In this sense, there may not be a more fitting reason (explaining this will have to wait for a later post) to break the silence than this: Google, in the person of Leslie Hawthorn who manages the Google Summer of Code program, just announced that Google will run the Summer of Code program again in 2009.

As I wrote previously, I have been fortunate enough to participate in the program for the last two years, as mentor and as organization administrator for NESCent. The program has allowed us to train future scientists in distributed software development skills and methods that aren’t normally taught in the university curriculum, and at the same to nurture a more sustainable developer community in phyloinformatics.

In previous years, Google wouldn’t publicly commit to the program until later in February. The much earlier announcement this year gives us an opportunity to better reach out to biology students with an interest in evolution and a bent towards computer programming who are waiting for the push to overcome their activation barrier towards contributing to an open-source project.

So, if that is you, or if you know someone who could be, please pass the word, and watch this place as well as our Summer of Code wiki for updates.

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!)

This part allows you to watch and hear me. To make the possibility for remote interaction bidirectional, Brian O’Meara, the mind behind TreeTapper, will concomitantly watch and moderate our IRC channel (#nescent on Freenode). You are welcome to log on and rant about the talk as I am presenting it, or ask questions, along with those people who are physically in the room.

In the future, there are many more capabilities of the Adobe Connect platform that we might want to exploit. Aside from having a chat feature built-in (which we won’t be using this time), there is a shareable whiteboard, which would actually allow you to send sketches and other visuals back to the presenter, and to the other remote participants.

If you are thinking about watching, I just need you to be aware of one big caveat — don’t expect a very formal presentation. Coincidentally, internally we have just recently debated whether the BBL seminars shouldn’t be more informal as they were originally intended to be. Inadvertently I am going to set an example for that, too. I have spent the last couple of days with the Evolutionary Informatics working group, which has just had their 3rd meeting at NESCent, and so have had almost no time to spend on a polished slideshow. In fact, I may improvise and develop some cartoons on-the-spot on a whiteboard or flipchart; theoretically, a swift turn of the camera should accommodate that just fine for the remote participants. You have been warned

I am serving on the Organizing Committee of BOSC this year (though obviously through my serving on the O|B|F’s Board I have been involved with the conference for years, but in rather minor roles), and for a number of reasons I am extremely excited (and in fact humbled) that we were able to recruit Julian. Julian is one of the principal architects of the Croquet Project, an open-source peer-to-peer software platform for creating deeply collaborative multi-user on-line virtual world applications. (He has a number of other claims to fame, which the Wikipedia entry on him lays out nicely and I therefore won’t repeat those here.) 

Why should this matter to people developing (or using) software that solves bioinformatics problems, who supposedly constitute most if not all of the BOSC attendees? The overall theme of this year’s conference are emerging technologies and how they might be used to tackle hard problems in our field. Most of us have probably heard about things like grid computing, Web 2.0, mash-ups, or even the semantic web and how they might impact our ability to advance science.

Personally, however, I think that at least as much if not more than any of those over the next couple of years 3D immersive virtual worlds (also called ‘metaverses‘) will fundamentally alter how we explore data, models, or even algorithms and code, and how we collaborate with each other to form teams and communities — or even “virtual organizations” — when and as we need them, to educate, innovate, and synthesize.

In fact, a number of early adopters ranging for example from an Open Notebook chemistry lab to Nature Publishing Group is setting foot in Second Life to examine its utility for teaching, communicating, and creating science. Virtual worlds have even become a research subject themselves; the peer-reviewed Journal of Virtual Worlds Research has just been launched, as has been a similarly aimed mailing list. 

What is particularly intriguing about Croquet in this regard as a platform, compared to, for example, Second Life, is that to me it fits so well into how we do science and its value system. Not only is it fully open-source, and hence other than skill poses no limit to the ability to tinker and to scrutinize, its architecture is peer-to-peer, rather than client and (centralized) server. The idea that the only server to run a BLAST search against would be at NCBI, and that they could only run against sequence databases at NCBI, sounds silly, if not inane — why should this be any different for our ability to collaborate?

