Category Archives: Computer tutorials

For one of our ongoing metagenomic projects I needed to split predicted proteins into cytoplasmic and transmembrane groups. After looking at a couple of different options I opted to use DeepTMHMM, part of the biolib framework. DeepTMHMM has a wonderful … Continue reading →

This post comes form Luke Piszkin, an undergraduate researcher in the Bowman Lab. Gnu Parallel is a must-have utility for anyone that spends a lot of time in Linux Land, and Luke recently had to gain some Gnu Parallel fluency … Continue reading →

It’s been a long time since I’ve had the bandwidth to write up a code snippet here. This morning I had not quite enough time between Zoom meetings to tackle something more involved, so here goes! In this case I … Continue reading →

A common exercise in environmental microbiology is counting bacterial cells with an epifluorescent microscope. During my PhD I spend many hours hunched over a microscope in a darkened room, contemplating which points of light were bacteria (and should thus be … Continue reading →

Self-organizing maps (SOMs) are a form of neural network and a wonderful way to partition complex data.  In our lab they’re a routine part of our flow cytometry and sequence analysis workflows, but we use them for all kinds of … Continue reading →

Introduction Hi! I’m Sabeel Mansuri, an Undergraduate Research Assistant for the Bowman Lab at the Scripps Institute of Oceanography, University of California San Diego. The following is a tutorial that demonstrates a pipeline used to assemble and annotate a bacterial … Continue reading →

Weighted gene correlation network analysis (WGCNA) is a powerful network analysis tool that can be used to identify groups of highly correlated genes that co-occur across your samples. Thus genes are sorted into modules and these modules can then be … Continue reading →

Hi! I’m Natalia Erazo, currently working on the Ecuador project aimed at examining biogeochemical processes in mangrove forest. In this tutorial, we’ll learn the basics of (free) QGIS, how to import vector data, and make a map using data obtained from … Continue reading →

It’s been a while since I was a new graduate student, and I’ve forgotten how little I knew about computers back then.  I was reminded recently while teaching a couple of lab members how to use ffmpeg, an excellent command … Continue reading →