[Baypiggies] Bioinformatics Python Programmer

Glen Jarvis glen at glenjarvis.com
Tue Oct 6 03:36:41 CEST 2009

My team is looking for another programmer (yeah!)
But, I must tell you, finding a fit for us here will be very difficult. You
need to know Bioinformatics well enough to be able to to understand the
directions given (a challenge for everyone when they start here -- even PhDs
in this field).

So, here are some basic questions to help you sort out, "should I even read

* Do you know the difference between DNA and Amino Acids? (Bonus if you have
all the Amino Acids memorized -- I still don't)?
* Do you know what is a gene (i.e., how is a gene different, if it is, than
a bunch of amino acids strung together as residues)?
* Do you know what a phylogenetic or phylogenomic tree is?
* Do you know what I mean by a predicted 'active site' in a molecule?
* Can you describe the shape of an amino acid (i.e., when formed and/or when
in an environment conducive to folding)
* Do you know what Biopython is and why it is useful?
* Do you know what a neighbor joining tree is? (Or Maximum Likelihood Tree,
Maximum Parsimony Tree, Quick Tree, etc.)
* Do you know what a Pairwise Alignment is and how it differs from a
Multiple Sequence Alignment (MSA)
* Do you know how to lookup an accession number in Genbank? (Or Switprot? Or

These are basic 101 questions, FYI.  You should know a lot more, like what a
Baysean network and Hidden Markov Models are. You don't have to know every
single thing listed above, but if it's all completely alien to you, you
*will* be in for a struggle -- especially if you don't know Python/Django
that well.

What would work in our team, you may ask?  Someone incredibly proactive and
who won't be intimidated easily. For example, if a PhD told you they needed
something to happen, described it graphically (what it should look like),
but not understand any of the difficulties (like databases, javascript,
html, etc.) to make that happen, would you get frustrated, or would you make
a plan on your own and make that happen? How could you deal with the
frustration if the PhD didn't understand what was taking so long because
they're focused on the result instead of infrastructure, how would you
address this proactively?

Can you read incredibly messy old HTML, JavaScript and Perl code, but write
incredibly pristine python/django/jquery code, and do it quickly? That is,
can you write code that JJ would give a thumb's up too, and write it
quickly? [JJ isn't involved in this job, I just use his high standards as my
internal barometer in my own code. I've not yet written code that JJ hasn't
found a problem with (good for me - I'm learning every time he does a code
review with me).]

Are you willing to take an incredibly low salary (comparatively) because
you're that interested in science, working for an very well known research
facility, etc?

I'm not asking the impossible - I fit the criteria above and will be working
along side you (as well as one other). I struggle with some of these things
a lot too. There are times it feels like a Dilbert cartoon here -- but, at
the end of the day, we're doing some pretty awesome things. You'll get
frustrated at the old system and how bad it is (PHP writing HTML writing
JavaScript writing HTML (Forms) writing more JavaScript writing
lord-knows-what at times). You won't be able to pull on all the old threads
(somethings can't yet be changed for fear of damaging processes no one knows

We're building a new system that mimics the functionality of the old system
- but clean and organized and well tuned. You'll be doing Python and Django,
but will probably also need to know a good deal of HTML, JavaScript, JQuery,
etc in the web stack. (I don't know JavaScript and JQuery that well, but I'm
working on it). Also, the new system is, thus far, organized/clean/and a joy
to create.

It's tough to find someone who's a good fit -- and willing to do this. But,
if you're looking and want to talk to me about it, I can help you figure out
if this is a position you may be interested in or not. I mean, heck, you got
this far, didn't ya :)

I'm not a recruiter -- just looking for a python peer who would be excellent
to work with.


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