Archive for Open Source

Summer of Code: tough decisions and how much competition is too much?

Posted in Open Source, Phyloinformatics, Summer of Code with tags , , on April 25, 2008 by drycafe

On Monday this week Google announced the students accepted into the 2008 Google Summer of Code, and therefore also those for our participation, dubbed the Phyloinformatics Summer of Code. We received 34 applications in total, which is about half as many as in 2007. However, unlike last year, only 1 of those was what we (and presumably Google) consider “spam,” and two have been withdrawn (one of which unfortunately was a really strong application, but the student needed a summer job and the deadline extension made it no longer an option to wait for the Summer of Code acceptance).

Of the remaining 31, about 80% were between reasonable to really strong, which presents a remarkable difference to last year, when the fraction of those was more around 25%. So in contrast to the total number of applications, we had more quality applications this year than we had last year.

By itself that’s a great development, though it already foreshadowed that we would have to make some tough decisions. On top of that, because our “popularity” (as measured by fraction of total applications received by all organizations) is only about half of last year’s, our current allocation of slots by Google is only 5, about half of what it was last year. Given that we offered 14 project ideas ourselves already (11 of which received strong applications), inevitably students ended up competing not only with those who applied for the same idea, but also with those who applied for other ideas. For many other participating organizations that may be the norm, but this level of competition was a bit new for us. Continue reading

Phyloinformatics Summer of Code is on for 2008

Posted in Open Source, Phyloinformatics, Summer of Code with tags , , , on March 30, 2008 by drycafe

GSoC Logo 2008After we participated in the Google Summer of Code™ program as a mentoring organization in 2007, we pulled together an application for this year, too — and we got accepted again! So the Phyloinformatics Summer of Code, as we are calling our program in reference to the emphasis on phyloinformatics, has been on for 2008 since March 17, when Google published the list of accepted organizations. The period during which students can apply opened on March 24, and was originally slated to end only one week later, on March 31.

The latest news is that Google may extend the application deadline for students by one week. We’ll hear the final decision on this early tomorrow morning (Pacific Time, obviously – so probably no news on this on the East Coast before noon). So if you are a student enrolled at a university in a graduate or undergraduate program, you are interested in evolutionary or comparative biology, and you have always wanted to get involved in a bioinformatics open-source software project or even possibly help found one, here is your chance for likely another week, and Google will even pay you a stipend.

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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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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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