Frequently Asked Questions

Why is it important to add as much biological information about my specimen as possible?

Say you collect a handful of mussels from the beach. You may be fairly confident they are all the same species, they all look the same and there are thousands of them lying around.

However when you barcode your mussels, you find out that instead of one species, you actually have two! And one of them is a new species that no one has discovered before!

You can bet lots of scientists will be very interested in your discovery. They will want to go back to that same beach to collect more samples to study.

As you can imagine, if you did not include your exact collection location on your BOLD-SDP record, no one else will know where to go and your discovery of a new species will likely go unnoticed.

If, on the other hand, you included all the information you can into your record, allowing other scientists to go back to your exact collection site, they will be able to investigate your findings further. Who knows, you might even end up with a new species named after you!

How do I create unique sample IDs?

Sample IDs can be anything you want them to be, as long as they are unique to BOLD. If you are unsure how to create a unique Sample ID try this method:

Year-School Initials-My Initials-Number

For example: 12-JFHS-JS-0001

School Name: John Frasier High School (JFHS)

Student Name: Jane Smith (JS)

It's best to keep your Sample IDs as clear as possible while still containing the information you need. Using a standard Sample ID format for all your samples, like the one shown above, will make it easier to remember it.

If I am unsure about the identification of my specimen, is it better to leave the nomenclature incomplete or to guess?

If you are unsure, leave it blank! You should add as much taxonomic information to your specimen as you can, but only if you're sure it is correct. You can always add more taxonomic information later.

For example, if you know the class of a specimen, but not the order, then leave the order and all the remain taxonomy blank. You can use the Notes field to list any hypotheses you might have about your organism's name.

Once you have a sequence for your specimen, you can use the BOLD ID Engine to determine, or confirm, the identification of your specimen and add it to the record.

What is the difference between region and exact site field in my collection details?

Region refers to a broader area of collection, such as a city, a neighbourhood, or a park, while exact site refers to the exact location where the specimen was found. It is important to make this distinction and fill out your data accordingly, so it is comparable to the data from other students. If you are unsure how specific you should be in describing your exact site, think of it as giving somebody directions to go back to that same spot where you found your sample.

For example: Let's say you found a beautiful beetle in Central Park, New York City. Here is one way to write your collection information:

Region: Central Park, New York City

Exact Site: Shakespeare Park, west of Turtle Pond

This would give a pretty good clue to anyone interested in going back to where you found your beetle.

How do I convert my coordinates into decimal degrees?

BOLD-SDP will only accept GPS coordinates in the decimal degrees format. This is an alternative viewing from the popular degrees, minutes, seconds (DMS) format, but both represent the same location on the map. Many GPS units will have the capability of displaying both formats when recording your coordinates in the field. However there are plenty of free online websites you can use to convert it afterwards too.

Here are a few choices, but feel free to look around and see if you can find one that works for you!

Option 1

Option 2

Option 3

Does the quality of the image I upload to my record really matter?

Yes, it really does! The images associated with your record should be in focus and as close-up as possible, so that all the diagnostic features for your specimen are visible. The images will help you, and other experts, confirm the identifications of your samples, even when the actual specimen is not available.

Comparing a high quality and a low quality image. Notice how the correct image is centered and covers most of image, while the incorrect image takes only 50% of the frame

You can add more than one image per record, so feel free to try all the different orientations – dorsal, ventral, lateral, etc – in case you can’t get all the features you need from just one photo.

What should I do if the species name for my specimen is not on the taxonomy drop down menu?

If the species name for your specimen is not on the drop down menu, it means there are no records on BOLD Systems for that species yet. If this happens, first use the taxonomic databases listed on the Explore Page to see if there are any synonyms for the name you have.

If you cannot find any synonyms for your species, then have your instructor email with the new species name and it will be added to the drop down menu. You may be barcoding a species that is new to the BOLD Systems database!

How do I tell the difference between a good trace and a bad trace?