Aside from all this, Julian gives great talks. He spoke at NESCent in November last year, and I found his talk both entertaining and inspiring. In fact, this let us to explore ideas on collaborating with Julian and others to virtualize the hackathons that we have run, but I’ll say more about that in a separate post.

And if that’s still not enough reason, consider the fact that he is actually a biologist (evo-devo or evolutionary biology, to be precise), though (I think) he no longer works in that capacity.

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.

In my mind, the context of this goes much beyond an easy means for our resident scientists to ask each other for advice on commonly encountered situations. Compared to IM (such as iChat or AIM) and email, IRC is always on, it doesn’t need to be initiated. Questions can be tossed on the table, everyone will see them immediately, and it’s at the leisure of every user at which level, and at which point she wants to engage, or disengage. In some ways I see it like a virtual coffee table that you can join casually right on your desktop, without leaving or even disrupting your work.

At a journal club-turned-brainstorming session last week, several NESCent postdocs distilled the keys to synthetic science (the ‘S’ in NESCent stands for Synthesis, and is what is supposed to set NESCent most profoundly apart from a more traditional “research lab” in evolutionary biology). The keywords that stuck out (at least to me) centered around thinking across scales, interdisciplinary, reductionist, and integrative, in ways that are unfamiliar, using a common language.

Nurturing synthetic science along these attributes in my mind inevitably seems to greatly benefit from, or even require collaboration, the basis of which is scientists from different disciplines, working at different scales, in fields or viewpoints unfamiliar to each other, talking to each other and establishing a common language between them. That is, nurturing synthesis needs incubators, providing of which is I guess one of our main distinct roles.

Which leads me back to our new IRC channel: maybe it can become one of those incubators, and it could serve that way much beyond the physical walls of NESCent. It’s always on, requires relatively minimal effort to join (see a comparison of client software — for example, XChat works really well on Macs — and a list of basic commands; our channel is #nescent on Freenode), and for now is open to anyone in the world. So if you want to meet a bunch of really smart people who do amazing work in evolutionary research and have a lot of ideas about taking the field to new levels, here’s your chance to do so at your leisure. (And yes, I’m hanging out there, too, though so far I’ve mostly supplied the light-hearted side

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.

So why is the quality of applications so much better this year? While of course I can’t be sure, the fact that we spelled out our expectations more unequivocally on the ideas page probably helped. We asked students to bounce their ideas and draft applications off our mentor mailing list before they submit, and we worked with all students who wanted to be worked with to improve their applications.

Another modification we made was to establish an IRC channel (#phylosoc on Freenode) and specifically encourage students and mentors to take advantage of it even before applying. Notably, or should I say sadly, my feeling is that in the end the students used it much more than the mentors did (with one notable exception – thanks Brian for all your help!).

That said, it was interesting to see that there really needs to be both – some of our students were very communicative and comfortable over email and some were over IRC, but almost none on both. One of the students who made it to acceptance probably did so to a significant extent due to how he presented himself in IRC, but the other 4 communicated mostly or exclusively over email – so it’s an option more than a requirement, and an advantage primarily for those who communicate more effectively in direct back-and-forth exchanges than by carefully composing what they want to say. 

Back to the higher quality level and low fraction of spam applications. It turns out that it also seems to be a general trend as many other organizations report the same, so it’s not even clear how much our own working with the students is to receive credit for this. On the other hand, many organizations report applying increasing rigor to the application process, in fact requiring actual code contributions in the form of patches as a prerequisite for applying seems to enjoy increasing popularity.

So maybe what we’re seeing is that the bar has been raised continuously for new students, and that word of this and of the competitiveness of Summer of Code has spread widely meanwhile. 

