Working in bioinformatics for three and a half years (Jan 2002 - Aug 2005)
was an interesting and enlightening work experience in my career. The
Virginia Bioinformatics
Institute (which is part of
Virginia Tech) was started with
some of the tobacco industry settlement money. I joined about a year after
it was started and in the time I was there it grew from 60 people to more than
200.
I built and led the software development arm that worked on many of the
institute director's research grants (totaling about $8 million when I left).
The funding came primarily from the US Army and the National Institutes of
Health (NIH). The grant that got it all started was from the US Army and
initiated the
PathPort
(Pathogen Portal) project. Later on, the
PATRIC and
ProteinBank
projects from NIH expanded the software development team to encompass more
than 20 members.
Prior to bioinformatics, I had not encountered a field in which the science
on which the computations were based was in constant flux. In biology, the
exceptions seem to outnumber the "rules". This is best exemplified by the
central
dogma of molecular biology, which at the very least, is significantly
incomplete as it ignores RNA genes (embedded within the "junk" DNA) and
RNA interference which can occur from the spliced out introns. Making matters
worse is the fact that not all organisms are the same. This is particularly
true of virus and bacteria, in which different species use different amino
acid encoding schemes. These elements (and more) made developing software
for bioinformatics quite challenging and required that the software systems
be flexible and developed on short time schedules. If the systems took too
long to develop, then the assumptions upon which they are based will be
altered by new scientific discoveries and understandings. Similarly, in order
to avoid having to throw systems away and start from scratch each time a new
biological discovery is made (which changes our scientific understanding of
molecular biology), these software systems must possess designs flexible
enough to enable rapid adaptation.
