Starting from scratch

[wrightaprilm]

Hi all,

I'm starting a faculty position in a few weeks, and I wanted to run some things by this group. I'm starting at a primarily undergrad institution (~9 Master's students), with immense support for both teaching computation and integrating computation in the curriculum (at home in biology and abroad).

Did any of you start from scratch building a bioinformatics pipeline? My first semester, I'm teaching genetics so I'm not too overloaded. But after that, I can start developing courses. I was thinking I might teach bioinformatics at the Master's level first, so I can have access to a TA pool for teaching undergraduates. What are the courses that should be on the books for undergraduates? I think I would ideally like to do a Carpentries-style project-based introduction to data management and biological data analysis to be taken freshman or sophomore years. If they complete that course with a passing grade, they can then take course work with computational labs (i.e., evolutionary bioinformatics lab in conjunction with the evolution course, ecoinformatics with the ecology course) and upper-level bioinformatics.

I like this approach for a couple reasons:

1. Taking informatics early lets me identify students who might be talented and motivated, so I can invite them into my lab :)
2. I want to integrate computation in the cirrciculum
3. But I don't necessarily want to teach ecology. So having an ecoinformatics lab means I can partner with the person who does teach ecology to codevelop a curriculum
4. Because the curriculum is somewhat sequential, I have a roadmap for development that isn't sticking me with too many preps at once.

What I don't like:

1. Students can opt out of learning computation, unless we want to make it a requirement. I think there's support for this, but I'm not sure how I feel about this. I suspect we would lose students along pretty predictable demographic lines.
2. I am worried about how much time we'd lose to reviewing the basics each time students signed up for a new computational lab.

Just some thoughts. Assuming a supportive department and no previous computational course infrastructure, what would you do?

[lexnederbragt]

You are in 'a good place' :-)

Have you seen the 'semester long DataCarpentry course'? https://jabberwocky.weecology.org/2016/11/14/fork-our-course-a-semester-long-data-carpentry-course-for-biologists/

[wrightaprilm]

I have. But that certainly shouldn't be the only course I put on the books for undergrads.