Initially the high quality of so many applications looked like a Good Thing™. However, since the last week I’m no longer so sure I like the result. With this level of competition it’s difficult to see how less experienced students would have a chance to get in. Along this line, we didn’t receive this year what I like to call an empowerment-type application, where we could envision someone going all the way from a user to a fully capable contributor, so a repeat of Erica’s story from last year is unlikely. 

I’m also wondering whether some of this is self-inflicted. We’ve had a few inquiries from biology students with very little or no programming experience who wanted to get into writing code, but we really only had one project idea (phyloXML support in BioPerl) that could be adjusted well enough to a beginners level and still be meaningful. None of those inquiries yielded an application. Were there too few options to pick from that seemed attractive? Did the expectations for a strong application seem too daunting? Aside from that, perhaps not surprisingly that project idea also turned out to be one of the most popular ones, and so I’m not sure a truly inexperienced student would have been able to successfully compete.

Other than ensuring that we sail an entirely smooth course over the summer to hopefully be able to snag more slots next year, I’m not sure what to do about that, though. Suggestions or ideas anyone?

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.

I’m serving again as the organization administrator. Last year, our participation originated out of the spur of the moment, when I came across a Google Summer of Code announcement on some mailing list (I don’t even remember which one) and thought this would be a great program to continue some of the activities started as well as the energy galvanized at the Phyloinformatics Hackathon that had taken place 3 months earlier. Despite a lot of skepticism and having had barely 2 weeks to pull together a competitive ideas page and application, we made it and became one of the 131 out of ~330 of applying organizations that got accepted.

The rest is history. The turn-out of applications was overwhelming (we received 65 in total), which gave us an even higher allocation of students (11) than we had anticipated in our wildest dreams (Google bases the allocation roughly on the number of applications an organization received, with adjustments for past performance and other things). Most of the top applications came from students with a strong background in evolutionary biology who wanted to gain or broaden their programming skills in a real-life context. Most of the students we accepted had not contributed in any significant way to open-source software before.

The applications showed that there is an audience for exactly this kind of program in our field. How successful were we in training the students, who are going to be the future researchers in our field, to not only (re-)use open-source software, but to be able to contribute to it? I’ll let you decide for yourself, for example based on the statistics I compiled for this year’s application (check section 5, Did your organization participate in previous GSoC years).

There is a nice overview of all of our 2007 Summer of Code projects in the Fall 2007 issue of the NESCent newsletter, which also has a group photo from the end-of-summer meet-up that we organized as an add-on. Moreover, one of the students (Mark Okada, if I recall correctly) assembled the mentors and students into a cladogram and every mentor received this motif on a mousepad. Isn’t that cool?

I can’t resist to highlight at least two of the projects here. One is PhyloWidget, developed by Greg Jordan (currently at the EBI), who has continued to work on it even after the end of the Summer of Code program. PhyloWidget is a Java applet based on Processing (an MIT spin-off initiated by Ben Fry) to allow navigating and manipulating even large phylogenetic trees; lately it has started to receive a lot of attention, for example in the AToL community, and Rod Page has covered it as well.

The other one is PhyloGeoViz, a project started from scratch and developed by Yi-Hsien Erica Tsai. Erica is my personal hero of the program and exemplifies what kind of empowerment the program makes possible. Though she had attended some programming classes before, she didn’t have any prior experience in the programming languages she ended up using (PHP and JavaScript) or the Google Maps API, and those were only a few of the obstacles she had to, and did surmount to finish reaching all her project goals! For me, her accomplishment alone was enough reward for the time I put into the program.

So I’m looking forward to enjoying this year’s Summer at least as much as last year’s. We have even received some blog coverage already (Panda’s Thumb, Your Bones Got a Little Machine, and TreeTapper) and if you can add to that please feel encouraged I have to say that based on our experience I disagree with Andrew Perry’s (over at Your Bones) suggestion that coding for a bioinformatics project is less interesting to Summer of Code students. The variety of interests among the students is huge, and so the observation that not all of them are into bioinformatics is no surprise (even if not fully understandable ). I also have no evidence to believe that Google limited the admission of bioinformatics projects in any way — unfortunately, and that is a surprise, aside from those admitted I really don’t know of any bioinformatics project that made the effort to apply (including, sadly, the O|B|F projects). Maybe bioinformatics is funded too well? Actually, believe it or not, almost everyone I speak to either isn’t aware of the program, or hasn’t thought that it might be for them too.

