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I joined the bioinformatics
group at Genetics Institute
in August 1995 just a few months after getting my undergraduate
degree from WPI. Dr. David Merberg
was my first supervisor and was the one responsible for triggering
and supporting my interests in computational biology and technical
computing
My post-college
plan was to pursue a straight scientific career in bioinformatics
or computational biology. It was only after Dr. Merberg let me teach
myself Perl on company time did I start getting drawn towards scientific
software development. I wrote small pieces of code to automate the boring
parts of my job (analyzing cDNA sequences) and shared them with people
in my group who encouraged me to take my one-off scripts and turn
them into a straightforward pipeline that could be used by everyone.
Those initial cheesy perl scripts,
CGI's and parsers ended up becoming the company's first high-throughput
analysis pipeline. Soon enough our group was looking to purchase
bigger Unix hardware. Once again Dr. Merberg let me get deeply involved
with things that I was wildly unqualified for on paper and I ended
up helping to purchase compute servers and storage arrays. Once
the new hardware arrived I was hooked - building out and managing
the technical computing infrastructure for our group consumed more
and more of my time.
The immeasurable amount
of value that the life science research community has gained from
freely available software cemented my views regarding open source
and led me to volunteer my own time and effort as a member of the
BioPerl Project and the Open
Bioinformatics Foundation.
As part of a promotion in 1998 I was formally taken
off the company scientific career ladder and was given an IT-style
title. This was also about the time that I started thinking that I could
focus my career towards being a generalist or "bioinformatics hybrid"
- a person who was not really an expert in any one field but had
skills and practical experience spanning several disciplines.
From 1998-2000 I spent
most of my time working on the scientific and technical computing
infrastructure used by various scientists involved in bioinformatics,
genomics and basic discovery research. I also proved without a doubt
that I am essentially a generalist and infrastructure geek
at heart.
The desire to concentrate
on scientific infrastructure projects combined with fears of growing
too complacent and comfortable after five years at Genetics Institute
lead me to accept a position with Blackstone Computing (Formally Blackstone Technology Group). At Blackstone I was a principal member of the life science consulting practice and my biggest solo project was building and integrating the VAMPIRE cluster for Vertex Pharmaceuticals.
I left Blackstone Computing
in December 2001 so that I could have more time to work on labor-of-love
projects like the Open Bioinformatics Foundation. A secondary reason
was that the cash-hungry VC's and investors ran the company into
the ground by transforming it from a respected consulting shop into
a wannabe software company with grand IPO plans.
In January 2002 I hooked
up with several of my ex-Blackstone consulting collegues. We had
been successful together as a team and wanted to continue working
together. Thus, BioTeam was born.
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