Sunday, April 26, 2015

Learning R: A Tutorial for Beginners

TryR is another great place to start learning R.
About a month ago, I put together an R tutorial for my departmental colleagues and classmates here at the University of Pennsylvania. In addition to getting my colleagues started with R, I also wanted to make the information available to anyone else who wants to learn. The tutorial was based entirely on a live demonstration and working through some examples, so there are no slides. All of the materials can be found on Github here.

The tutorial package can be downloaded as compressed source code according to the README file. This includes the R script that you can run and work through, as well as an R notebook file that includes the R output so you can see what examples of result output. Finally it includes an example dataset as a comma separated value (csv) file, which I use to illustrate how to import data into R.

Sunday, April 19, 2015

Defining Microbiome Engineering and Our Realistic Expectations

Microbes, including bacteria, viruses, and fungi, are all around
us. <Source>
Most of us are aware of the impacts the human-associated microbial communities (the human microbiome) have on our health. These communities consist of the bacteria, fungi, viruses, and other microbes that live on and in our bodies. As I have mentioned in previous posts, the field of human microbial ecology has really taken off in the past decade, primarily as a result of next generation sequencing that has powered our scientific abilities to discover a more robust human microbiome than previously appreciated.

Sunday, April 12, 2015

Updates on Fecal Microbiome Transplants, Microbiome Study Reproducibility, and Basic Research (IHMC2015)

Paul Wilmes, one of our Luxembourg hosts, presenting
the congress opening remarks.
A couple of weeks ago I had the amazing opportunity to attend the International Human Microbiome Congress (IHMC2015) in Luxembourg. This congress got together the leading microbiome researchers from around the world to share and discuss their science. I met a lot of awesome microbiome researchers, saw a lot of the most recent microbiome research, and even had the opportunity to represent the Grice lab by talking about my research.

Sunday, April 5, 2015

The Scientist’s Obligation to Public Communication

Get out there and share your science! Source
I recently had the opportunity to attend a talk given by the popular and insightful Vincent Racaniello. For those of you who don’t know, Vincent is a virologist who made significant advances in Polio research, but has since taken on science communication and outreach later in his career. He is the host of the popular podcasts TWIM, TWIVTWIP, and Urban Agriculture. On a more personal note, Vincent has been one of my role models in my endeavors in science outreach and communication, including this blog.