Monday, July 30, 2012

Presenting In Absentia

One of the lovely things about having good colleagues: just because you're having a major life event doesn't mean everything has to grind to a complete halt.  For the month preceding my daughter's expected due date, I was grounded---not travelling anywhere, in case she should decide to come early.

That time also overlapped with a couple of conference presentations, and fortunately my colleagues were able to go in my place.  Aaron Adler took over my invitation to present on our synthetic biology tools at the Biological Systems Design meeting at ISMB, a major computational biology conference,
and Hala Mostafa presented our paper, A Manifold Operator Representation for Adaptive Design, at the Generative & Developmental Systems track of the GECCO evolutionary computation conference.

From their reports, it sounds like both meetings went very well, and that our work was well received.  Frankly, though, I'm quite glad I didn't take the risk of missing my daughter's birth.  Professional life continues, and there will be many more chances for me to travel in the future---and perhaps even take a baby with me, if she turns out to be social and a good traveller.

Monday, July 23, 2012

Non-Maskable Life Interrupt

Last Tuesday, my daughter was born.

I've been mostly off the Internet ever since, and certainly not doing any scientific work.
Fortunately, this was planned for: I've got six weeks of paternity leave scheduled, and am looking forward to taking all of this time to learn what parenthood is like and who is this little person who is my daughter.

And yet... I find that my reactions as a parent are clearly shaped by my inclinations and education as a scientist.  Rocking a fussy neonate to sleep, cooing to her in woogie-woogie tones, "Oh, don't you worry little thing, you don't know how to regulate your emotional state yet, so you're just counting on us your parents to do it for you... isn't ooo?  Yes, yes, you're using your parents as an externalized regulatory mechanism, you silly little mammal you."

I've had to set down and ignore two position papers that I was in the middle of writing --- hopefully I'll be able to come back to them before my colleagues completely run out of patience, but maybe I won't.  Work/life balance has an entirely new meaning now, and I will be utterly fascinated to find out how I am able to navigate this balance between fatherhood and science.

Right now, though, I'm taking everything one hour at a time, and I think that's the right way to do it.

Monday, July 16, 2012

Synthetic Biology: End-to-End and Also in the Middle

Dear reader, you must not, of course, expect this run of publication posts to extend indefinitely, but for the moment we're hitting pretty well and experiencing a good bit of synchronicity as all my different projects seem to have long gestating papers maturing all at once.

The latest in the series: over the past week, we've had not one but two of our synthetic biology papers accepted for publication, both in ACS Synthetic Biology, as part of a special issue on design tools.

The first, "An End-to-End Workflow for Engineering of Biological Networks from High-Level Specifications," is essentially a summary of the key results of the whole TASBE project---the "Tool-Chain for Acceleration of Synthetic Biology Engineering" that I led  last year, with Ron Weiss and Doug Densmore collaborating.  The big result: coming up with a series of models and tools for turning high-level computer programs into DNA for controlling the behavior of cells.  And we made it work, at least for our version of "hello world"---a program that fluoresces one color when it detects a signal molecule, and a different color when it's not there.  Not the most complicated thing in the world, and there's a lot of duct tape and baling wire used to hold the tool-chain together, but it took a lot to sort this much out and it's a good starting point.  Moreover, now that we've showed it's possible, we (and others) can expand and do more and more complicated things---the hardest part is getting anything at all to go reliably from end to end, and now that we've got that, we've got a foundation to build on top of.

The other paper, "Automated Selection of Synthetic Biology Parts for Genetic Regulatory Networks,"
is all the details for one of the new key pieces of the tool-chain, for selecting which DNA parts can actually be used to correctly implement a computation.  This was led by my colleague Fusun Yaman, who worked with the folks over at BU and came up with a nice mapping of the problem onto a graph problem (NP-complete, of course), and a good set of heuristic algorithms for solving it.

I'm quite proud of both of these papers, since I think they're an important milestone in the progress of synthetic biology, and especially of raising the level of abstraction at which it's actually practical to design organisms.  There's a long, long way to go, but we're making progress and (eventually) reporting and publishing it as well.

Monday, July 09, 2012

Energy Management = Cover Story!

There's a nice article about my distributed energy management work with Zome Energy Networks
in the MIT Energy Initiative's "Energy Futures" magazine.  We're the cover story (though the cover image is of a simulation from a much older generation --- they really liked the Proto graphics, even if our current simulations don't use Proto any more).

Monday, July 02, 2012

Coordination Languages vs. Proto

Got an interesting new paper for you folks, a little bit into a different space than the last few: Linda in Space-Time: An Adaptive Coordination Model for Mobile Ad-Hoc Environments.  This was just published in Coordination 2012, and is another collaboration with Mirko Viroli, who really did the bulk of work in the paper --- my last author position means "consultant" rather than "supervisor" on this one (on a completely side note, it bugs me that the semantics of author position are so ill-defined, but that's a post for another time...).

The interesting thing about this paper for me is it's really pushing my boundaries on how to think about spatial computing languages.  Mirko comes much more out of the coordination languages community, where they think about programming more in terms of a blackboard that a whole pile of different processes can write to.  So everything folds down into one or more "tuple spaces" and you have no idea what might be shoving itself into the tuple space or deleting stuff out of it, or even any way to guarantee that names mean the same thing to different programs---the whole point is that you can have a bunch of different programs written by different authors all coming into the same place and sorting things out between them as they go.

To me, this is scary --- anarchy!  With Proto, you always know exactly what everything means in every scope --- it's exactly the sort of control-freakiness that's so elegant and so often limiting with Scheme.  To Mirko and others in his community, coordination languages are a wonderful world of open pervasive ecosystems.  So when Mirko approached me about bringing ideas from Proto into the Linda coordination language, I struggled but ended up finding the challenge interesting.

Overall, I think we're still very early in figuring out how spatial computing programming languages can and should work.  There are certainly some key ideas that keep popping up over and over again: neighborhoods, distributed distance measures, vector fields, restriction, broadcasts, gossip, etc.  A group of us had a discussion of this after the spatial computing workshop, and decided that we ought to start building a table of the useful primitives, and which variants are being made available in all of our languages (kind of an obvious next step after the Spatial DSL Survey).

Linda in Space-Time is a start on another perspective, and I'm looking forward to where it goes next, and what the tension between it and Proto can teach us about computing on space in general.