Quick Start Guide

Navigating the Student Consoles

An instructor must first register a course in order for students to login.  Every student in a given course will have the same login information (username and password) provided by their instructor.  Once a course has been registered, students will login using the course login account. Click on the Students icon from the homepage to bring up the Student Login page.

Student Login Page

Figure 4-1: Login page for students, which can be accessed from the BOLD-SDP homepage by clicking on the "Students" icon.

Once a student is logged in, the Main Student Console will appear. The Data Management Console permits student users to upload specimen data, images of specimens, and forward and reverse trace files generated from their amplicons. This console also contains an integrated tool that enables users to assemble, edit, and upload nucleotide sequence data from trace files.

Main Student Console

Figure 4-2: The Main Student Console is the landing page after students log in. Here students can upload and manage their barcode data, view and download the data already available, and utilize powerful analytic tools to examine their barcode data.

Submitting New Data

There are four data components that form a complete barcode record: Specimen Data, Specimen Images, Trace Files, and Sequence Data. Each of these components should be uploaded separately and in this order. Attribution data for the work must be submitted at each step. Detailed instructions on the correct way to fill out the various fields are provided on the left side of each upload form.

Data Management Console

Figure 4-3: The Data Management Console is central on the Main Student Console.

New Specimen Form

Figure 4-4: The New Specimen form is accessed through the Data Management Console of the Main Student Console. This is the first of 4 blocks of data that must be completed by the student. This page includes the Specimen Identifier, Specimen Details, Taxonomy, and Collection Details. Instructions on the correct way to fill out the various fields are given in the menu on the left side of the screen.

Upload Images Form

Figure 4-5: The Upload Images form is accessed through the Data Management Console of the Main Student Console. This is the second of four blocks of data that must be completed by the student.  Students must first enter the correct Sample ID to connect their uploaded images with the corresponding specimen. Instructions on the correct way to fill out the various fields are given in the menu on the left side of the screen.

Upload Traces Form

Figure 4-6: The Upload Trace form is accessed through the Data Management Console of the Main Student Console. This is the third of four blocks of data that must be completed by the student. The Sample ID field is used to connect the correct traces with the corresponding specimen. Two traces should be uploaded per record whenever possible, one for the forward read and one for the reverse read.

Add Sequence Form

Figure 4-7a: The Add Sequence form is accessed thought the Data Management Console of the Main Student Console. This is the final block of data that must be completed by the student. Every step MUST be followed in sequence.  Subsequent steps will only be displayed once the preceding step has been successfully completed. The first step is to connect the correct specimen to the corresponding sequence through the Sample ID.

Figure 4-7b: After entering a Sample ID and clicking on "Add Sequence", the next step is to paste a nucleotide sequence in FASTA format into the pop-up text form.

Figure 4-7c: Once the sequence has been entered, it is ready to be processed. This will involve three steps that will be performed automatically by BOLD: primer trimming, contamination checking, and sequence alignment. If all steps are completed successfully the sequence is ready to be uploaded to the record.

View Data and Download Data

Students logged in to BOLD-SDP will be able to view and download all the data submitted by their coursemates. This is useful for comparing records and performing various types of sequence analysis.

Main Student Console

Figure 4-8: Main Student Console with the View and Download Data buttons available on the right side of the screen. The View Data button allows students to access the records submitted by themselves and their coursemates. The download tools allow students to download the course specimen records, trace files, and sequence data.

The download tools provide the following files:

• Download Specimen Data
           Specimen Data will be downloaded in Excel format
  
• Download Trace files
           Trace files will be downloaded to a folder containing each trace file in .ab1 format and a list of trace
            files in .txt format.
  
• Download Sequences
           Sequences will be downloaded as FASTA files.

The View Data options are described below.

Record List

Figure 4-9: From the View Data button, students have access to the course record list. This provides a quick overview of the taxonomy, sequence lengths, and record flags for all the records in the course. Each Sample ID and Process ID are linked to a specimen page and a sequence page respectively. Analysis tools are available on the left menu, once more than 3 records have been submitted for the course.

Example Specimen Page

Figure 4-10: This page provides an overview of the submitted specimen data for the record including identifiers, taxonomy (if known), specimen details, specimen images, geography, and collection details. Under the Contributors section of the Specimen Details, attribution data is also displayed including a list of students and their contribution to the generation of the record. A student may annotate a record and add comments by clicking on "Add Tags and Comments" under the Annotation section. 

Example Sequence Page

Figure 4-11: This page displays the nucleotide sequence, amino acid sequence, illustrative barcode, raw trace files, primer information, and sequence quality for the genetic data generated from the specimen. A student may annotate a record and add comments by clicking on "Add Tags and Comments" under the Annotation section. 

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

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

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

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

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

Figure 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

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