[Baypiggies] Hiring / Bioinformatics Tutor/Hack day

[Jeremy Fishman]

+2

  - Jeremy


----
Jeremy Fishman
http://jfishman.org
Software Developer, Realtime @ Quantcast
jeremy.r.fishman at gmail.com


On Thu, May 13, 2010 at 11:02 AM, Greg Cheong <gregcheong at gmail.com> wrote:

> +1
>
> -Greg C.
>
> On Wed, May 12, 2010 at 5:21 PM, Glen Jarvis <glen at glenjarvis.com> wrote:
> > This email covers two topics (although they can be, but don't have to be,
> > inter-related):
> > * A job opening
> > * A tutor/hack day to give the computer scientists a real Bioinformatics
> > problem to solve
> > I put them together as a benefit for those who may be considering a job
> in
> > this field. You can have a day to work on these types of problems to see
> if
> > it interests you or bores you to tears..
> >
> > === Job Opening ===
> > Some time back, I sent out an email regarding my bioinformatics lab
> hiring a
> > programmer. I tried to give a feel for what work would be like on a daily
> > basis. And, I tried to set your expectation for pay (less than industry).
> > We still have that job opening -- probably because I set your expectation
> so
> > well  :( .
> > I was intentionally not involved in the interviewing/hiring process
> because
> > I wanted to have no appearance of impropriety (as I was also interviewing
> > for a position to move from contractor to full time employee). So, if you
> > weren't hired, I don't really know why.... I intentionally stayed out of
> > that loop to keep as professional as possible. I only know the position
> is
> > still open.
> > With that said, my boss is talking about hiring another programmer again
> for
> > a short term (possibly a year or less).  Although, if it works out on
> both
> > sides, it could turn into a permanent position (as it was for me - I was
> > hired full time). Finding a fit for this position is actually difficult
> (on
> > both sides).
> > Sooooooo......  I'm going to stick my neck out and try something new:
> > Working on a small bioinformatics problem in an open source environment.
> >
> > === Tutor/Hack day ===
> > I've been wanting to get the open source community more involved with
> some
> > of the problems that we're tackling. Open Source code is *so* much better
> > than code reviewed by only a few eyes. And, this would also give everyone
> a
> > chance to see what a problem would be like.
> > There are some *real* bioinformaticians on this list (I don't yet
> consider
> > myself on that level yet -- although I'm getting there). So, if you're a
> > real bioinformatician, this may be a trivial problem for you. But, if you
> > want to come and help explain things/help others work this out, that'd be
> > cool!
> > I'd like to get together (on a weekend, possibly) and hack on this
> problem.
> > I will describe the things that I think you need to know:
> > * What is FASTA format (http://www.ncbi.nlm.nih.gov/blast/fasta.shtml)
> > * An brief introduction to BioPython (http://biopython.org/)
> > * What is a genome
> > * What is a gene
> > * What are amino acids (contrasting against DNA data)
> > * What is a 'percent identity' between genes
> > * What is a species
> > * What is a strain (loosely defined because it seems to be very loose in
> > this problem)
> > * The term taxa (plural) and taxon (singular)
> > * How can genes vary and still be the same gene
> > * How errors can exist in different databases
> > * An introduction to the JGI (http://www.jgi.doe.gov/) database
> > * An introduction to the UniProt (http://www.uniprot.org/)
> >
> > With this introduction, you should have a theoretical understanding of
> all
> > that you need to solve this problem -- the rest is coding. (That is, if I
> do
> > my job and explain things well -- and don't fall into pot holes of
> > information that I don't know).... Also, I over simplified things that
> you
> > don't need to know for this problem (e.g., We won't talk about open
> reading
> > frames at all or what that means. Since we're already given amino acids,
> we
> > don't care).
> > The problem is:
> > I will give you a file in FASTA format of the genes for a particular
> species
> > (let's say: Chlamydophila pneumoniae). That file will contain a list of
> > genes, one after the other, again in FASTA format. The file will have the
> > JGI unique identifiers. However, we also want the UniProt identifier for
> > this same gene.
> > Now, this should be as simple as: "Take the gene from the JGI database,
> > look-up the same gene in UniProt, record the number, dust off your hands
> -
> > you're done" -- There are lots of little tedious problems, however, that
> > keep it from being this easy.
> > For example, if two genes are absolutely identical (they have the same
> amino
> > acid sequence) except for in a single position, are they actually
> identical?
> > What if the sequence found was in a strain instead of from the original
> > exact species?
> > Let me ask another question: If you were to somehow magically sequence
> your
> > personal entire genome (everything - not just genes) from a cell in your
> toe
> > and also sequence your entire genome from a cell from your nose, would
> they
> > be identical?  I bet not... I'll explain why. Now, we expect less
> > differences in actual genes (not in other parts of your genome), but even
> > then, there can be some variation...
> > These are the types of questions/problems that we'll be getting into if
> > you're so interested...
> > Who's up for this?  We'll get date and time once we have a set of
> interested
> > people...
> > You don't have to be interested in this job to be interested in this
> problem
> > (and/or to do more in bioinformatics).
> >
> > Cheers,
> >
> >
> > Glen
> > --
> > Whatever you can do or imagine, begin it;
> > boldness has beauty, magic, and power in it.
> >
> > -- Goethe
> >
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