Archive for the 'Other Stuff' Category


Back to posting (and numpy)

Jesus, when it rains, it pours.

I haven’t had time to post in quite a while – somewhat due to the NIH goldrush and somewhat due to the fact that I have been trying to get some manuscripts out the door that have been hanging around for far too long. Then, there’s planning-time wasted for NIH projects that didn’t pan out or that we couldn’t get together before the deadlines.  I’m pretty sure everyone is sort of in the same boat.

Anyway, I’ve been working today with some things in numpy, which is probably one of my favorite libraries (in the whole world) for python. There’s things that you can do in numpy, that quite honestly, are probably far simpler than they should be.

Generally speaking, numpy is meant for calculations involving large arrays. That said, the flexibility of numpy continues to amaze – recently (within the past year), I’ve used it with great success for sequence comparisons and SNP characterization (numpy arrays can hold string values). This morning, i’ve used it to calculate summary counts of interactions between many objects over periods of time (essentially 100 x 200 x 200 element arrays). Of course, the array based nature of numpy lets you maintain structure (i,e. temporal structure) within the data, while performing the needed summary operations over the data.

Numpy wouldn’t be quite so great if it weren’t for the impressive number of methods available for numpy objects or it’s integration into the larger SciPy project. Per usual, numpy can be subclassed to do whatever you want.

Anyway, if you haven’t used it – do. And if you have, then you’re probably as impressed with it as I am.


a new day dawns

Today, I felt prouder of my country and its citizens than at any other point in my life. America the beautiful, indeed.


No time like the present…

Well, well, well.  I guess I have finally decided (after much internal debate) to take a more personal step into (onto?) the intertubes that have served me well since the the time when just having an email addy was the shit. It’s exciting, fun, a little scary, and, I hope, a good idea.

That said, this step is not – ahem – as personal as it could be. Given the nature of this blog (genetics, computers, molecular biology, whatever I want), my potty-mouth, and my current and future position(s) in academia, I have chosen to write using a pseudonym.

Of course, pseudonymity does not ensure that the writing will be interesting or good. However, in a backwards way, it does ensure that I can write openly about what I perceive to be the truth – while avoiding repercussions. Recently, The Boss and I were discussing the utility of blogging and writing under a pseudonym just the other day. Our consensus was largely that:

  • blogging is an outlet that can help us (generally) perform better at other, similar tasks (journals, lab notebooks, etc)
  • blogging/writing are fundamentally different from writing research manuscripts, therefore they are “good” or at least “fun”
  • pseudonymity is probably best, particularly for those at the early career stages

Of course, good things can be used for evil, and writing under a pseudonym is certainly no different. But, don’t come here for unsupported tirades, slander, etc. That’s not how I roll.

So, you may be wondering how I do, in fact, roll. Well, since this is a new thing for me, I can’t say that I’m exactly sure. I am likely (and, hopefully, consistently) to write about some of the subjects with which I work, the environment in which I work, and my interests. These include, but aren’t limited to: genetics, behavior, molecular biology, organismal biology, bioinformatics, life in academia, music, mountain-biking, cooking, reading, etc.

If you like these things, then you’re in luck. If not, tough shit.