Thoughts about #ngs2014

Posted on Posted in Bioinformatics

As many of you know, I recently spent a week at MSU\’s Kellogg Biological Station. No, I haven\’t betrayed my Maize and Blue, instead, I was there after being invited by Titus Brown to participate in the 5th installment of ANGUS workshop. I have to admit feeling a fair amount of imposter syndrome going in – after all, these guys and my co-instructors (e.g. Meg Staton, Aaron Darling) are the who\’s-who of bioinformatics, each with his or her own niche. Why would they want me????

Anyway, I have to say that it was an amazing experience, though it\’s not clear if I taught the students more than they taught me. Doing something like this – a super intensive workshop leading novice bioinformaticians through some pretty heavy material (sometimes early in the AM, after late night social events), was hard, and it tested my ability prep and present material, including tutorials without much lead time. I was literally writing materials up to the minute before I presented them. Next year (hopefully there will be a next year), I will have a much better idea about what the present, and at what speed and depth.

When I was not lecturing, I sat in the back of the classroom and did a lot of observing. Here are my thoughts.

  1. The students were awesome. Clearly a lot of thought had gone into the picking of students to achieve a good mix of gender, ethnicity, experience, etc. Although the class was reportedly \’less wild\’ than those of other years, they clearly gelled. They learned an amazing amount, so whatever anybody says, the way the class is taught is powerful and effective.
  2. Group students by interest: An alternative model to teaching the course how we did (everybody receives same content) would be something like this. Week 1. Core concepts and tutorials presented. Week 2, continue core content in AM, PM focus groups. A group for RNAseq, genome assembly, metagenomics, etc.. These groups delve more deeply into the specific material.
  3. Students checked out. Sitting in the back allowed me to see what student were doing. It was clear that some material was pretty difficult for a lot of them (e.g. stats). I think this was a combo of the timing (taught 1st thing in the AM), and that it is simply a challenging topic. I\’m not sure if the answer is to really streamline the section (teach only the most critical points) as a solid understanding of this material is really important.. Maybe some of this coupled with teaching later in the day. This is a general problem, not limited to this class, obviously.
  4. UNIX skills required: I was taken by surprise the difficulty that students had in understanding the basics of UNIX, e.g. $PATH, relative vs. absolute path, IO, files and folders.. Seems like a more solid footing here, given earlier in the class would really benefit the students in the later parts.
  5. Get a minION. Sequence something as part of the class. (just kidding about this one, kinda). As this technology becomes more mainstream it might make for a nice complement to the existing structure.
  6. Instructor office hours: Some student were really proactive about coming to talk to me and others, but some were clearly shy.  I wondered if the quiet students were totally lost, or bored, or whatever.. Finding a way to engage these students is needed. Maybe this was happening and I was just unaware.
  7. Lightning talks. Maybe this happened before I arrived, but I really wanted to know what students (and co-instructors) were working on.