As part of my training to become an instructor-trainer for Software and Data Carpentry, I want to help further develop the material used during instructor training workshops. Greg Wilson, who heads the instructor training, and I, decided to make some videos to demonstrate good and not-so-good practices when teaching workshops. Greg recently released his “example of bad teaching” video focussing on general teaching techniques.
make two 2-3 minute videos with contrasting ways of doing a live coding session
one demonstrates as many ways as possible how to not do this
one uses as many good practices as possible
during the instructor-training workshop, participants are asked (in small groups) to discuss the differences and their relevance.
With help from colleague Tore Oldeide Elgvin (the cameraman) and local UiO Carpentry organisers Anne Fouilloux and Katie Dean (playing the role of learners), we recorded the videos. It took about two hours and a dozen attempts, but it was fun to do. Amazing how difficult it is to not doing your best while teaching…
Here are the videos – watch them before you read on about what they were supposed to show. Note that (part of) the unix shell ‘for-loop’ lesson is what is being taught. It is assumed the instructor has already explained shell variables (when to use the ‘$’ in front and when not).
Many thanks to Tore, Anne and Katie for helping out making these videos!
instructor ignores a red sticky clearly visible on a learner’s laptop
instructor is sitting, mostly looking at the laptop screen
instructor is typing commands without saying them out loud
instructor uses fancy bash prompt
instructor uses small font in not full-screen terminal window with black background
the terminal window bottom is partially blocked by the learner’s heads for those sitting in the back
instructor receives a a pop-up notification in the middle of the session
instructor makes a mistake (a typo) but simply fixes it without pointing it out, and redoes the command
instructor checks if the learner with the red sticky on her laptop still needs attention
instructor is standing while instructing, making eye-contact with participants
instructor is saying the commands out loud while typing them
instructor moves to the screen to point out details of commands or results
instructor simply uses ‘$ ‘ as bash prompt
instructor uses big font in wide-screen terminal window with white background
the terminal window bottom is above the learner’s heads for those sitting in the back
instructor makes mistake (a typo) and uses the occasion to illustrate how to interpret error-messages
In March 14-18 2016 we organised the first Carpentry week at the University of Oslo. After a mini-Seminar on Open Data Skills, there was a Software Carpentry workshop, two Data Carpentry workshops and a workshop on Reproducible Science as well as a ‘beta’ Library Carpentry workshop.
The Software and Data Carpentry effort at the University of Oslo, aka ‘Carpentry@UiO’, really started in 2012 when I invited Software Carpentry to give a workshop at the university. The then director, Greg Wilson, came himself and gave an inspirational workshop – recruiting Karin Lagesen and I to become workshop instructors in the process. Karin and I graduated from instructor training spring 2013 and have been giving a couple of workshops in Oslo and elsewhere.
Teaching in general, and at Software and Data Carpentry workshops in particular, gives me great pleasure and is one of the most personally rewarding activities I engage in. With Software Carpentry, I feel I belong to a community that shares many of the same values I have: openness, tolerance, a focus on quality in teaching to name a few. The instructor training program is the best pedagogical program I know of, and it is amazing to see how Software and Data Carpentry are building a community of educators that are fully grounded in the research on educational practices.
Being an instructor is my way of making a small, but hopefully significant, contribution to improving science, and thus the world.
I get asked about this a lot, so I thought to put together a quick blog post on it.
Disclaimer: this is the advice I usually give people and is given without warranty. As they say, Your Mileage May Vary.
Main advice: bite the bullet and get the budget to get 100x coverage in long PacBio reads. 50-60x is really the minimum. Detailed advice:
Sequencing and assembly
get 100x PacBio latest chemistry aiming for longest reads (make sure provider has SAGE Blupippin or something similar)
get 100x HiSeq paired end regular insert
run PBcR on the PacBio reads, this is part of Celera. It corrects the longest raw reads, assembles them using Celera (long run time). Make sure to install the latest Celera release which uses the much faster MHAP approach for the correction.
At the workshop, I presented a poster based on my recent blog post on “Active learning strategies for bioinformatics teaching” (the first time I turned a blog post of mine into a poster…). The poster can be viewed on FigShare. I managed to make the poster a bit interactive itself, by having a small quiz on it. The results speak for themselves:
A quiz to make a poster on active learning techniques interactive
The more I read about how active learning techniques improve student learning, the more I am inclined to try out such techniques in my own teaching and training.
I attended the third week of Titus Brown’s “NGS Analysis Workshop”. This third week entailed, as one of the participants put it, ‘the bleeding edge of bioinformatics analysis taught by Software Carpentry instructors’ and was a unique opportunity to both learn different analysis techniques, try out new instruction material, as well as experience different instructors and their way of teaching. On top of that the group was just fantastic to hang out with, and we played a lot of volleyball.
I demonstrated some of my teaching and was asked by one of the students for references for the different active learning approaches I used. Rather then just emailing her, I decided to put these in this blog post.
The motivation of turning to active learning techniques is nicely summarised in a post on the ‘communications of the ACM’ blog entitled “Be It Resolved: Teaching Statements Must Embrace Active Learning and Eschew Lecture”. I highly recommended reading it and checking out the references mentioned. I am by no means an expert in the area, and simply am learning by doing. I have no ways to measure whether the techniques I use are beneficial, but student responses strongly encourage me to keep applying them. My teaching is also very much influenced by my being a Software Carpentry instructor.
The following describes what I do in the de novo genome assembly module of the ‘High Throughput Sequencing technologies and bioinformatics analysis’ course I organise (link to materials). I used part of that module for the NGS Analysis Workshop (link).
As before, full run throughput in gigabases (billion bases) is plotted against single-end read length for the different sequencing platforms, both on a log scale. Yes, I know a certain new instrument seems to be missing, hang on, I’m coming back to that…