Pre-Conference Training

Participants in the Adelaide Barcode Conference will have the option of attending two days of Pre-Conference Training events. The training events have been designed for beginners and early users, and for technicians in laboratories that are expanding their barcoding operations.

Registration for the training events is now closed.

Monday, 28 November: Informatics

Course Materials:

Agenda

Session 1: Introductory Level Topics

Session 2: Domain Specific Studies

Session 3: Mirrors and Data Partners

The informatics training workshop sessions were designed with both beginner and advanced users in mind. The morning session will cover introductory level topics to help new users get started on BOLD and other barcode databases. Presenters will showcase new features and functionality available in BOLD 3.0 and explore connectivity to partners such as GenBank, the Barcode Of Life Data Portal, Geneious, Specify and more. The afternoon will be organized into domain-specific sessions to cover workflows designed for ecological studies, regulatory use, regional inventories, iBOL campaigns, student training and more.

For more information about this workshop please contact info@boldsystems.org.

A significant portion of the workshop will be devoted to an overview of BOLD 3.0 features and use cases on BOLD. The morning session will cover introductory level topics to help new users get started on BOLD, showcase new features and functionality available in BOLD 3.0 and demonstrate workflows for standard uses. Speakers from BOLD and other institutions will present on the following:

  • Introduction to BOLD 3.0
  • Data life cycle
  • Using the system
  • Data sharing and publication
  • BARCODE Data Standard including animals, plants & fungi
  • Plant barcoding workflows

The afternoon will be organized into domain-specific sessions that cover workflows designed for various domains, including ecological studies, regulatory projects, and student training initiatives from the point of view of experts in these areas. Finally a lightning talk session will explore connectivity from BOLD to partners such as GenBank.These talks will be presented by the partner organizations, with a short question and answer period following each.

 

Tuesday, 29 November: Lab Procedures

Course Documents

Agenda
  • Module I: Introduction to Barcoding and its pipeline
      Brief introduction to barcoding and the current goals and campaigns/working groups (Dario Lijtmaer)
    • The Barcoding Pipeline (Amy Driskell)
      • What is the barcoding pipeline?
      • What data and objects need to be tracked through the pipeline?
      • What possible entry and exit points exist
    • Barcode Data Standard compliance (David Schindel)
      • Vouchering and archiving of vouchers
      • Imaging and archival of e-vouchers
      • Provenance data quality
      • Sequence and trace file quality
  • Module II: Acquisition and Handling of specimens and tissue samples
    • Pros and cons of collecting specimens for barcoding vs. sampling existing collections (Sally Adamowicz)
    • Field Collection (Sally Adamowicz)
      • Legal issues
      • Logistics
      • Data quality and acquisition (overview of available field data entry tools)
      • Collection/preservation methods
    • Museum Harvesting (Jeremy deWaard)
      • Deciding which collections to use
      • Deciding which specimens/samples to use
      • Destructive vs. non-destructive handling; voucher recovery protocols
      • Biological material transfer policies
    • Front-end processing (Michelle Van der Bank)
      • Specimen arraying, databasing, imaging, sampling
      • Pre-lab challenges and solutions:
        • Individual tracking of collection specimens
        • Avoiding human error when working with large batches of specimens
        • Streamlining front-end processing of large specimen batches
  • Module III: Laboratory methods and information management for small, medium and large-scale facilities.
    • DNA Extraction (Dario Lijtmaer)
      • Equipment
      • Methods/protocols
      • Storage and shipment of DNA extracts
    • PCR Amplification (Dario Lijtmaer)
      • Equipment
      • Methods/protocols
      • PCR product verification
      • Shipment of PCR products
    • Information management and data quality (Amy Driskell)
      • Tracking progress through the laboratory pipeline
      • Keeping all required products together
      • Consistent data assessment
      • Analysis-lab feedback loop
      • Key elements of a data management database (LIMS)
  • Module IV: Taxon-specific aspects of the barcoding pipeline

This short course, organized by CBOL's Leading Labs Network, will focus on laboratory procedures and DNA barcoding methods. The course will cover different aspects of barcode-related activities, including an introduction to barcoding and its pipeline, information about the acquisition and handling of specimens and tissue samples and a brief description of laboratory methods and information management. The training will cover the ways in which these activities are carried out in small, medium, and high throughput facilities, and it will also include a series of talks and a round table about how this methodology is implemented in the major groups of eukaryotes and which particular considerations are necessary in each of them.

The course is designed specifically for researchers and students who are starting to work on barcoding or are planning to do so in the near future. The course will also be beneficial for members of institutions that are expanding their research on barcoding (for example to groups of organisms with which they haven't worked before) or are increasing the scale at which they are generating DNA barcodes.