Pushing the envelope on remote interaction: my talk, live, interactive

Posted in Open Source, Phyloinformatics, Synthesis, Talks, collaboration with tags , , on May 22, 2008 by drycafe

You may have seen the weird sounding item in the NESCent news feed (which I am syndicating in the left bar). This is the talk that I am giving tomorrow at noon (12pm EDT) at NESCent’s weekly Brown Bag Lunch seminar series, titled “Incubating Cyberinfrastructure: Community Building and Open Collaborative Software Development at the Transition Between Mostly-Off and Always-On.”

I will be speaking about my interests in open collaborative software development as a vehicle (in fact, in my opinion requirement) for promoting effective cyberinfrastrucure development, using various examples from our Hackathon and Summer of Code activities. In addition, I’ll connect these objectives to social networking, blogs, and related tools, and hope to instigate some brainstorming on how much we should be at the forefront of technologies that allow us to broaden participation much beyond the physical walls of NESCent.

Regarding the latter, part of the presentation is the setup itself. You can watch the talk — myself and the slides — live as a videostream, complete with audio, using most modern web browsers, without installing separate stand-alone software. Unlike the expensive and bulky Polycom that we have been using for video-conferencing, which only allows up to 3 concurrent client connections (and which has shown to be highly vulnerable to occasional network bottlenecks), this time we will be using much lighter equipment on the production end (in essence a video camera and a wireless microphone), and a much more powerful solution on the broadcasting end (Adobe Connect), allowing up to 100 (!) people to connect via their browsers. (Note that this will be a live stream only — it’s not a downloadable videocast, and there is no recording!)

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Julian Lombardi will speak at BOSC

Posted in Incubator, OBF, Open Source, collaboration with tags , on May 19, 2008 by drycafe

As has been announced recently on the home page of this year’s BOSC (the Bioinformatics Open Source Conference) and as I just posted on the O|B|F News, Julian Lombardi will be giving the keynote address this year at the conference.

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Incubating synthesis: NESCent goes IRC, and you can join

Posted in Phyloinformatics, Synthesis, collaboration with tags , , on May 1, 2008 by drycafe

As I noted earlier, one of the things we did differently this year for our Summer of Code participation is to maintain a presence on IRC (Internet Relay Chat) almost from the get-go. This not only proved useful for some of the students, but also inspired Brian O’Meara, one of our mentors who also happens to be a postdoc at NESCent, to propose a NESCent IRC channel as a means for our resident scientists (primarily postdocs) to stay in communication even when it’s not lunch break or teatime.

So here we are in #nescent on Freenode, and this week is declared as trial week to help everyone overcome the activation barrier and evaluate the utility for themselves. I’ve been very impressed by the willingness of almost everyone to follow along and give it a try. The first three days have seen some lively conversations, and even though some were on the light-hearted side (I guess I’m at fault here), some weren’t.

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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. Read more »

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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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R-Phylo launches on the Ides of March

Posted in Open Source, Phylogenetics, Phyloinformatics with tags , , , , on March 18, 2008 by drycafe

R-Phylo LogoOn March 14, 2008, the website R-phylo.org and the Special Interest Group (SIG) mailing list R-sig-phylo launched. Or, more precisely, their existence was announced on several channels (EvolDir, Ecolog) hopefully reaching as many as possible of the community that we have created the site for: developers and users of phylogenetic and comparative methods in R. R is the open-source clone of S/S-plus, and a powerful statistics platform and programming language at the same time. As Samantha Price, a postdoc at NESCent and one of the driving forces behind the site, writes in the announcement:

The wiki currently contains information on analyses and packages available in R and provides step-by-step tutorials for those just getting started.  We strongly encourage new users, experienced users and developers to both use and modify this resource to create a thriving comparative methods in R community.       

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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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