Workshop on Genomics January 12-24, 2014
Greetings Bioinformatic Campers!
I trust everyone had a lovely Christmas and have plans for a most happy New Year!
It’s that time of year again…where we rehash the glory and heartache of next generation sequencing data analysis as well as update you on the latest and greatest in the field. Two weeks of hands-on and lectures with some of the best people in the field today!
By way of introduction, I am Dr. Mel Melendrez, a researcher and bioinformaticist working in Washington D.C. I was an attendee of the workshop last year and blogged about my experience in the two week intensive. The organizers of the workshop seemed to enjoy my blogging shenanigans so much that they offered me a spot on the evomics website to blog live and tweet this year during the workshop! My background is microbial/viral ecology and evolution and of course I use next generation sequencing to answer questions in this field. Currently, my focus is on dengue and influenza viruses. I was particularly excited by the new faculty additions this year who will be talking on Metagenomics both clinical and environmental. If you would like to learn more about who I am, feel free to stalk me at:
The field of bioinformatics can be quite daunting for those with little or no background in computational biology. Bioinformatics is also a catch-all for all the specialized fields within the discipline. For instance, there are researchers who only focus on whole genome sequencing and comparision studies, others deal primarily in transcriptomics/proteomics, still others are metagenomic analysts. Additionally, those in the field of epidemiology have their own bioinformatic analysis packages; not to mention all the bioinformatic programmers who create the packages and pipelines used today. Personally, I have experience with whole genomes, single and multiple gene analyses, microbial/viral evolution analysis and some metagenomics. I have dealt with sequence data derived from sanger and next generation sequencing platforms (Roche, MiSeq, Ion Torrent). I don’t program beyond shell and bash scripts, though I have some working knowledge of python and R (stats package) but I only program when I have to and my knowledge of transcriptomics is minimal; hence why I was drawn into this workshop last year. The field itself moves at lightening pace and it is not unusual to feel as though you are in a constant state of ‘catch up’. Just when you acquire useful knowledge, it suddenly becomes ‘outdated’. This can prove to be an immense frustration.
The goal of this blog is to provide a download of topics covered, direct you toward and facilitate the practical tutorials as well as resources and anecdotes on things I learn in real-time. It will also serve as an archive…it helps to have decipherable e-notes readily available. I also desire to make what we do as bioinformaticians more ‘accessible’ to other investigators who would like to manhandle their own data (or have a grad student or technician learn how to do it) instead of waiting several months for a potentially incredibly busy bioinformatic collaborator to get back to them (I’m not pointing fingers at myself at all! Ok, maybe one…or all 10). It is easy to get bogged down, so let’s dispense some knowledge and hopefully lighten everyone’s load!
If you are here reading this blog I will assume you are an investigator, student, technician or generally interested party who knows what sequencing is, what a nucleotide is, what an amino acid is and if I show you ‘ATGC’ versus ‘AUGC’ you know what both are. Background in software packages, evolutionary or genomic analysis and programming would be helpful but will not be assumed.
The workshop covers a variety of topics and while it is useful to have some background knowledge the workshop was not designed for you to be an expert when you arrive. That being said, I do have some prepartory advice! On the website there is a page under Information called Preparation it has a lot of good links to introduce you to the various topics that will be covered over the course of the two weeks and I highly recommend it. In addition, last year I wrote several preparatory blogs on the different subjects for those that needed more background information on certain topics so feel free to peruse those in preparation as well.
- Modern Genome Sequencing (minus Nanopore or any single-molecule sequencing, this is as of Jan 2013).
- Genome Structure
Also we will be ‘officially’ twittering during the workshop this year!
Have a question you’re too nervous to ask? Twitter it! I’ll ask for you! #evomics2014
Like I said earlier we have some great faculty on board this year, and this year, since I don’t have to write prep blogs, I will be writing up some faculty highlights so we can get to know the men and women behind the bioinformatic madness…so stay tuned!
Looking forward to a great workshop this year and everyone that will be attending…2 weeks-ish and counting!
Signing Off…Dr. Mel