Sunday, January 20, 2013

Workshop on Genomics 2013: Final musings, anecdotes, mutterings and OCD tendencies garnered...

Greetings bioinformatic campers!

Last blog from ever so idyllic Prague, Czech Republic.

It has been a long two weeks, jam packed with beer, wine, sequencing, programs like RAD and programs like CRAP--mmm, haha; fun-guys, snow ball fights, genomics, scary math, more oddly named software, tutorials galore, unix ninjas and sequencing gurus, enough 'considerations' to have us spinning for years to lets rehash the glory a little bit shall we?

Of life, love, linux and latent twitching... Highlights from 2013 Workshop on Genomics, Cesky Krumlov, Czech Republic in no particular order--most of the below is in good fun, a lot intellectually was learned, see all the previous blogs! But in reflection there were some truly golden moments both scientifically and personally as those that attended and those that ran the workshop were indeed awesome like that:

  • "Beer, Bethesda and Biology"
  • "We are drowning in information and starving for knowledge": sequencing has gotten so cheap now that we are producing so much data that we haven't the people, expertise and/or resources to remotely scratch the surface of analysis. Don't be afraid of learning the tools, handling the data yourself, asking questions and teaching others!
  • Mike Zody is a sequencing guru
  • Julian Catchen is a unix ninja
  • Wait til you are in the air before taking OTC sleeping meds
  • We need more workshops like this.
  • "Adjust your expectations!"~Scott Handley. This is applicable to what is about to happen in your various research programs whether you are grad student, postdoc or trained PI. Scott's advice applies even after this workshop is over. Everyone has different levels, some will be faster at Unix, some will be better at constructing graphics, some will catch onto subject and concepts 10x faster than patient with yourself, relax and drink much as possible.
  • Bioinformatics software is seriously, there is some massive PMS going on in some software packages. Again, be patient.
  • Don't touch the frescos
  • Seriously...the painter is dead...don't touch the frescos
  • Bioinformatics is FUN!
  • Programming is FUN!
  • Unix is FUN! this point we wonder if our instructors are high. Later we realize that in fact they aren't and once you get the hang of it...yes, it is fun. Fun mixed with cuss words, keyboard banging, beer drinking, more cuss words and a huge HUZZAH when it finally works!
  • "If you are typing, you are doing it wrong" ~Julian Catchen
  • "There are two types of users in this world those that have a white background with black type (emacs users) and those that have a black background with green type (Vim users)" ~Julian, "What if you have a black background with white type???" ~student, "Then you are confused" ~Julian, "It's been years and I use a black background with white type still..." ~Daniel McDonald (python course instructor)...collective silence as no one wants to reveal to Daniel he is still 'confused'. :)
  • "Vim or DEATH!" ~my husband, Tyghe Vallard--python programmer at WRAIR
  • "Alright, you are my may use Emacs, but you must never speak of it." ~Tyghe
  • Seriously...don't touch the frescos
  • What's an isochore again?
  • There are ALOT of programs
  • Amazon sponsors us $100!
  • The QIIME tutorial failing yet still managing to be hella cool program.
  • There are a lot of sequencing platform options, make an informed decision!
  • "Sequencing means nothing without biological and evolutionary context"
  • 60 people logging onto instances at once? Amazon instance FAIL! DOH!
  • ChIP-seq is scary...and after Manuel's talk, it's better but still scary.
  • Watch your phred score interpretation! It'll depend on platform.
  • One *ome to rule them all?
  • Snow ball fights at 3am are fun...
  • Getting up for 9am lecture after a snow ball fight that goes til 3 am is not fun.
  • "It all depends"
  • "What is your question?"
  • "Garbage in garbage out"
  • Ctrl+V, tab
  • hacking up tinkerbell.txt
  • There is no push button solution...damnit
  • A student suggests we should have an "IKEA catalog" of options to pick from to make it easier.
  • RStudio makes some damn pretty figures
  • When in it, then ask Daniel....or Luke...or Konrad....or Pete....or Kristina
  • Always consider normalizing your data
  • metadata, metadata, metadata
  • Sea dragons are cool why wouldn't you want to study them?
  • Tree of Life versus Networks of microbes
  • "UniFrac is robust against garbage trees" ~Daniel McDonald
  • Joseph Bielawski thought it was really cool when he saw my card and that it stated I worked for the Cherokee Nations and was a Bioinformaticist for they are my actual employer, though WRAIR is my 'client'. Hence that'd make me the head bioinformaticist for the Cherokee Nations. Epic indeed.
  • Fungi like whisky
  • "The search for homologous genes is quite futile except in very close relatives" ~Ernst Mayr, 1963.
  • CRAP
  • and just so you don't forget...
totally serious about those McDonald fries...

Well, 12 days (3 sessions a day)...hashing, rehashing, learning, re-learning... I do hope that this teaching blog series proved (and continues to prove) useful for those of you looking to get into bioinformatic analysis, looking into buying a sequencing platform or attended the workshop and have completely forgotten what we talked about as your eyes glazed over after the 15th session...

Don't forget about the website!!! It has all the links to presentations, tutorials and anything I didn't touch on because I was too lazy and linked it instead!

And as I mentioned in one of my blog posts when dealing with a field that moves as fast as computing and bioinformatics does, it is important to Not Panic! This blog will stay up for future reference and hopefully it'll take longer than 6 mos before it's 'outdated'. Still there's a lot of good foundational information to be learned from what was presented in this workshop and I encourage you to continue learning...always. When you stop learning, your career is dead. Workshops like this one are so valuable for continuing education and networking...broadening your outlook, increasing your toolset, de-mystifying the mystified and if you ever have the opportunity to go to the Cesky Krumlov workshop (genomics or evolution) or Woods Hole, MA molecular evolution workshop, good on you--you will have one of the best most intense experiences in learning you can have...and it will be awesome.

And because I like to cover all my bases... should you die in the pursuit of your genomics aspirations, perhaps this quote from the Irish bar I was at tonight will help:

"May you be in heaven an hour before the devil knows your dead"

Totally unrelated to anything in the blog series, but I'm sharing it anyway...because it's awesome. I hope everyone had safe trips back to their respective countries, homes, labs etc... It was an absolute privilege to get to know you all, instructors and students alike.

This is Dr. Mel signing out from Prague...she has wine to be drunk, a hot shower to take, flannel pajamas to put on and a husband to return to on the morrow....


Melanie Melendrez, Ph.D.
Chief, Bioinformatics, Lead Scientist
Walter Reed Army Institute of Research
Viral Diseases Branch
Silver Spring, MD 20910