Ecology of Infectious Marine Diseases TA Recap
Things I did at FHL that were not my research
For the past five weeks, I’ve been at Friday Harbor Laboratories as a Teaching Assistant for the Ecology of Infectious Marine Diseases course! I thought it would be good to recap what I did, since I was working but didn’t have time for my own research. In addition to finding lab equipment and helping out with fieldwork, I gave some lectures, helped students with a genomics project, and spearheaded the formal science communication section of the curriculum.
Teaching molecular methods
For my first lecture, I taught students about Github and basic Linux commands. I had students navigate to this Github repository and clone it to their machine. I then walked through the steps I laid out in this document. I had students learn to change their working directory and navigate through directories using the command line interface. I opened up a Terminal window and placed a Finder under it so students could see how the commands I typed in the Terminal changed directory structure and files. I also emphasized the use of tab-complete to make things easier and avoid typos in code. The next set of commands I walked through involved downloading FASTA files from web links. Looking back on it now, I probably should have taught them about checksums, but I think their brains may have exploded a bit. I had them create new directories, move FASTA files into directories, and remove extra files. Finally, I went through commands to explore files from the command line.
Later that day, I taught them how to
blast from the command line! I wanted them to type the code themselves, but we were unable to download
blast on the computers in the Computer Lab. I walked through the code in this document so they could try reviewing it themselves later. What was more useful for them was going to the Uniprot SwissProt database and teaching them about the database and how to get GOterms.
At the end of our genomics block, I gave a lecture on my own work! Since Colleen focused on transcriptomics, I used my work as case studies on the use of proteomics and epigenetics to study how abiotic stressors affect organismal physiology. Students were really interested in specific methods, so I added in a lot of detail. I think those extra details may have prevented some students from seeing the big picture. I’ll need to work on that if I give that lecture again.
A large component of the course was working on projects. For the project examining NIX prevalence in Kalaloch Beach razor clams, I assisted students with DNA extractions and qPCR. I spent most of my time assisting with the transcriptomics project looking at eelgrass wasting disease host-pathogen interactions. I created this Jupyter notebook to merge transcriptomic data with
blast output and Uniprot Swiss-Prot annotations. I also streamlined isoforms into genes. In this R Markdown file, I formatted input files for gene enrichment with GO-MWU. I used the GO-MWU pipeline for eelgrass and pathogen transcriptomic data, but only found two enriched GOterms for eelgrass. I also created this R Markdown document to help students create heatmaps of differentially expressed genes. They used the code I created to create their own heatmaps for genes of interest. I think any molecular method is difficult to follow if you have little to no experience, and if you don’t have a great understanding of R or Linux. One thing that (I think) helped while I was teaching was to constantly remind students the purpose of each step.
The other part of the course I helped with was science communication practice. Students were required to write one blog post for a public audience and create a short talk about a disease for the class. I worked with each student on their blog post and provided targetted feedback when editing their initial drafts. I also had students give practice presentations to me so I could help them if they needed. Most of my comments were directed at improving the organization of their pieces or talks. I took it upon myself to help them outline their final papers and reviewed their final presentations so they would not have similar issues.
Overall TAing at FHL was a lot of work but really rewarding! I learned a lot about what it means to be a good instructor and I cannot wait to flex those skills soon.