Quick Start Guide

Registering an Instructor Account

New instructors may create a BOLD-SDP account by following the instructions on the right hand side of the Instructor Login page (available by clicking on the "Instructors" button in the middle of the SDP home page). To register an Instructor account, users need to fill in an appropriate group-code. If one was not already provided, the group code ‘BOLD-EDU-SDP' can be used to submit the New User Application to register as an Instructor.

*Please note that standard BOLD accounts do not qualify for access to the BOLD-SDP. A new BOLD-SDP Instructor account must be generated, even for those who already have a regular BOLD account. If a user no longer needs a regular BOLD account, this account can be converted to an SDP Instructor account by emailing [email protected] with this request.

Instructor’s Login

Figure 3-1: Login screen for instructors, which can be accessed from the BOLD-SDP homepage by clicking on the instructors icon.

New User Registration

Figure 3-2: When registering for a new teacher account, BOLD-EDU-SDP should be entered into the ‘Optional Group Code’ field, unless Instructors were provided with a different code.

Registering a Course

*Please note that the course registration process REQUIRES a valid Registration Key. If you do not have course registration keys, please contact [email protected] for more information.

Each course that an instructor plans to facilitate must be registered independently with unique registration keys. Once a registration key is obtained, the registration process involves the entry of institution information and course information, including student names and their contact information (strict adherence to privacy policies is assured), and the listing of any collaborating instructors. Co-instructors have the same level of access to student data as main instructors. Each course must be registered with a unique name. If the same course is being taught in different semesters, semester information should be included in the name to disambiguate the classes.

Once registered, an instructor will be provided with student login information for the course. Every student within that course will use the same account information (username and password) to access the site and to submit/analyze their data. The use of a single account simplifies the management of accounts for instructors, without compromising their ability to track contributions made by individual students.

Manage Courses Page

Figure 3-3: Landing page for instructors after logging in. From this page it is possible to Register a New Course or go directly Course Management, where instructors can monitor student work in existing courses.

Classroom Registration Form

Figure 3-4: A course can be registered with more than one instructor, if required. Email addresses for each student are recommended, but not required. Upon registration, a shared account with a single username and password will be generated for all students in the course to use. Instructors are asked to circulate the login information to their students.

Course Management

Once a course has been registered, instructors can select Course Management on the Instructor landing page to view the following details for each course: course information, a list of students, and the barcode records the students are in the process of generating.

Management Console

Figure 3-5: Management console for instructors. From this page instructors can monitor and validate student work from multiple courses. A logging system keeps track of the work students are doing and displays it on the activity wall

Course Information

Figure 3-6: Course info popup. Clicking on Course Info next to a course will display course summary and a list of each student’s progress.

Course Record List

Figure 3-7: This interface provides a list of the taxonomy, Sample IDs, Process (BOLD) IDs, sequence lengths, and record flags for all the records in the course. The record flags are defined in a legend on the page. Each Sample ID and Process ID are linked to a specimen page and a sequence page, respectively. When more than 3 records with sequences have been submitted for a given course, a range of analysis tools is also available in the left menu.

Specimen Page

Figure 3-8: This pop-up page provides an overview of the submitted specimen data for the record including identifiers, taxonomy, specimen details, geography, collection location, and specimen images. Under the Contributors section of this page, attribution data includes a list of students and their contribution to the generation of the record. An instructor may annotate specimen records, by adding comments through the "Add Tags and Comments" in the Annotation section.

Sequence Page

Figure 3-9: This pop-up 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. An instructor may annotate specimen data elements by adding comments through the "Add Tags and Comments" in the Annotation section.

Approving Student Work

Before student-generated records can be added to the BOLD library and sent to GenBank, they must be approved by an instructor and submitted for additional data validation by SDP Administrators. The Course Management console shows the records queued for instructor review from all courses in the section called "Record Approval Queue".

Analysis Tools

It is recommended that instructors utilize the built-in analysis tools provided by the BOLD-SDP to help confirm the quality of the records assembled by their students. These tools can provide further insights into the quality of the records as they allow all records in a course to be compared at once, which could include highlighting errant records (such as a taxonomic mis-identification found via using the ID Engine). The analysis tools are available from each course record list. Here is a brief overview of the analysis tools available for instructors to use on the barcode records in each course they manage:

• Barcode Gap Analysis
  Determines the distance to the nearest neighbour for each species, where distance is a measure of sequence similarity. Distances between specimens of the same species will tend to be much smaller than distances between different species, since larger distances indicate higher sequence divergence.
  
• Alignment Browser
  Visualizes how the sequences of a project are aligned together.
  
• Accumulation Curve
  Estimates how diverse and complete collection efforts for a certain site have been. A steeper curve suggests high diversity, not yet included in the data being analyzed. Curves with flat tops indicate that most species have been collected from that site.
  
• ID Engine
  Queries the existing database for nearest matches.
  
• Taxon ID Tree
  Illustrates how the specimens in the project cluster together based on their sequence similarity, with horizontal lines in the tree indicating how similar sequences are to each other.
  
• Map Collection Sites
  Provides a Google Earth image with mapped collection sites
  
• Image Gallery
  Creates a library of selected specimen images. By default, a single image is picked for each specimen in the course. You may click on images to zoom in a new window.

In the Record Approval Queue, instructors can quickly access an overview of the record, including the number of images and trace files uploaded and the sequence length and quality. Instructors may carefully examine each Specimen (using the Sample ID) and Sequence (using the sequence link) page to ensure that there are no mistakes and that the record meets data compliance standards. If the record does not meet standards for approval, the instructor may annotate individual specimen and sequence pages to provide feedback and guidance to their students.

• To approve a record, and forward it to the next step in the validation process, instructors can click on the green check mark in the validation column. This adds the record to an SDP administration queue, which allows project leaders and members of the scientific community to vet these student-generated barcode records before moving them to the BOLD researcher workbench and submitting corresponding nucleotide sequences for publication in GenBank. The green check mark will not be available to click unless the record meets the basic requirements for specimen and sequence quality and completeness.
• If a record is unable to be completed, or is of low quality, instructors can remove it from the SDP by clicking on the red x in the validation column. This permanently deletes the entire record and audit trail from the BOLD-SDP, so should only be used when a record is no longer needed for course grading. There is a confirmation message pop-up that requests a confirmation before a record is deleted.
• Should a record need further work by the students, it should be left in the Record Approval Queue until it meets the criteria to be validated.

Queued Records List

Figure 3-10: Queued records awaiting instructor approval before being sent to an SDP administrator.