It is usually pretty easy to tell the difference between a good trace and a bad one. Each of the 4 DNA nucleotides are represented by a specific coloured line, and when the trace quality is high you can decode the sequence of the nucleotides just by looking at the peak of each colored curve one after another. In a bad quality trace file the peaks tend to blend together, so it can be difficult to determine the order of each coloured curve.

The 4 nucleotides are represented by the following colours:

Red = Thymine

Green = Adenine

Black = Guanine

Blue = Cytosine

Good quality trace file

Bad quality trace file. As shown in the image, an N means that the nucleotide is unable to be assigned to one of the 4 nucleotides (unknown colour: yellow).

What are primers and how do I identify them in my sequence?

Primers are short strands of nucleotides used to deliminate the start of DNA synthesis, amplification and/or sequencing. Primers can occur naturally as short RNA strands, but for DNA amplification and sequencing experiments they are usually manufactured in a laboratory. These manufactured primers are typically designed specifically for a group of organisms that share similar DNA sequences, but some primers have the ability to bind to a multitude of organismal groups, and are known as Universal Primers.

In DNA barcoding, where only the mitochondrial COI gene needs to be amplified and sequenced, primers are fundamental because they determine the exact portion of the gene that should be targeted during PCR and sequencing. The sequence codes for the primer are available through the manufacturer, and can be easily recognized in the nucleotide code after DNA sequencing is completed.

It is advisable to trim out the primers before aligning and analyzing your sequences. BOLD-SDP has a built-in sequence processor that will identify and trim your primers automatically. Compare the primer sequences provided by the manufacturer with those identified by BOLD-SDP, chances are they match up very well!

Why didn't my traces appear on the Sequence Page after uploading?

Traces with file names that contain special characters (such as semicolons) can cause errors in uploading traces. Please rename your traces to contain only numbers and letters, and try uploading again.

How can I tell if a record is ready to be send to BOLD Systems and GenBank?

The first step is making sure all of the data elements have been added to a record the specimen data, the images, the trace files, and the sequence. Once all of the elements are present, you will need to verify their accuracy and quality. There are several components of a record that should be checked. Here is a list to help you can get started: 

1. On the Specimen Page, check the image(s) and GPS coordinates uploaded to the record:

• How is the quality of the specimen image? 
• Can you tell which species it is suppose to be based on the photo? 
• Does the image(s) match the taxonomy provided?
• Do the GPS coordinates map to the correct country/state provided?

2. On the Sequence Page, check the quality of the sequence and compare the sequence in the record with the BOLD ID Engine

• Are there any stop codons in the amino acid sequence?
• Does the taxonomy provided match what was found on BOLD Systems?

BOLD-SDP analysis tools, such as the Taxon ID tree, Collection Site Map, Alignment Browser, and Image Library allow you to compare all the records for the course at once. This is useful for detecting outliers in your dataset right away. For example, if all but one of th GPS coordinates for the samples collected in your course fall within the state California, there maybe an issue with the GPS coordinate for the one record outside the state, and it should be examined more closely. 

Does it matter if there are stop codons in the sequence?

A stop codon, by definition, is a short sequence (three nucleotides long) which signals the end of a sequence translation. In protein coding genes stop codons will not naturally occur in the middle of the sequence read because this would indicate to the messenger-RNA that the translation of nucleotides into amino acids is complete and it would result in a lot of functionless pieces of proteins. 

COI, the mitochondrial gene used in DNA barcode of animals, is a protein coding gene used in cellular respiration and it should no have stop-codons present in the sequence.

Finding a stop codon in a sequence can be the result of many factors, most commonly it either involves an incorrect base calling from the original trace file or a shift in the reading frame of the sequence. It is important to try to fix stop codons before approving a record by confirming the base calling in the original trace file is correct and by re-running the sequence alignment. If rechecking these steps does not resolve the problem, the record can still be approved with the stop codon and it will be checked by an administrator. 

How can I grade my students?

