Saturday, September 7, 2013

Still Here...new series of blog posts coming

Greetings to my 6 followers and many others who peruse this blog via google, facebook or other link.

Rest assured I have not fell off the planet; the purpose of this blog was to be a communication, teaching, disseminating tool for when I attend workshops, conferences, develop courses or read literature. Indeed apparently I don't travel as much as some in terms of conferences and workshops so I've had little write about...

That and I got swept away in the bid for grant funds available at my institution...was successful--HUZZAH, 4th year of trying was the charm apparently and now am in the thick of my own research as well as what I do on a daily basis as the Viral Diseases Branch bioinformatician.

However following the Workshop on Genomics this last January (and coming up again this January) I have been teaching a basic class on bioinformatic sequence analysis and recently attended a meeting on the NIAID - Dengue Vaccine Initiative.



Now the classes I've been teaching "in-house" where I work and at affiliated laboratories in our organization were designed with the 'beginner in mind'...you know what A,G,C,T is ...you know what an amino acid is and you know that three nucleotides 'make' or code for said amino acid. Pretty basic stuff; we build from there up to understanding different sequence statistics generated from analysis of alignments, antigenic analysis (since I had many flu enthusiasts) and basic phylogenetic construction followed on with how to start looking at and interpreting phylogenetic trees.

Everyone I meet wants to use, understand and be guru's at BEAST...my response is:
'Know the BASICS first'.
I decided to construct this "small" (40 hrs) set of lectures/slide presentations/datasets to assist those within the bioinformatics section and PIs who were interested in being able to actually do a first pass at their data. Not that I don't enjoy analyzing everyone's data for them and possibly getting on publications...but there is only one of me and well...a lethal dose of data out there...

credit: xkcd

Much of what I have done over the past year has been more or less 'reporting' with requests to look for the needle in the haystack should it pop up. I won't lie...it's tiring and when it's not my own research, tedious. I don't mind doing it, but I think there is more to be gained by empowering PIs and others interested in dipping their toes into bioinformatic sequence analysis to look at their own data. The goal being that hopefully they'll like it, they'll 'catch the bug' of excitement of being able to process massive text files not using notepad or wordpad (though we can start there if they need and work our way out!); they'll reap the benefits of looking at software tools that aren't as 'scary' as they once thought...and perhaps they'll seek more education increasing their knowledge, improving their own understanding and ability to conduct analysis.

That being said...I have to clean out all 'work' data and references to make the presentations and datasets 'clean'. While much of the data will end up in Genbank...as soon as I find my 36 hr day to get everything submitted, for the time being I need to unaffiliate my work. Not that they don't appreciate my teaching...but it's the PC thing to do for right now. SO...gleaning all the presentations etc takes time...so that blog series hopefully will go up by the end of the year.

OK...more Updates and Coming Soon...
  • A year ago I started a pdf newsletter for bioinformatics enthusiasts, minions and beginners highlighting tidbits from the 80+ blogs I follow, the literature, anecdotes etc that I come across in my job and on the web. This newsletter has grown so much that while I still email the one page wonder once a month (message me if you want to be on the list)...I have now transitioned to online newsletters of various bioinformatics and viral themes all hosted by Scoop.it which allows me to post so much more...in all it's geeked-out glory. Feel free to peruse.
  • Research Blogging
    • So I forever live in envy of my counterparts who find the time to do 'Research Blogging'. Seems like there are never enough hours in the day for me to do lab work, conduct analyses, 'bash' around on my Linux, keep up with my attempts to learn/get better at Python, teach/train, write manuscripts, write for money and read the literature...and yet I need to find the time. Processing the literature rather than skimming is ever more valuable...research blogging will force me to do that. So I'll start small and hopefully work my way up to the amount of research blogging that my peers do. Small meaning...once a month...ya, I said small. It will all be labeled under a tag of Research Blogging for future reference. So hopefully my blog won't go completely quiet as it did the past 8 months if I'm posting literature reading blogs.
  • NIAID Dengue Vaccine Initiative: Consultation on Dengue Vaccines
    • So earlier in the summer I had the opportunity to attend the Dengue Vaccine Initiative meeting held locally where all the 'big wigs' of dengue vaccine development get together and rub shoulders for 3 days highlighting advancements and considerations in vaccine design for dengue. While I am not an immunologist...so much of this was woohoo-- well over my head, I will be highlighting the speakers and summarizing what happened, similar to what I did in the Workshop on Genomics blog series, though less instructional, more just 'Here's what's up in the world of dengue vaccine design'. Mostly because I'm a genetics/sequencing geek...hell I'd barely know what a T-cell is if it weren't for wikipedia and my basic immunology book on Kindle. It was a free meeting and I don't think anything was proprietary or classified, ha! Unfortunately I won't be able to share the presentations/slides from the meeting, but I'll do my best to bring you up to speed for those that are interested in vaccine developements in dengue.
  • Course Content/Discussion: Bioinformatics: Basic Sequence Analysis
    • Per my earlier mention...I will be cleaning this up for posting on this blog. The presentations will most likely go up on figshare or slideshare; I haven't decided where I can host the datasets yet.
  • Workshop on Genomics 2014 in Cesky Krumlov, Czech Republic will be coming up in January...huzzah! I'll be back blogging...the drama, the heartache...the shear sadness of when a student hears "One does not simply email Illumina runs".
Credit: bytesizebio.net (ps. ahhh game of thrones...<3)

This year they've asked me to return as an instructor to help with lab sections, tutorials, general mischief, whatnot etc...which I am so honored and happy to oblige.

Until next time oh Minions of Bioinformatics...

Next Up:  Blog Series: NIAID Dengue Vaccine Initiative: Consultation on Dengue Vaccines heretofor abbreviated NIAID-DVI because I work contract for the Army where acronyms you can never remember are a way of life...