A non-coders attempts at writing useful code
Posted in Uncategorized on Jan 7th, 2009
Almost two years ago I first started writing the codeitch weblog about my code ambitions on wordpress ( codeitch.wordpress.com) .This blog was driven by a strong desire to get better at writing code and importantly building solutions that enabled better science. To do that I had decided to pick up python , Java , javascript [...]
Posted in Uncategorized on Jan 2nd, 2009
As a crystallographer we routinely travel to the national synchrotron light sources at Chicago , NSLS on Long ISland NY, the BCSB at Lawrence Berkeley etc to collect X-ray diffraction data from our protein crystals at the various beamlines. A beamline is basically a station or a lab room at a synchrotron facility where out of [...]
Posted in Uncategorized on Dec 24th, 2008
Everytime I have struggled with syntax in Excel I have always longed to break free from the tyranny of its visual basic syntax. Although very powerful, excels formulae and their complex mix of parenthesis , square brackets , dollar signs and brackets always had me wishing that spreasheets spoke a language with a more readable [...]
Posted in Uncategorized on Dec 22nd, 2008
I have written in the past on my frustrations with the mess that is 32bit browsers and 64 bit plugins. I was desperately trying to get a java web start application to play on my 64bit ubuntu linux box. I of course imagined that upgrading java to java 6 update 11 would be the way to go [...]
Posted in Uncategorized on Nov 24th, 2008
One of the fun parts of learning a programming language yourself is when you get stuck at solving a trivial problem . When this happens I generally try to do a few things generally involving searching . I have tabulated these activities and also the apparent value to me , both for my short-term solving [...]
Posted in Uncategorized on Nov 7th, 2008
If anyone feels this post is provocatively titled. I can only offer as defence sagging traffic to this blog. But serioulsy! I am writing to defend what I perceive as a tendency among bioinformaticians to complain about Biologists and their tendency to not respect things like structured data , file formats , data portability and various other [...]
Posted in Uncategorized on Oct 7th, 2008
If I were to list one of the most attractive things about python , the interactive command line would rank among the top few. Well today I was forced with a rather simple task. I had to order a primer for a sub-cloning experiment that was the reverse primer corresponding to the last twenty bases of a [...]
Posted in Uncategorized on Oct 1st, 2008
First for some disclaimers: I have not yet used chrome since I mostly use Linux and Mac OSX . Although I believe that forking and straying from the beaten path are great things , my gut reaction to the chrome announcement was that it was definitely going to dull the impact of firefox which google [...]
Posted in Uncategorized on Sep 23rd, 2008
I came across a submission to Nature Precedings this morning detailing the creation of a "semantic - natural language processing " based search for the Pubmed database by Cognition Technologies in collaboration with a team at the Department of Biochemistry at UT Southwestern Medical centre in Dallas. A few searches later, I can definitely say the technology [...]
Posted in Uncategorized on Sep 12th, 2008
I have been to three of the four Boston ignites and even spoken at the second one, but yesterdays keynote by Tim oreilly at Bostons Ignite-4 was truly exceptional . It takes someone with Tim Oreillys vision to put it the way he did. It was one of those talks you walk away from inspired [...]