Archive for January, 2008

Remote tree reconstruction is (almost) here

Posted in Phyloinformatics, Programmable Web with tags , , , , , on January 27, 2008 by drycafe

This week the CIPRES project released a REST-based API for running optimized versions of some of the most powerful programs for phylogenetic tree reconstruction on the CIPRES compute cluster at the San Diego Supercomputer Center (SDSC). This lays the foundation for developing the same infrastructure for seamless remote execution of phylogenetic tree inference as is being widely used, for example, for BLAST-based sequence similarity searches run at the NCBI.

Continue reading

The greatest danger to the success of most artists is not piracy but obscurity

Posted in Open Source with tags , on January 19, 2008 by drycafe

I stumbled upon this quote the other day on Web4Lib, a mailing list for librarians concerned with, well, web-based access to libraries and their services. What a great motto to start off this site.  

The poster was paraphrasing Cory Doctorow, a writer and one of the founders of, who said in a USA Today interview in 2005: 

For almost every writer, the number of sales they lose because people never hear of their book is far larger than the sales they’d lose because people can get it for free online. The biggest threat we face isn’t piracy, it’s obscurity.     

The quote immediately struck a chord with me for several reasons. First, Cory Doctorow wrote When Sysadmins Ruled the Earth, a great (and in parts disturbing) short story that I would have never read had he not posted it freely on-line, and that since then has stuck in my mind (I have children, too). I might, in fact, not have read anything from him ever, as I’m normally not very interested in science fiction writings.

The second reason is that I like to think of writing, or designing, elegant, compact, resistant code as an art (yes, I do own The Art of  Computer Programming): the art of writing code that does one thing and does it well. And indeed, what is the biggest threat to the recognition of programmers who strive to write beautiful code? Their code being stolen reused over and over by others? 

Even if I never end up buying one of Cory’s books, he has touched my life and has anchored himself in my memory as an artist. How many artists can say that?


Get every new post delivered to your Inbox.