[Baypiggies] Bioinformatics Python Programmer

RYAN DELUCCHI bender at onsrc.com
Tue Nov 3 21:00:40 CET 2009

Congrats!  Yes: that sounds like a good time.


On Nov 3, 2009, at 11:46 AM, Glen Jarvis wrote:

> I've gotten several inquiries about this post the past few days.  
> Please also note that they were, and as far as I know, still are  
> hiring at least one other person. I intentionally stayed out of that  
> loop so not to risk any appearance of favoritism or impropriety. I  
> don't even know the candidates that were reviewed and was not  
> involved in the process. So, I don't yet know the status of that  
> situation at all...
> However, hopefully someone from our great community has applied,  
> gets it, and we can rock writing Python and doing science :)
> I'm sorry I can't be more helpful right now.
> Warmest Regards,
> Glen Jarvis
> On Mon, Oct 5, 2009 at 5:36 PM, Glen Jarvis <glen at glenjarvis.com>  
> 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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