Friday, May 10, 2013

Crosspost: Woohoo – two more genome announcement papers from our undergraduate project on built environment reference genomes

Crossposting this from the microBEnet blog.
Two new papers out from the microBEnet Undergraduate Research: Built Environment Reference Genomes  project:
These go with two previously published ones:
And two more coming. So proud of the undergrads in my lab who did this work and David Coil for coordinating it with help from Jenna Lang and Aaron Darling.  Undergrads at UC Davis sequencing genomes of organisms they isolated. So cool.


  1. Just discovered this project via @caseybergman, so cool! Glad to see that we're not the only ones doing such stuff.
    Our time to publication is much longer because the students also do annotation, and then we try to tell a biologically relevant story. Maybe we should have gone with a simpler approach like yours. On the other hand, the annotation step is very interesting for the students, teaches them what can be done with a genome and some of the power and limits of bioinformatics.
    In any case, there should be more such initiatives. This is really the way for students to learn about genomics and bioinformatics.

    1. Our goal in this project was to have the students learn something about microbial genomics. I agree that annotation and biological interpretation can be very educational but in our case we simply did not have the time given our students schedules to do that. So we decided data release papers would be it for now. But if we do this again actually we would probably want to copy your approach more ...

    2. I'd be curious to know what your students took from the course. I'll try to get our students' impressions on our blog at the end of the semester.

    3. Well, one difference with us vs. you -- it wasn't a course. This was part of a research project and was to give them research experience but it was not formalized into a course. Next time we will probably do this as part of an actual course.

    4. I gathered impressions from our students and put them on our blog: