barcode data.
Mallory Van Wyngaarden Data Manager and Outreach Assistant As a data manager, Mallory validates and uploads batch submissions as well as provides user support. She has been with BOLD for over a year and a half and recently joined the Communications and Outreach team to support educational barcoding initiatives as well as geographical barcode surveys, most notably the National Ecological Observatory Network. Mallory's most recent contribution has been developing workflows for educators using BOLD. Follow Mallory on Twitter!	Eddie Ma Ph.D. Candidate Eddie is currently doing his Ph.D. in Computer Science at the University of Guelph. As part of his thesis, he is developing an automated pipeline for the assembly of barcode sequences from raw trace files using machine learning methods.

Social Media

We will be using social media tools to get feedback, respond to questions and provide updates on our activities at the conference. Please also feel free to contact us via email at ">info@boldsystems.org.

	Follow us on Twitter!	@BOLDteam
	Join our group on Connect!	BOLD Group
	Like us on Facebook!	BOLDsystems