Displaying posts categorized under

open source software

PLoS-1 published a “creationist” paper: some thoughts on what followed

As everyone knows by now, PloS-1 published what seemed to be a creationist paper. While references to the ‘Creator’ were few, the wording of the paper strongly supported intelligent design in human hand development. A later statement from the first author seemed to eschew actual creationism, but maintained teleological (if not theological) view of evolution, […]

Choosing a software license

(With apologies to the memory of Elizabeth Barrett Browning) How shall I license thee? Let me count the ways I license thee to be free to distribute and embed My code can be buggy, when I wrote it late last night “While” loops have been made without a stated end I license thee to change […]

BOSC 2014 Guess the Keynote Competition

(From Peter Cock, via the OBF News Blog)   We’re pleased to officially confirm that one of the two keynote speakers for the 15th annual Bioinformatics Open Source Conference (BOSC 2014) will be C. Titus Brown, as he announced on Twitter recently: Titus Brown (@ctitusbrown): Excited to be a keynote speaker at BOSC 2014! My […]

The Bio* projects: a history in graphs

Yesterday I received an email from Kristjan Liiva, a student at  RWTH Aachen University Germany. Kristjan has developed a really cool dashboard to analyze and visualize the development of collaborative OSS projects by mining their mailing lists and software repositories.  (If the link doesn’t work, try again later; the project is heavily under development). The […]

Should research code be released as part of the peer review process?

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 […]

Can we make accountable research software?

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 […]

Open Access: the Revolution Will be Convenient

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 […]

My Hype Cycle

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 […]

Bioinformatics Open Source Conference 2010 (and a poll)

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 on Ubuntu

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 […]

Short bioinformatic hacks: reading between the genes

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 […]

Thankful for…

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 […]