[Baypiggies] Bioinformatics Python Programmer

Glen Jarvis glen at glenjarvis.com
Sat Oct 10 19:51:52 CEST 2009

Wow! This is *such* a big topic. Although it's impossible to squeeze two
semesters of classwork into an hour, I could definitely speak on it, but I'd
have to keep it on "just the basics"... I'd also drag one of my peers from
work in to do this talk (he has a degree both in Microbiology and in
Computer Science and can field a lot of the questions)....
We could do a tech talk which answered just the self-evaluation questions I
sent in a recent email and did some very basic BioPython and webqueries. I
know BioPython has fallen out of favor in the past few years, but it's great
for doing things like iterating through FASTA sequences, getting sequence
lengths, converting from one sequence format to another, etc. And, it's very
simple to use - which makes it a great fundamental tool for a basic tech
talk. I saw at least two people who were much more qualified than I was on
this list - I'd happily speak with them. My topics, however, would assume
the audience has zero Biological background.

If there's an interest, I could certainly try to put something together. I
guess the fundamental question is, how many people would really be
interested?  Especially since this is 95% basic science and the programming
is dead simple (iterating through a sequence and getting some results). We
don't have the science to do more complex programming examples.

We could also do a basic demo of Pymol too - but that would be showing
pretty 3D models of molecules (proteins in our case) using a tool that's
already created.

I could do this starting January -- but again, I'm not certain how
interested our entire group would be since it's heavy on the science you
need to understand as background and very light on the actual


P.S. Feel free to comment off list to me if this is something that doesn't
have to be said publicly.

On Sat, Oct 10, 2009 at 10:19 AM, jim <jim at well.com> wrote:

>   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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> > Baypiggies at python.org
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