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.
For my contribution, I wanted to demonstrate as many aspects as I could of what I wrote in my “10 tips and tricks for instructing and teaching by means of live coding” post.
So here was the plan:
- 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.
I was recently asked to provide a testimonial on why I am an instructor for Software Carpentry and Data Carpentry. Here it is:
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.
This testimonial can also be found here.
I attended the ”FEBS-IUBMB workshop on education in molecular life sciences”, 18 – 19 SEPT 2015, in Oslo, Norway. Although ‘molecular life sciences’ is part of the workshop title, many of what was discussed was applicable to a much wider range of subjects.
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).
Open source, open data, open course
We recently had the third instalment of the course in Throughput Sequencing technologies and bioinformatics analysis. This course aims to provide students, as well as users of the organising service platforms, basic skills to analyse their own sequencing data using existing tools. We teach both unix command line-based tools, as well as the Galaxy web-based framework.
I coordinate the course, but also teach a two-day module on de novo genome assembly. I keep developing the material for this course, and am increasingly relying on material openly licensed by others. To me, it is fantastic that others are willing to share material they developed openly for others to (re)use. It was hugely inspiring to discover material such as the assembly exercise, and the IPython notebook to build small De Bruijn Graphs (see below). To me, this confirms that ‘opening up’ in science increases the value of material many orders of magnitude. I am not saying that the course would have been impossible without having this material available, but I do feel the course has become much better because of it.
‘Open’ made this course possible
This course used:
- openly available sequencing data released by the sequencing companies (although some of the Illumina reads are behind a – free – login account)
- sequencing data made openly available by individual researchers
- code developed for teaching made available by individual researchers under a permissive license
- open source software programs
(for a full list or resources, see this document).
I am extremely grateful to the authors/providers of these resources, as they greatly benefitted this course!
‘Opening up’ is the least I can do to pay back
In exchange, the very least I can do is making my final course module openly available as well.
The rest of this post describes the material and it’s sources in more detail.
About a year ago, I attended a Software Carpentry Bootcamp. Software Carpentry aims ‘to make scientists more productive, and their work more reliable, by teaching them basic computing skills’. As I described in a previous blogpost, attending the bootcamp changed many aspects of the way I work. I also decided to become a Software Carpentry instructor. Together with Karin Lagesen, we recently taught a BootCamp in Oslo. Our group at the Centre for Ecological and Evolutionary Synthesis (CEES) is working on different aspects related to fish genomics. This more or less started with our leading role in the project for the sequencing and assembly of the genome of Atlantic cod. As part of that project, many group members had to learn basic unix shell commands, making small pipelines, running programs, and sometimes a bit of scripting. Now, we see many more people at the CEES are moving into bioinformatics, often as a result of them starting to get high-throughput sequencing data. Thus, we have many self-taught bioinformaticians at the centre, in other words, the ideal target audience for Software Carpentry.
To help the bioinformatics work in our group apply the principles of Software Carpentry, we are going to have an ‘extended’ workshop, spread over several weeks with one half-day session each week. In this post, I will present the intended subjects. Continue reading