LifeFormulae Blog » Posts for tag 'molecular biology'

“You can’t do Bioinformatics if you haven’t worked in a wet lab” No comments yet

The line “you can’t do bioinformatics if you haven’t worked in a wet lab”, has been used as the basis for the “you need to know where the data comes from” argument time and time again.   I actually saw this in print in a slide presentation at the Next-Generation Sequencing Data Analysis conference in Providence, RI, in September 2008. 

I can sympathize with this viewpoint, but I don’t agree with it.  For instance, I designed the data system, compiled the data, and did the field testing that certified a re-engined aircraft, but I can’t pilot a plane.   I did do a lot of field laboratory work and it was “wet” - if snow, sleet, and rain count, along with desert dust and volcanic ash.

Knowing where the data comes from is very important, but what is of more importance is whether or not the data is actually measuring what it is supposed to measure  — data validity (are your instruments correctly calibrated and is the sampling rate sufficient), what is the format of the data, what is the size of the data, and to what sort of analysis will the data be subjected.

If the lab experience is so very important, a simple systems analysis is a very good tool to use.  As I’ve done it, the observer/programmer/engineer would “live” in the lab for a period of time — usually two to four weeks, or until they have a good grasp of the processes involved, taking copious notes and asking lots of questions.  That person may actually perform some of the work involved if desired.
This person should have some understanding of molecular biology, etc. to fully appreciate the lab experience. 

This activity has the potential of illuminating possible bottlenecks or methods that may need modification or fine tuning.  If more that one site is involved, so much the better, as discrepancies in processes will be made obvious.

My biological wet lab experience got me a “you have excellent lab technique” and a job offer, which I declined.

Bioinformatics training also comes into question.  Many courses just help the student determine which internet site to go to for information, or how to construct a FASTA-formatted sequence, or parse a BLAST output or a GenBank report.  They can’t do much except offer a survey of things “bioinformatic”. Not much time is spent on information management or engineering approaches.

I jumped from engineering to bioinformatics in the early 90’s.  The object-oriented data model I presented apparently found an audience.  I did some reading up on genetics, etc. before the interview, but most of the knowledge used to answer interview questions such as, “what are the four basic building block of life”, came from watching X-Files.  Things have gotten a lot more complicated (the textbooks have gotten heavier), and keeping up with new discoveries can become quite a task.

Next week I will offer a series of “horror stories”, or some of my experiences in the bioinformatics arena.

Top of page / Subscribe to new Entries (RSS)