Monday, January 7, 2013

Blog Series: WoG, Cesky Krumlov; Day 1: Introduction


Day 1: Introductions, Reasons, Rationales and Methods to the Madness amounting to the creation of this workshop.

So last night we had the opening reception where everyone was able to meet; it is quite the diverse crowd but I simply had to corner Scott Handley and ask the question I'm sure he gets several times over--so much so that he's got slides worked into his introduction presentation talking about how the workshop came about and how it ended up in an isolated idyllic town 3 hours south of Prague.

Scott and his colleagues have been hosting workshops for several years now. Originally he'd attended, then TA'd for the workshop out of Woods Hole, MA which focused on molecular evolution. A workshop I tried for many years to go to as a graduate student, but alas was unable. But from others I have heard over and over how amazing of a workshop it is and therefore I highly recommend you look into it if that's the direction you'd like to go in your research. From a Woods Hole start they commenced doing workshops in other areas such as doing one for the CDC in Atlanta at the Smithsonian as well as Fort Collins, CO. Then they decided to do one in Europe and in the course of their research and contacts, found Cesky Krumlov. Cesky Krumlov was ideal--it had infrastructure for computer analysis (internet, ability to charge laptops easily), it was beautiful and different, but not so exciting that you'll miss classes to 'see the sights', and inexpensive. The workshops pay for themselves via the registration fees, there is no  outside grant that covers workshop costs here. If they get enough registrants the workshop is on, if not it's cancelled. So far attendance has been good and the workshops have all been rewarding experiences for all involved-so they've continued to host them.

Through the course of our conversation it came up, the rationale for this kind of workshop. When they first hosted the genomics workshop most of their attendees were PIs that had just gotten next generation sequencing capabilities and now had all this data they had no idea what to do with. Now in it's third year the attendance has moved more toward graduate students and postdocs who now are wrestling with mass quantities of data produced in their labs. He used the analogy of a tidal wave of data, easily overwhelming anyone in its path. There are simply not enough folks with the training and skills to manage and analyze this deluge; hence the workshop on genomics was borne.

Another topic of consideration is the value of continuing education in our field. Many times family members are asking me 'what? you're taking classes?...didn't you get your Ph.D.? Aren't you done with school already!?' Quite frankly in our line of work, the 'schooling' never stops, when it does, your career will be dead. If you are not moving as fast or at least attempting to catch up with your field through continual reading, workshops, collaborations, short courses, conferences...then you will become a relic before your career even starts. In the past it took 30 years to become a relic in biological research--then they invented high throughput sequencing--curses! Now if you don't keep up you can be easily outdated within a year--a year! Not only that, but it takes a skill set in order to conduct bioinformatic analysis, a skill set that has be learned flexibly so that it can easily and quickly change and adapt as the technology does. And it takes time to learn that skill set and perfect it's flexibility, so you have to invest that time (and money) to seek out those opportunities that allow you to grow and learn with the field.

Often times I think researchers have the impression that once the laboratory experiment (as in, wet lab) is run that the hard part is truly over. Not so much. Bioinformatics is not a 'magic black box' you push data into and out comes the next Science paper. Utilizing software, writing code, implementing bioinformatics is an experiment in and of itself. It can malfunction, you can put the wrong 'reagents' (Parameters) into it causing you to have to re-do it, it can break altogether, you can set up the experiment incorrectly and the computer gives you garbage back--after running for 48 hrs--doh!!! In silico computer based 'experiments' can take just as long or even longer to obtain results from as any laboratory experiment and more and more there should be a growing respect for this in the field. Quite frankly, though things are moving faster--they are still going to take as long as they take. And believe me I scream and yell at the computer runs as much as any gel or culturing experiment--both can take days and days to run, only to find our you missed one small crucial point and now have to start all over. SO, have the same patience and respect for bioinformatics as you would any wet lab experiment, believe me--it'll save you frustration, anxiety and exhaustion in the long run.

And that's just getting to the point of getting output from your computer experiment...

Now you have to figure out if the result makes sense or if you goofed and have to troubleshoot. See, no different than the wet lab. Honestly, sometimes I wish I could fix the problem with duct tape, new wiring, cleaning the system and tubing as opposed to having to glean through hundreds of lines of code or parameters to find the misplaced semi-colon! In the lab you visualize everything on your bench, in bioinformatics, it's all in your head, in the computer software (be it code or software parameters) and of course 500 little sheets of paper littering your desk with the schematics and flow of what you are doing or trying to do at each computational step.

Continuing education? Best thing ever.

Ready, set, sequence! Read on for todays highlights...

Highlights from this mornings introductory/welcome talks:
  • Everything and I mean everything will be posted on the website: including presentations, links, tutorials, projects--you name it, so check the website often. I will attempt to point you there as well, when I am too lazy to re-post here.
  • The important stuff was covered: Restrooms, coffee and internet
  • We get discounts for wearing our name tags...oh by the way, wear your name tag
  • Need a pub? There's one every 20 meters or so. Drink responsibly.
  • Computer lab is in the prelate--it's an older building that has been revamped by the awesome people of the town for our use to have charging stations and internet. So...
  1. Don't touch the frescos
  2. Wipe your feet
  3. It was used to house a Brewery at one point, hey that's cool (1596-1865).
  4. It dates back to the 14th century and has been renovated many times.
  5. Did I mention don't touch the frescos...ya don't lean on them either
  6. no food or drink
  7. The painter of the frescos died in 1791 so he can't come back and fix them if you touch them...
  8. So don't touch the frescos on the wall.
One of the best pieces of advice and perspective handed out from Scott (I'm paraphrasing):
Adjust your expectations. As of this year SEQwiki that houses most bioinformatic analysis software packages had 587 registered. That's a lot of software to sift through to find the program that will suit your needs most and it's still growing. Combined with the tidal wave of data this can often lead to getting tied up in the semantics of data processing and forgetting the biology
My advisor (Dave Ward, MSU-Bozeman, MT) in grad school often called this "missing the forest for the trees"...while detail is important, you can't get so hung up on procedure and detail that you miss the cool things actually being produced or coming to light via your analysis. When you focus on one tree, you may very well miss the forest fire raging in your data.
So keep calm, you will get frustrated, everyone has different threshholds of patience, expertise and computing hardware. One person may have a tricked out MacBook Pro while another has a hand-me-down Dell laptop and spins up so loud and high pitched it causes dogs to bark. Help each other, work in groups.
My advisor in grad school also liked to immortalize the words from the back cover of the Hitchhikers Guide to the Galaxy...
image credit:
So lets jump right in...