Course design

Many of my students could do work on GitHub Classroom; some got an error and had to fork a repo instead. The only ones who ended up committing changes as pull requests back were those who did the forking; the Classroom students didn’t seem to do this. I’ll dig into why, but overall, seems like just using regular repos one forks works better for now. GitHub Classroom looks like it has potential, especially as this class scales up, so I’ll check it out again next year.

Leaving GitHub classroom

About a quarter of the students are getting the message “You are forbidden from performing this action on” when they try to check out an assignment. This may be due to not yet approving your email account in GitHub, but it may be a different issue. GitHub knows about this but doesn’t have a fix yet. In the meantime, if there’s an assignment you want to do but can’t, instead go to, go to the appropriate assignment, click Fork (button in upper right), then make (and commit and push) changes in your fork of the assignment, then do a […]

GitHub Classroom bug

PhyloMeth poster
I have put up a poster for recruiting students locally (PDF here); advertising the course online will happen later (when there’s more material available). Content from poster: Spring 2016: Phylogenetic Methods (new course) Instructor: Brian O’Meara EEB603, Thurs. 12:40-3:25, 3 credits Learn how and why to: Build, test, and date phylogenies Study diversification, trait evolution, & more Create new methods Test using simulations Modern teaching best practices: Flipped classroom Active learning Group and solo work Ongoing discussions (offline and on)   Requirements: Scientific question(s), basic familiarity with R (no need to be an expert), laptop. In class you’ll be guided […]


I was already going to be doing GitHub for assignments: lets students proceed at their own pace, plus ease them into best practices in research (tracking changes, commenting, testing code) and, eventually, software (unit testing of code, package structure, etc.). Just saw a post about GitHub Classroom which looks like it might work well: lets students fork the exercises and develop it on their own. Not sure yet about doing checking with TravisCI (some of the checks will be rather slow), but considering it.

GitHub Classroom

How to design useful exercises is an important question for a class like this. I’ve taught in many workshops and such (SSB’s workshops at Evolution, Arnold & Felsenstein’s Evolutionary Quantitative Genetics workshops at NESCent and NIMBioS, phrapl workshops) and have gotten the best student feedback by teaching with a skeleton of a solution that has sections where we stop and talk about what is needed and which has some bits for students to figure out themselves but still in a framework. For example, from the EQG workshop: #Let's go back to coin flipping in R. Let's have three hypotheses: prob.heads.hypotheses […]

Exercise design

How to best host class discussions is an important question: need to make it accessible to students, and world-viewable, but also prevent spam (“Learn how I made money from home using ….”). I thought of a WordPress plugin but that can result in a static discussion: basically a series of posts, which can relate to each other, but lacks the fluidity of an IRC-like chat. IRC itself is fun to use, but it has declining usage. Slack is popular, but requires students to hook into a new system and the free version has a limited number of saved posts. I’ve […]

Class discussions

For first run, I’ve chosen not to go with edX, coursera, or the like but instead host locally. This is a trial run, so I think it’s premature to deal with the overhead that may come with having an official University course run through one of those services. I also don’t like how most free courses don’t seem accessible there until you register; maybe this is an optional setting, but I’d prefer for people to be able to stumble into a lecture or exercise through a web search. I’m thus doing a WordPress site for now. I’ve explored some plugins […]