Most programming languages have facilities of some sort to enable the developer to execute commands on the OS’s shell prompt. Maybe it’s just me, but I’ve never been able to have an easy time at managing system processes properly (i.e., representing processes individually through the language’s constructs). Representing multiple processes piped from one to the next properly seemed like a pipe dream (sorry). I think the first painless way of doing this, at least among all the different options that I’ve seen, is in Clojure with the clj-commons-exec project. At the moment, it seems like a hidden gem. A side benefit of the project is that the evolution of the code for piping one process to the next, at least for me, is instructive on the difference between object-oriented and functional paradigms.
Continue reading Executing System Processes and Illustrating FP in Clojure
Since learning Clojure will most often require a lot of experience in coding in Clojure, a practical consideration for any new learner will be having an effective environment for editing code, testing, deploying, etc. On the Clojure development (developer?) website, there are instructions on getting started with Clojure. I believe that these instructions are intended to be the official help resource for everyone, and people are making good effort to keep it up-to-date and authoritative. My attempt, with this post, is to formalize what I know, and then contribute over to the official documentation whatever others might find a useful addition.
Continue reading The Newbie’s Guide to Learning Clojure, Part 2 – Tooling
There are many ways to dabble in Clojure. My approach has been to read something, retain some fraction of it, and then repeat this process until those fractions equal a whole. When stepping into functional programming for the first time, especially after OOP, it’s not easy to grasp it right away. Sooner or later, the ideas will stick, right? That means learning in multiple passes, where some deeper level of understanding happens during each pass compared to the last. Kind of like iTunes Essentials with “The Basics”, “Next Steps”, and “Deep Cuts”. So that is what I want to present to you, in an ordering that will minimize your difficulty along the way.
Continue reading The Newbie’s Guide to Learning Clojure
On Wednesday and Thursday, I’ll be volunteering at a Software Carpentry boot camp that’s happening in Berkeley/Oakland. I’m looking forward to it.
Previously, I’ve created an episode of the online lectures for secure shell. I also wrote the initial code for the episode using phylogenetic trees, although it got re-written by Greg. So I was more like just the narrator in that episode, but now I know how triangular matrices can be handled by maps. It’s always nice when you can work alongside smart people and can imbibe some of their knowledge and wisdom.
For a while, now, I’ve been trying to explain to people what makes someone effective — productive and efficient to do programming and/or science research. Until very recently, I was working in a genetics research lab, and I was asked by coworkers about what it takes for someone to be productive. Whether it was in terms of programming productivity or ability to intuit scientifically, I had been on both sides of the non-/productive divide. I distilled the differences to being resourceful and resolved.
Continue reading Essence of Productivity
Everything in technology seems to increase in exponential fashion. There’s the ever-quoted Moore’s Law, where CPU speeds seem to double every 1.5 years. RAM capacities and HD capacities seem to follow this rate, although the correlation might be coincidental more than anything else. However, network speeds have barely increased in the past decade, it seems. The boon in high-tech, high-throughput technological advancements in modern genetics labs is also a bit of a curse. As the New York Times reports in DNA Sequencing Caught in Deluge of Data:
Continue reading DNA Sequencing Moving Too Fast for Computers and Bioinformaticians