Hand-crafted relational databases for fun and science

Mon, 05 Dec 2016 00:00:00 +0000

This post originally appeared on the Data Carpentry website

I’m a microbial ecologist that is primarily interested in understanding the ecological causes and consequences of plant-microbe interactions. Like many ecologists these days, my research spans the gamut from field to lab to laptop. Often the work involves collecting some leaves from plants in the field or from plants in a greenhouse, and then culturing from those leaves the fungi that live asymptomatically within them (a.k.a. endophytic fungi). Sometimes studying these communities relies on culturing the organisms in Petri dishes, and sometimes on directly extracting the DNA or RNA from the samples and sequencing that. One of the hardest things for me has been simply keeping track of what samples came from where, when, and who did what to which samples. To give an example: Let’s say I’ve got a fungal culture growing in a Petri dish, and I want to know how many times it has been subcultured (that is, regrown from an existing culture), when those subculturing events happened, what kind of plant tissue the original progenitor culture came from, and where that plant tissue itself came from out in the field. Oh and then downstream, I also want to know something about all the other such fungi that came out of that same plant and all their metadata as well. And I want to be able to get all of that programmatically.

Teaching to the Workflow

Tue, 15 Sep 2015 00:00:00 +0000

This post originally appeared on the Software Carpentry website.

"Teaching to the test" has a deservedly bad reputation, but what about "teaching to the workflow"? A group of us came together at the NCEAS Open Science Codefest last year and put together a paper on open science in ecology. In it, we sketch three examples of possible open science workflows (Figure 2 in the paper). In response, I was asked what Software Carpentry should teach to prepare people for working in those ways. My top three things are (in order):

Naupaka Zimmerman on The Carpentries

Hand-crafted relational databases for fun and science

Teaching to the Workflow