A successful class project pilot! Update on our Genetics class project

In an earlier post we described a  Genome  Analysis project we have now (successfully in my opinion) piloted into a Genetics class taught by Loren Launen (author of this post). Here’s an update!

We have finished running the project with students, the only thing left is for students to complete their final reports (and for me to grade them). Once they have done that I’ll add to this post.

We spread the project over four class sessions (described earlier), which took a couple of weeks as we fit the material around ongoing lecture and tutorial practice sessions in other topics. Below is a summary of the highlights, from the teacher’s perspective.

What went really well:

Completion of all technical stages by all students: All of the students were successful in navigating the server, trimming data, running reference assemblies and using PROKKA and QUAST to analyze the data. Students were literally zipping along by the end!

Mining of useful data with biological relevance: All students were able to use their data to determine the identity of the isolate (a Vibrio vulnificus strain that was shared with our lab by Dr. Anita Wright from the University of Florida). They did this by looking at the reference alignment in QUAST, and by using nBLAST to identify the best match to the 16S rRNA gene. Students also found genes that encode the production of hemolysin toxin, and capsule synthesis genes, both important virulence factors in Vibrio vulnificus.  Great for learning and teaching, and also immediately useful in the research project in our lab!

Connecting the project with biological relevance: The assessment of student learning in this project is broken up into a pre-assignment, a final report, and participation points. The pre-assignment included questions about the biology of Vibrio vulnificus, it’s human health relevance, and the fundamentals of genomics (the purpose to the tools and steps we would be conducting). Students were provided with appropriate sources of information to help them answer these questions, including a lecture that I gave on the topic. The students did really well with this pre-assignment, demonstrating a really good understanding of the topic area.

* Note – I will update this post once I’ve been able to read the students final reports. The final report requires students to correct their pre-assignment based on feedback I provided them, to draw conclusions about their data, and to read more broadly into an an area of their choice to consider how genomic analysis can inform important questions in Biology today. 

Reinforcing concepts and skills learned in class: There are so many ways genome analysis can reinforce fundamental biological knowledge, especially in Genetics! This project gave students hands on experience looking at nucleotide and amino acid sequences for genes, reinforcing the genetic message. They also had to scratch their heads (figuratively) to understand why the 16S rRNA gene was NOT in the amino acid sequence file….reinforcing the modern concept of a gene and the concept of “functional” RNA. Students had learned about and used BLAST earlier in class, so using it again in the bacterial genomics project context seemed to come easily and quickly to them. Looking for capsule synthesis genes allows us to “remember” Fred Griffiths work on bacterial transformation. The integrative aspects of projects like this are incredible -we just need to figure out the best way of helping students make the connections.

What needed improvement:

Pacing: The students came into the project with diverse backgrounds ranging from highly proficient on computers (those with previous coursework in computer science) to less proficient (those with no computer science experience). This resulted in what must have been frustrating delays for some (of course, my students are all so nice I could not really spot this), and anxiety for those who needed more time (definitely easy to spot). In the research group we discussed how we could work to alleviate this. Our initial approach was to have students link to the day’s directions online, and follow along as the lead instructor moved through the steps on the lecture screen (live). This didn’t work well. What we tried in our last class was to hand out hard copy (!) directions, and then demonstrate the steps in one short, quick session, then having students work at their own pace. We moved around helping at that time. This seemed to work much better.

We didn’t measure student interest in bioinformatics/genomics: We think measuring this somehow before and after the project would be good to do. We’re just not sure how to do it (well).

Ideas for our next iteration (next semester): 

Now that we have run through this project once, we’d like to change a few things. These are:

1. We have the resources (see postings to this blog) to more fully explain tools such as SPADES and PROKKA. We need to figure out how to do that without losing students in applied math (or losing ourselves for that matter!).
2. We would also like to have students analyze different bacterial genomes. We know these methods work on a known, well sequenced Vibrio vulnficus now (which was information we gained from doing this work with the students). We’d like to have each student take on their own isolate data in the next iteration, and then compile it at the end to move forward the research project, and to allow students more opportunities for novel discoveries.
3. We’d like to have students contribute directly to this blog. Perhaps by summarizing their research findings as a class?
4. We’d like to have students directly interact with a graduate student from Kelley’s lab, as part of the project and to learn more about careers in bioinformatics. We wanted to get Jordan Ramsdell here this semester to give a talk and interact in person with students, but we just didn’t quite make that happen in this pilot.
5. We would offer a more thorough tutorial on using the Terminal before the students start working with the bioinformatic tools.  The pace at which the students worked increased dramatically as they became more comfortable with the Terminal.  This directly ties in with the pacing discussion earlier, as we didn’t account for how comfortable they would become with the Terminal.

Going forward into next spring, we are planning to scale this project up quite a bit for an upper level “Genome Analysis” project.

Now off to hatch some evil plans for that…

Loren