[Baypiggies] Bioinformatics Python Programmer

jim jim at well.com
Sat Oct 10 19:19:21 CEST 2009

   is there a BayPIGgies talk in this? 
   generally the issue seems to be bringing 
application-specific experience to programming 
skills. more specifically, biology and medicine 
application areas and python--this growth area 
includes non-intrusive hardware solutions. 

On Mon, 2009-10-05 at 18:36 -0700, Glen Jarvis 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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