On the Management Console it's easy to see student contributions by selecting Course Info beside the course listing. This gives you an overview of how many specimens, sequences, images, and traces each student has generated, which can help you gauge participation and can be useful in grading your students. In addition, the Activity Wall allows you to keep track of daily student activity and monitor the students' involvement in the project. You will be able to easily detect which students have been actively contributing data to the course and which students may be struggling through the process, and will need assistance. 

What should I do with a record that does not meet the approval standards?

If a record does not meet approval standards, the first step is to determine if any data element can be edited to correct the record for approval. For example, this may include having to re-shoot a photograph, or re-edit a sequence, or simply assisting a student upload a component they are having difficulty with. If a record cannot be edited to meet approval standards, it can be rejected from the Record Approval Queue.

It is important to note that all components of a rejected record will be deleted from the course dataset and all individual student contributions will be lost. Therefore rejecting a record should be the final resource. 

Even records that do not meet international DNA barcoding standards can contain useful information. These records can stay in your class project and can even be used as teaching tools. Records with poor quality trace files, contaminated sequences, or even missing specimen data can all be used as examples to help students understand why it is important to create the highest quality records possible - one that includes specimen data, images, trace files, and sequences.

What should I do once my students have uploaded all their data on BOLD-SDP?

Once your students have uploaded all their data, they can begin to use the tools built in to BOLD-SDP to analyze and study what they have collected.

Questions derived from DNA barcoding research can encompass a range of science and societal disciplines including ecology, genetics, molecular biology, conservation, and socio-economic issues. Several resources already exist to help guide you through your lesson plans and more information on how to use the BOLD-SDP tools and what questions can be answered can be found in the BOLD-SDP brochure. 

Why can't I add a co-instructor to my course?

Co-instructors will need to create an account on BOLD before you will be able to add them to your course(s). Students and co-instructors can be added from the Course Info pop-up on the Course Management page. 

Co-instructors will have the same rights as the instructors and will be able to validate and approve records. 

What will happen to my project once a project is done? 

If you are generating reference barcodes, once your project is done your records can be approved to be sent to BOLD Systems and ultimately GenBank. Once you approve the records generated by your students, BOLD-SDP administrators will have the opportunity to further scrutinize the records to ensure they meet the standards of the global DNA barcoding community. Following this, the records will be queued to be sent to GenBank. Once the records have been published in GenBank, your students will be able to see their record (with their name included) on GenBank and BOLD Systems where it may be used by professional scientists around the world.

If you are creating records to utilize BOLD's ID Engine features (for example, if you are conducting a fish market survey), your records do not have to be approved and sent to BOLD Systems - they can be analyzed and studied through BOLD-SDP and left in the class project once the students are done working with them.

Once your course is completed, you can Retire it from your Course Management console. The data will remain on BOLD-SDP and BOLD but the course will no longer appear on your Course Management console.

What is the difference between a reference barcode and an investigative barcode? 

DNA barcoding is a very powerful tool for species identification, but before any sequences can be identified there needs to be a database of reference sequences to compare them to.  Reference barcodes make up this database, the BOLD DNA Barcode Reference Library.  Reference barcodes are created from samples with well established taxonomic identifications such as those in museum collections. 

Investigative barcode records are generated from samples with unknown or questionable taxonomic identifications, such as fish market samples or tea leaves.  By comparing these sequences to those in the BOLD DNA Barcode Reference Library, identifications can be determined and confirmed.

If your class is creating reference barcodes, you will need to include as much specimen and collection information as possible and make sure that all your specimen and sequence data is accurate.  These records will be referenced by other scientists to determine the identity of their samples, and if you have mistakes in your record, it can lead to serious data errors in the system. 

On the other hand, if your class is creating investigative barcodes you will likely have less details about your sample, however it is still extremely important to include information about the restaurant or supermarket where your sample is coming from and when it was collected or purchased. This will help you interpret your results and determine the outcome of your experiment.