Saturday, January 18, 2014

Details and Perspectives as Illumina Announces their Newest DNA Sequencing Machines and the $1,000 Human Genome


A couple of days ago, at the healthcare investment JP Morgan Healthcare Conference, the CEO of Illumina (one of the major DNA sequencing technology companies) announced their newest line sequencing machines.  The two new DNA sequencers are the NextSeq 500 and the HiSeq X10, with the NextSeq 500 being marketed for everyday laboratory use, and the HiSeq X10 being marketed as a factory level, population sequencer (this is the higher power model).  These are going to be powerful, state-of-the-art machines that are going to have a significant impact on both research and clinical applications.  Here I am going to briefly cover what these new machines are and what their release means for contemporary research and clinical applications.  As always, I will also point you in the right direction for further reading, in case you are interested in more.

Sunday, January 12, 2014

Recent Publication: Our Ongoing Study of The Traumatic Wound Microbiome

A few days ago our lab, in collaboration with some folks here at the Hospital of the University of Pennsylvania Orthopaedics Department, published a manuscript in the Journal of Orthopedic Research.  The title of our manuscript was "Culture-independent pilot study of microbiota colonizing open fractures and association with severity, mechanism, location, and complication from presentation to early outpatient follow-up".  This is a report of our ongoing prospective study in which we are characterizing the microbial communities associated with open fracture wounds and their adjacent healthy skin, as well as describing correlations between the microbiome and clinical factors (such as healing complications and wound severity).  Unfortunately this paper is not open access, so you are going to have to access it through a university or local library subscription to the journal.

Sunday, January 5, 2014

Learning Linux: How I Turned My Old PC Into a Linux Server


I do a lot of computational microbiological research, so having a basic understanding of how computers work is essential.  Because computers play such an important role in my research, and because I am just genuinely interested in them, I decided to dive further into the linux world by setting up and maintaining my own personal linux "server".  I always find this kind of thing is a great way for me to learn because it gives me the chance to immerse myself in the environment and forces me to keep learning about how the systems work.  So far this has been a pretty cool experience.  In this post I am going to outline my process of setting up my own linux "server" using an old PC, and go over the pitfalls & decisions I encountered through the process.  I hope this will be an enjoyable little story of my short linux adventure so far, and also hope it will provide you with helpful resources in case you want to try the same thing (and if you do try this on your own, ALWAYS backup your hard drive before you start).  And let's be honest, I will forget how I did it if I don't record it somewhere, and blogs are great places for recording these kinds of outlines.