PhyloWS and BioSQL are my hackathon targets

Posted in Open Source, Phyloinformatics, Programmable Web with tags , , , , on February 12, 2008 by drycafe

After the cold rain and stinging wind yesterday this day in Tokyo presents itself most magnificent. The sky is blue, the wind is still cold but the air is clear and crisp, and, best of all, I am writing this post with snow-covered Mt. Fuji in clear sight from the 8th floor of the CBRC building in the Tokyo Bay Area.

The Open Space session on Monday and ensuing discussions resulted in two main targets for me to work on this week. Rutger Vos and Chris Zmasek are joining forces with me to define a basic Phyloinformatics Web-Services API, or PhyloWS in short (pronounced “phylowiz”). (You can also watch some of our ramblings on the PhyloWS workgroup page at the BioHackathon wiki.) 

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BioHackathon 2008 has started

Posted in Open Source, Phyloinformatics, Programmable Web with tags , , , , on February 11, 2008 by drycafe

After a long 14 hour flight (not counting the connecting flight, and the additional 90 minutes train ride to get to the hotel), passing over the vast, beautiful, snowy landscape of Nunavut, the Northwest Territory, and the breathtaking Alaska Range, including majestic Mt. McKinley, I arrived last night in Tokyo for the BioHackathon 2008.

BioHackathon 2008 logo

This event is a meeting of more than 60 programmers and service provider representatives from around the world to work on improving support for interoperability and web-services for the life sciences. Today we are on the 40th floor of Roppongi Hills, with an awesome sight on the dazzling sea of high-rises in Tokyo. As we learn later from Dr. Hideaki Sugawara, the Director of the CIB at DDBJ, today is also National Foundation Day, a public holiday celebrating the founding of the Japanese Nation.

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Entertaining (a) poster session

Posted in Open Source, Talks with tags , on February 8, 2008 by drycafe

Owen McMillan, who we collaborate with on the Natural Diversity extension module to Chado, is teaching an undergraduate class on “Genome Science” this spring. In an interesting variation on the typical class schedule, he decided to intersperse the class with five poster sessions where students create posters presenting a chosen paper. 

In addition to that, Owen invites an outside speaker to those poster sessions to entertain the students, and I had the honor to be the guinea pig for the first session, titled ‘Genomes and Genome Databases’.

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Integrating ontologies is a mess

Posted in Ontologies, Programmable Web, Semantic Web with tags , , , , , , on February 4, 2008 by drycafe

Using ontologies, controlled vocabularies, and thesauri to aid integration of data, and in fact also services, has come a long way over the last several years. Vocabularies help to make sure we use the exact same terms to say the same thing, and ontologies provide for computable semantics over a conceptualization of reality. The semantic web crucially relies on these so that software agents can actually interpret the data and the services they encounter. With integration at the core of the mission of the ontology effort, wouldn’t one assume that a common infrastructure for integrating vocabularies and ontologies would be in place by now that is straight-forward to use yet powerful and flexible, well documented, widely adopted, and solidly a part of the Programmable Web? Well, it turns out, no, not by a long shot.

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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.

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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?


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