So there have been a few reactions to my latest post on accountable research software, including a Tweeter kerfuffle (again). Ever notice how people come out really aggressive on Twitter? Must the the necessity to compress ideas into 140chars. You can’t just write “Interesting point you make there, sir. Don’t you think that your laudable goal would [...]
Preamble: this post is inspired by a series of tweets that took place over the past couple of days. I am indebted to Luis Pedro Coelho (@LuisPedroCoelho) and to Robert Buels (@rbuels) for a stimulating, 140-char-at-a-time discussion. Finally, my thanks (and yours, hopefully) to Ben Temperton for initiating the Bioinformatics Testing Consortium. Science is messing around with [...]
Some time ago an article in Linux Journal discussed the adoption of free/open course software (FOSS) by the general public. The article (I can’t seem to find it now) talked about the people that do not care about the distinction between Free as in Free Beer vs. Free as in Freedom (libre). They want software [...]
The hype cycle characterizes the over-excitement and subsequent disappointment with new technologies. I expanded this a bit to include research and social trends in science which seem prevalent nowadays. Any views represented in this hype cycle diagram are my own, and in no way represent the views of my employers, family, friends, neighbors, greengrocer, auto [...]
The 11th Annual Bioinformatics Open Source Conference (BOSC) 2010 is coming up in Boston, July 9-10 2010. The BOSC meetings are a great get-together of a community of programmers who are like-minded in their advocacy of open source code for science, and specifically for bioinformatics. The whole thing is run by volunteers who take a [...]
AMOS is a suite of genome assembly and editing software. It includes assemblers, validation, visualization, and scaffolding tools. I have been having some issues installing AMOS on Ubuntu 9.10. Specifically, Ubuntu 9.10 has gcc 4.4, which breaks the compilation of the AMOS release version. However, the development version has been fixed to accommodate that. If [...]
In celebration of the biohackathon happening now in Tokyo, I am putting up a script that is oddly missing from many bioinformatic packages: extracting intergenic regions. This one was written together with my student, Ian. As for the biohackathon itself, I’m not there, but I am following the tweets and Brad Chapman’s excellent posts: Day [...]
In no particular order or context. No personal stuff and by no means a complete list: WordPress (like, duh). Wikipedia (default for looking up new stuff) Wikis in general (great lab management tool. Don’t need LIMS) Open Access Publishing and Creative Commons licensing. FLOSS licensing (90% of the software I use, and 100% of what [...]
