The learning curve

It is interesting to look at where in my current state as a programming newbie I fall on this curve.  My first experience with Perl (or any programming language for that matter) was during the CSHL Programming for Biology course in mid October.  I came away with a very large three-ring binder and an array of books with different animals on them…essentially the tools needed to tackle any data analysis situation that could be simplified or made manageable using perl.  I am very fortunate to have since been working alongside a group of very helpful friends in the Ware lab.  Reaching my spot this far along the learning curve would have been very difficult without them.  Even so, in these last 2 months I have experienced a series of peaks and valleys corresponding to momentary jumps of joy and periods of frustration where I feel seemingly unproductive.  As I move along the learning curve, although I continue to experience valleys, they are becoming increasingly more complex and my intermittent peaks are actually beginning to produce useful information for my research.  For example, earlier in the week I spent an entire evening trying to figure out whether the data structure that I had constructed in my code was an array of hashes or a hash of hashes or a hash of arrays, etc.  After systematically trying to isolate elements of the code line-by-line and commenting on what each gave back, I felt I had made some progress and went to bed.  As usual, I curled up with my camel book and a glass of wine.  What was not usual was my erratic sleep and the visions of arrays and hashes looping through my head.  I am not even kidding a little bit…I must have woken up about 10 times, each after hitting an error message.  The next day I felt tired and stressed, but when I sat back down at the computer, I realized almost immediately that I had a hash of arrays in which one element was a hash reference!  Ok, a little weird and probably not uncommon among programmers since I think if you stare at anything long enough it tends to come back to haunt you in your sleep.  Perhaps complete immersion is a little unhealthy since I dreamt of hashes again last night.  But I am happy about my progress along the learning curve.  

So in a nutshell, aside from the technical aspects of things, what have I learned thus far?  First of all, programming is really fun!  As a biologist working with deep sequencing data, it is also really essential…at least a basic knowledge anyway.  Even knowing only what I know now would have made my research as a graduate student that much easier.  There are only so many lines you can populate in an excel spreadsheet before the computer crashes.  Especially with some of these Solexa datasets…such analyses would be virtually impossible without the proper codes.  Also, very importantly, I learned that programmers love Starbucks.  Nuff said…I’m in good company :)