Quick Start Guide
Video Tutorial
1. Registering an Account

An introduction to the BOLD Student Data Portal website. This video provides an overview of the system and describes how to register and create a course.
2. Submitting Data

This video follows the submission of a DNA barcode record from the specimen data all the way to the sequence. It focuses on the student interface, but it allows instructors to follow the steps students will need to undertake in order to create their records.
3. Overseeing a course

This video provides an overview of the tools available to instructors to monitor student work and participation. It also describes the steps needed in validating and approving student-generated data for publication on BOLD and GenBank.
 

Data Analysis Tools

Once more than 3 specimen records and sequences have been added to a course, students can analyze the data using a variety of BOLD analysis tools, including: Taxon ID Tree, Identification Engine, Barcode Gap Analysis, Specimen Image Array and Map of Collection Sites.

Analysis Console
Analysis Panel Figure 4-12: The Data Analysis options available to students.

The Taxon ID Tree allows students to visualize how the sequences are genetically related using a Neighbour-Joining tree. This allows students to see how all the specimens in their course collection cluster together.

Taxon ID Tree Parameter Page
ID tree Figure 4-13: This page allows students to select branch labels and highlight problematic records, in order to create a cluster vizualization of the barcode records in the course.

The BOLD Identification Engine compares all of the sequences uploaded in a course to the BOLD Barcode database to determine the most likely match. The top matches are displayed for each sequence that was identified. Students can view the Taxonomy Browser page for the species that are the most likely matches for the sequences. The matches can also be visualized through a Taxon ID tree.

Identification Engine Result Page
Identification Engine Figure 4-14: The result page for BOLD ID Engine highlighting the most likely species match and where it was collected. Individual results pages are available for each barcode record in the course.

 

The Barcode Gap Analysis shows the variation in barcode sequence between members of a species and between different species using the sequences in a given course.

Barcode Gap Analysis Result Page
Barcode Gap Figure 4-15: This page shows the divergence between sequences from different species in the course.

The Specimen Image Library allows students to view all of the images uploaded to a project in a single page. Students can filter the images by specimen orientation (eg. Dorsal, Lateral) to view all of the images of a particular orientation at once. This tool helps assist in record validation by allowing students and instructors to quickly verify that the images are uploaded to the correct specimen.

Specimen Image Library
Image LibraryFigure 4-16: The library containing all the specimen images for the course.

Map Collection Sites shows the collection locations of all of the specimens in a course, based on GPS coordinates. This allows students to see where their specimens were collected and detect issues by making it easy to spot any major errors in GPS coordinates.

Collection Site Map
Collection Map Figure 4-17: Display of GPS collection points for all of the records in a course.