That said, I’ve been really pleased to see some new organizations there, such as quite a few related to grid and workflow computing (among them Taverna), and the Squeak development environment, which includes project ideas for Croquet. These examples also show that in reality more bioinformatics projects may be represented than one might think, as some listed organizations in reality act as umbrellas. In fact, two of our own project ideas (phyloXML support in BioPerl and BioRuby) are Bio* projects, so in a sense they are here.

Update 1 (March 31, 1.54pm): The student application period has now officially been extended to April 7.

Update 2: Added blog coverage by TreeTapper in the text.

Update 3: Failed to mention Plazi who I am positively surprised to see participate, as it is from the intersection of biodiversity informatics and digital archiving.

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.       

The site itself has actually been up since several weeks. After the documentation on how to do comparative analyses in R, which was created at the Comparative Methods in R Hackathon in December, was moved over, Sam Prince, Brian Sidlauskas, and Brian O’Meara, all postdocs at NESCent, worked on polishing up the initial content, determined to formally launch the community on the Ides of March. Sam is also the one who created the logo – I wish my own logo designs were only half as good!

The site right now is a wiki. The hope is that it is not only for, but eventually also by the community. Everyone can create an account for themselves and edit or create content (anonymous edits are disabled at present, though). And yes, in case you were wondering, despite the uncommon style (or ‘skin‘ as it’s called) it is indeed a MediaWiki. The URL layout of the site (i.e., putting the wiki under /wiki) allows to add other components to the site later, such as a blog (any volunteer writers?), or static content, or services.  

The community mailing list, which we decided to make a special interest group (SIG) hosted on the same server as other R Project SIGs, has actually been up even longer, namely since the beginning of the year. The interesting thing, and a strong indication that we’ve really hit a need here, is that seemingly by word of mouth (or web sleuthing?) a number of scientists from various institutions have discovered and subscribed to the list in the meantime, and two discussions involving some of the preeminent experts on the topics already took place without any formal kick-off. I hope that’s a good sign for this becoming a lively and self-sustaining community over time.  

Aside from signifying the beginnings of the first resource of this kind for this community, the launch of the site is also noteworthy from another perspective. We are using it as a pilot for moving towards decentralized, user-centric, globally unique user identity and authentication, in this case using OpenID. We all know the problem of proliferating user account/password combinations too well. For R-Phylo, using the “Login with OpenID” link in the upper right corner you can use an existing identity of yours (provided it’s an OpenID) as login and authenticate against your OpenID provider. For example, I (re-)use my claimID identity.

I’ll be blogging separately about our ideas and the experiences we make employing this technology on a larger basis; global user identity is becoming increasingly important for us not only to control the number of user accounts we ask our numerous scientific visitors to create when in all likelihood they already have more than their share of identities when they come to us, but also to lay the basis for authenticating data access and querying authorization across databases and digital data repositories.

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.) 

Obviously this could be a rather monumental task, so we are trying to break it down into manageable units. We are starting with defining possible scopes (such as along the axis of broad phyloinformatics data types), use-cases, and distilling an initial set of API requirements from those. It is quickly becoming clear that the number of possible queries and desirable operations is nearly endless. Rutger already attracted the awe of our fellow programmers in the room by creating a gigantic matrix of all possible inputs versus all possible outputs, with the cells being the operation(s) that the combination would correspond to (see the workgroup page). Chris’ insights from a comparative genomics perspective (see, for example, his recent paper in Genome Biology) are also invaluable; it is interesting to hear how different the obstacles are that he encounters in his data analyses from, for example, the issues with disseminating research trees of life.

