[Baypiggies] Hiring / Bioinformatics Tutor/Hack day

Brice Lemke blemke at gmail.com
Mon May 17 18:37:58 CEST 2010


On Mon, May 17, 2010 at 7:05 AM, chukwuweta chukwudebe <
neoafricanus at gmail.com> wrote:

> Is this still open?  if so, I am interested,
> (In the problem/hack day part- not the job)
> 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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