[Baypiggies] Hiring / Bioinformatics Tutor/Hack day

[Tung Wai Yip]

+1.

And feel free to bring your problem from work if you think it can be  
solved by newbies.

One time I was considering to enroll in a deck building class. The  
instructor told us that the students would go to a site for hands on  
practice, like to a habitat for humanity site or some student's home. At  
the end of the day the students would learn how to build a deck, and  
someone also has a new deck built!

Wai Yip


> +1
>
> 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)
>> CSC
>>
>> 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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>>
>>
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