I interviewed our students on the last day of annotation on their impressions and take-home message from the two semesters of this class, from extracting the bacterial DNA to summarizing their annotation of a specific subset of the genome. The following summary is of course subjective.
There is a strong constrast in the experience of the students between the sequence assembly in the autumn, and the annotation in the spring.
The sequence assembly was more abstract, with theoretical explanations of algorithms which were often difficult to follow for the students (De Bruijn graphs, k-mers, and friends), and all the work needed to be done on a distant cluster using the dreaded Unix command-line interface. So the students often felt that they were copy-pasting commands and using ready-made scripts without truly understanding what they were doing nor why.
Another source of frustration is that, although we try to provide a full A to Z experience, the sequencing is done without them in a facility to which we just send the DNA. Then, miracle!, the sequences are on the cluster a few weeks later. On the plus side, several students appreciated getting much closer to these new and fashionable techniques. Illumina and PacBio stopped being just names they had heard, became more real.
After the bioinformatics part of the assembly, we did some experiments which were a bit frustrating because they take quite a bit of time for a small progress. I’m told a lot of experimental biology is like that. 😉
Overall, the assembly was more interesting for the students who have chosen to specialize in Bioinformatics in the master, relative to the others. One student called assembly “putting pieces of the puzzle together”. Some bioinformatics students also liked the experimental part of the course, which they otherwise don’t have during their master. Of note, one non bioinformatics student found the bioinformatics of assembly “hard but cool”.
On the other hand, almost all the students appreciated the annotation, which is closer to biology, and allowed them to use multiple bioinformatics tools independently. By using these tools to pursue a biological aim, several students felt that they improved their understanding of the tools (e.g., flavors of Blast, differences between SwissProt and Pfam). It also allowed them to have more initiative, to pursue leads which they found interesting. And then, in the words of a student, “we see how the bacteria use their genome”.
A few students would have appreciated spending more time on the annotation, they feel that they barely scratched the surface, found tentalizing leads, then had to stop because the semester was ending. We will consider in the future allowing motivated students to continue for extra credit.
A difference between the two semesters which was purely practical, but influenced the experience of the students, is that in autumn classes were every two weeks, whereas in spring they were over half of the semester every week. The weekly rythm was unanimously judged more adequate, allowing students to carry on from one session to the next more easily.
While many students found the assembly more difficult and less interesting, many also appreciated having seen the whole process from begining to end. Or as one student put it, “from A to W”, since we didn’t really have time to finish everything which we would have liked to. But isn’t it always so in research…
Those students who are doing microbiology appreciated that the whole course gave them a better knowledge and understanding of what goes into a bacterial genome and gene annotations, since they are confronted with these data in their work at some point or another.
Finally, one student, after telling me everything which he didn’t like about the course (Unix! algorithms! we didn’t have time to finish!), concluded “It was challenging but interesting” with a smile.
I can only encourage colleagues to organize similar courses everywhere.