Monday, December 31, 2012

Time for a Tutorial...or how about 10

Greetings, Salutations and Happy New Years Eve!

So I have decided to run a 'live-blog' starting January 7, 2013 with the expressed intent of conveying whatever I learn to you--the blog reader.

For those unfamiliar with who I am, you can read my byline: aspiring infectious disease ecologist. I am currently a bioinformatician at Walter Reed Army Institute of Research (WRAIR) in Silver Spring, MD. My educational background is quite varied and if that interests you click over to my LinkedIn Profile which also has a list of my recent scientific publications.

Crib Sheet Bio: Grew up everywhere...ended up in Hawaii and graduated from Maui High School in 1997. I did my undergraduate degree at Pacific Lutheran University in Tacoma, WA--Major PreMed/Biology and Spanish Language and Literature, graduated in 2001. Worked for a plastic surgeon 2 years back in Hawaii then promptly opted out of medical school and in 2003 entered into a Ph.D. program in Ecology and Environmental Sciences at Montana State University in Bozeman, MT (microbiology focus; Advisor Dr. David M. Ward, Land Resources and Environmental Science Dept). I graduated in 2010 and immediately started a post-doctoral fellowship courtesy of the National Research Council in Bangkok, Thailand at the Armed Forces Research Institute of Medical Sciences (AFRIMS; Advisor: Dr/MAJ Richard Jarman, Virology Dept). In May 2012, I was offered a position at WRAIR helming the massive amounts of sequence data being generated through the introduction of their 454 Roche FLX and Ion Torrent sequencing platforms. We may also be obtaining a MiSeq at some point as well. So I am currently running the gauntlet of various sequencing technologies and implementing bioinformatic pipelines developed in-house as well as utilizing the best of what academia has been able to offer in terms of open source software. I am also coincidentally (or not so coincidentally perhaps) a 2013-2014 ASM/BWF Science Teaching Fellow, so as you might surmise--I enjoy research and teaching and aspire to an academic posting in the future.

My current research muse is dengue virus. Specifically, dengue virus quasispecies characterization and dynamics over time and space. I have also worked on sequence data from thermophilic Synechococcus spp. bacteria, influenza A (pH1N1, sH1N1, H3N2), influenza B (Yamagata and Victoria lineages) and Hepatitis E virus. 

WRAIR as well as other military institutions have certain restrictions on what software can be installed and there is a lengthy approval process to ensure information assurance policies are followed. For that reason, those of you following this blog may not be able to immediately use the software, pipelines or even access certain internet links. Fear not, I feel you pain. I will make every attempt to make sure links I provide will allow you to access the information no matter where you are at. This means I will provide links to the sites where you can find downloads for academic open source software, I will not be providing actual downloads through this blog (see disclaimer).

DISCLAIMER: Please do not attempt to install any software discussed on this blog without prior authorization and approvals if you work for an institution with enhanced security policies in place. 

This disclaimer will appear at the top of any blog post that contains links leading you to software download sites to remind you to be aware; annoying but necessary. If you work at WRAIR and need assistance with the approval process, please contact me directly. If you work elsewhere, please check the regulations of your institution for guidance on policies regarding software downloads, installation and implementation.

I am not a professional science blogger so apologies if the the prose is less than polished. As you also probably noticed, I opted for the fantastically bland and ever-so boring 'simple' display for this blog, but that was by design. I plan on conveying as much material (text, links, diagrams etc.) as possible and want that to be the highlight of this blog as opposed to fancy displays which can get distracting for me. I have always been the girl who gravitates to shiny objects--great for picking up pennies, not so great when I am attempting to focus.

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. 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 the attractiveness of the workshop I will be blogging about. 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, hopefully, practical tutorials and resources on things I learn in real-time and to serve as an helps to have decipherable e-notes readily available. I also desire to make what I do 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 am going to sheepishly raise my own hand on this as I have reports and data to get back to collaborators myself in addition to my own research and routine obligations at WRAIR. Granted I only started 7 mos ago, so I'll catch up--BUT it is easy to get bogged down, so let's dispense some knowledge and hopefully lighten everyone's load! The only way I personally learn things is to keep copious notes and re-write/view them in different ways--we'll see how this works out.

Blog Series #1: Workshop on Genomics, Cesky Krumlov, Czech Republic, 7-18 Jan 2013.
First Blog: 7 January 2013
Last Blog: 18 January 2013
Assumed Audience: Investigators, students, technicians who know what sequencing is, what a nucleotide is, what an amino acid is and if I showed them 'ATGC' and 'AUGC' they know what both are. Background in software packages, evolutionary or genomic analysis and programming would be helpful but will not be assumed. So for some this may be a little more of a hand-hold than you might like--feel free to skim. 

I have obtained approval to 'live blog' this workshop from Dr. Scott Handley, many thanks!

I will post a preparation blog prior to officially starting on 7 Jan 2013. Blog posts will arrive in the evening as I cannot blog what I have not learned!

Comments and questions are welcome, what I cannot answer I will ask someone at the workshop--please identify yourself in your comment if you don't use a profile, I'm not a fan of anonymous posting and will not bother to answer/reply to anonymous posts.

Following the workshop, I cannot guarantee how often posts will appear as I stated earlier; I'm not a science blogger really, but feel free to subscribe and then you'll get a notice when postings do happen. You will probably only see postings on this blog site when I feel I have something functionally useful to convey or I am attending a workshop where I have organizer permission to live-blog or a conference.

Ok! For those of you without 2 weeks to spare to flit off to the Czech Republic to learn the latest and greatest in genomic analysis, care to join the journey and have a somewhat 'virtual-workshop' experience?

Excellent, I wish us both luck then.

Kind Regards,
Melanie Melendrez, Ph.D.
Chief, Bioinformatics, Lead Scientist
2013-2014 ASM/BWF Science Teaching Fellow
Walter Reed Army Institute of Research
Viral Diseases Branch
Silver Spring, MD 20910