Help I'm New to the Lab

Here’s a checklist and resources of things for people that are new (or not so new) to the lab. Before freaking out, be sure to read this blog post from Pat.

Logistics

The first week in the lab can be a bit hectic, welcome! Here are a number of items that we have found are critical to getting off on a good foot…

Boot camp

Very few people join the lab with the foundation to do reproducible microbial ecology analysis (Pat didn’t!), but over time, we’ve found a set of tools are pretty critical to success in the lab. We think of this as our full stack for doing the analytical end as a microbial ecologist who is concerned about the reproducibility of their analysis. Don’t feel like you need to master this stack in your first week of being in the lab. By going through these tutorials and actually using the tools in your daily work you’ll eventually get it. The Schloss Lab Full Stack includes: mothur, R, knitr, git, bash, and make. In your first week or two of being in the lab, you should do the following tutorials and do them all on Flux, the high performance computer cluster that the lab uses:

You can supplement those materials with these tutorials and cheat sheets:

Useful software

We are primarily a Mac OS X lab and we make use of a Linux-based computer cluster. Thankfully the tool set that we use can be ported to any operating system.