Our next step will need to be narrowing down by API scopes, query priorities, and implementation feasibility. As a start, the way I am looking at API scopes is from the viewpoint of the types of possible service providers. For example, one type of service (or, in this case, data) provider is a database of phylogenetic trees, such as TreeBASE, or a taxonomy database, such as ITIS. Another type of service provider would be one offering to execute phylogenetic analysis methods, such as CIPRES. In reality, service providers may fall into more than one category; for example, TreeBASE also stores character data (such as alignments).

We have already gathered a substantial amount of documentation along the lines of the above, and if you read this you are very much invited to comment on any of the aspects, ranging from how we are organizing this, to what we are missing, to what in your opinion we should focus on.

My other main target is working towards the long-overdue v1.0 release of BioSQL, and serving as a readily available consultant to the BioSQL interoperability and web-services group. When I’m not watching Mt. Fuji, I’m sitting next to Mark Schreiber - one of the great things about a hackathon is that interaction just can’t get any easier. In addition, our PhyloWS documentation work has already pointed out several pieces of information a phylogenetic tree database should have available, but that the current version of BioSQL’s PhyloDB module can’t store, so in a related goal I intend to make several additions to the schema module to close those gaps. 

As is always the case for a hackathon, there are many times more tasks I would want to work on than I could possibly accomplish. The main goal for the remaining time is to get enough done such that the main activation barriers have been surmounted, so that the rest of the work can be completed when we return home and are engulfed again in our normal daily obligations.

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.

The event is sponsored in part by the Database Center for the Life Sciences (DBCLS), a new center that was only founded last year, as Dr. Toshihisa Takagi, the Center’s Director, points out in his opening address. In fact, he says, the hackathon is the first event sponsored by the Center, and he looks forward to us setting the mark for future events.

The event was organized by Toshiaki Katayama, who I have known for a long time. Toshiaki founded BioRuby in 2000, and has himself been at several Bio* hackathons in 2002 and 2003, and in fact attended NESCent’s Phyloinformatics Hackathon in 2006 as well. As he tells us, he also co-founded the Japanese Open Bio* Research Group — a Japanese sister organization of the O|B|F and I had not been aware!

I’m very excited to be here, and honored to be invited. Interoperability and the programmable web, of which web-services are a key part, are among my core interests, and there are a lot of smart people convened here from really interesting projects. This afternoon, we will use Open Space Technology to nail down the concrete goals each of us will work on. I am looking forward to some stimulating discussions.

Personally, I’m very interested in making progress towards a common phyloinformatics web-services API, which I am for now simply calling PhyloWS, but more on that separately. In the past two weeks, several other suggestions have been made for possible subgroups (see the public archives of the mailing list), some of which would also be gratifying for me to be involved with, for example a Bio* interoperable BioSQL-based web-service API. In fact, Heikki Lehväslaiho reminds me that if I only got around to finally releasing BioSQL it would be a great outcome…

So watch the space on the list of topics page, and you can in fact watch us live through the BioHackathon2008 stream on UStream.TV.

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’.

The small twist is that the speakers he invited aren’t local faculty colleagues, but instead people from the private sector, possibly to bring a fresh, applied, perspective to the subject, and in terms of showing alternative career possibilities. (You may have the exact statistics, but simple numerics alone suggests that a majority of undergrads will not proceed to faculty careers.)

As I haven’t ever worked at a genome database or sequenced a genome (and at present also don’t work in the private sector), I’m not sure why Owen invited me. Moreover, Owen’s direction was not to say anything about genomes, or genome databases. Instead, he asked me to talk about how I got into the field.

After scratching my head for a long long time, in an epiphany I thought choosing the title of this blog as the guiding motto could be a good idea. Sure enough, once I had that the rest started falling into place, and it ended up being a thoroughly enjoyable experience that I’m glad Owen invited me to. The slides in PPT format are here, though don’t expect much substance if you do take a look.