I’m currently a post-doctoral researcher at Penn State University. I honestly don’t know how to classify myself as a scientist. I have a bachelor’s degree in Biochemistry and a MS and PhD in Plant Biology, but I’m basically a microbial ecologist who studies plant (and sometimes Human) associated fungi and bacteria. My computer skills developed a decade ago as I started at the command line to do phylogenetic analyses of gene sequences. In the last five years I’ve tried to develop my programming skills to deal with a deluge of genomic data from new sequencing technologies. My recent time has been spent working on several “big data” microbial and plant genome sequencing projects and metagenomic studies with soil and animal gut microbiomes. While I still spend most of my time using command line tools, I code most frequently using the languages R and Python and very rarely use Perl. I also enjoy web programming and have become fairly proficient in JavaScript (including D3), PHP, and MySQL for communicating data via the web. I’ve been involved in teaching a few bioinformatics workshops and semester long courses, but I’m here to attempt to take my teaching skills to new levels. I’m very excited and honored to be involved with Software Carpentry.
You can find out more about me at these locations:
Web: joshuaherr.com
Twitter: @number_three
Blog: cymeandcystidium.com
Github: jrherr
BioStar: Josh Herr