[Baypiggies] Bioinformatics Python Programmer

Glen Jarvis glen at glenjarvis.com
Tue Nov 3 20:46:23 CET 2009

I've gotten several inquiries about this post the past few days. Please also
note that they were, and as far as I know, still are hiring at least one
other person. I intentionally stayed out of that loop so not to risk any
appearance of favoritism or impropriety. I don't even know the candidates
that were reviewed and was not involved in the process. So, I don't yet know
the status of that situation at all...

However, hopefully someone from our great community has applied, gets it,
and we can rock writing Python and doing science :)

I'm sorry I can't be more helpful right now.

Warmest Regards,

Glen Jarvis

On Mon, Oct 5, 2009 at 5:36 PM, Glen Jarvis <glen at glenjarvis.com> wrote:

> 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
> on?"
> * 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 Pfam?)
> 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
> about).
> 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.
> Cheers,
> Glen
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