The weather has been awfully clement of late, so we’ve been flinging the doors and windows wide this week and inviting the bugs and other assorted fauna in. A particularly large junebug was flitting around our living room last night and developed an apparent affection for my hammered dulcimer. (I was a bit chagrined to note that by dint of crashing randomly into the strings, it played the instrument slightly better than I usually manage to.)

While standing in the back door after dark listening to the nocturnal symphony from the backyard, Emily asked me “What’s that sound?” “I think it’s frogs,” I said, listening to the unusual creaking cries coming in on the breeze. “Can I go look?” she asked, and bolted out the door.

Since I was in the middle of several other things at the time, I gave it no more thought. A little while later, I noticed Emily at the kitchen sink, apparently washing dishes. “Good for her!” I thought absently. As Kathy passed a few minutes later, however, she said in a surprised voice “What are you doing?”

I joined them at the sink to discover that Emily had filled a bucket with toads, all of which she scooped out of our pool which, due to its winter neglect, made a very nice habitat for the creatures. She had then dumped her dozen-strong catch into the kitchen sink, where four of the toads were trying to escape while another four busily tried to make more toads with the last four. It was quite a scene!

We let Emily and her amphibian circus play in the kitchen for a while longer until Kathy finally chased them all off to their various (flower)beds.

For any of you Wii-toting friends out there, here’s my Wii number: 4947 6945 6170 9931. Let me know what yours is so we can get hooked up!

Our bodies are made up of, among other things, a large array of proteins. The creation of those proteins is directed by our genetic code — the instructions encoded into our DNA as a long string of nucleotides, groups of which specify particular amino acids to be used in protein construction. Since the human genome has now been mapped, one might be excused for thinking that we would have an excellent grasp on the proteins in our body and their function at this point.

The problem is that proteins don’t come off the cellular assembly line and remain a long, snake-like string of amino acids. Instead, they fold up after they’re produced into a structure that determines what role they can fulfill. When this process works correctly, one ends up with useful enzymes, antibodies, and other vital biological machinery. When it goes awry, the malformed proteins can cause diseases like Alzheimer’s, Mad Cow, Huntington’s, and cancers.

This folding process, while near-instantenous, is mathematically incredibly complex, as it involve simulating all the intermolecular forces at work over the length of the amino acid chain. In fact, to simulate the folding process of a single protein would take about 30 years using the computer that’s sitting on your desk.

So, is simulating protein folding impossible without giant supercomputers or decades of time at your disposal? Yes, absolutely. However, the clever folks at Stanford have realized that a giant supercomputer doesn’t need to live all in one place, but can be cobbled together out of a whole pile of machines connected over the Internet. It was this realization that led to the birth of the Folding@Home project.

Folding@Home allows volunteers to install a screen saver which, when their computers are idle, will download bits of a protein folding simulation and work on it until the computer’s user needs it again. It periodically sends the results back to Stanford where they are aggregated and used to further the biological research that’s going on there. The project has been going on for several years now, and has yielded a great deal of useful data, though it remains constrained by the amount of computing power available to work on these complex simulations.

The recent interesting news in this area is that Sony and Stanford have developed a Folding@Home client for the new PlayStation 3 console so that its computing power can be harnessed and contributed to Stanford’s distributed computing cluster. While it was being developed, Sony touted the PS3’s cell processor as more powerful than a PC, and it does appear to have the most computing power of the next-gen game consoles. While a standard computer switches between tasks rapidly to create the illusion that it can do more than one thing simultaneously, the PS3’s 7-core processor can actually work on several tasks at once, further enhancing its potential number-crunching advantages.

So, do the Folding@Home statistics bear out Sony’s claims? Check out these numbers from the statistics page (a TFLOP is 1,000,000,000,000 floating point calculations, like “5.5÷22.3”, per second):

To bring that home a bit more clearly, I divided the number of CPUs by the TFLOPS Folding@Home reports to give an idea of how many TFLOPS each computer of each type is contributing and graphed the results:

So, the PS3 is contributing more than 6x the computing power per machine than Linux, the next closest operating system. Now, admittedly, there are going to be a lot of older machines in the other platform’s statistics, where all the PS3s are obviously of recent vintage, but this still seems a win for Sony. More importantly, it’s a huge boost for Stanford, which has more than doubled the computing power of their Folding@Home cluster by writing a client for the Sony console. Kudos to Stanford, and to all of the generous PS3 users who have chosen to participate in this project.

Here’s a video on the subject from GameVideos.com (warning: salty language at the end):

If you’re interested in contributing to the Folding@Home project, you can do so by grabbing and installing a client from their download page.

There’s a good article up at the L.A. Times site on Ross, his partner Andy, and their work at Boom! making new and interesting comics. Here’s the link. (If you don’t have an account on their site, feel free to use mine: latimes.5.seanmctex@spamgourmet.com/password.)

Holy cats, do I want one of these:

via Jason

I’ve been thinking some lately about all the great software and services that I use during the course of an average day. While I’m excellent about whining when a business or product doesn’t meet my expectations, I’m not as consistent about shout-outs to the good ones. In order to help remedy that, here’s a list of the stuff I like and why I like it.

For normal people:

• Google Calendar: (web) Managing a calendar for a family of 6 is a challenge. I used to use iCal, but was frustrated with keeping it synced across several different machines. Having the data on a central server eliminates the syncing hassles, the sharing options make it easy for multiple people to help keep things up to date, and the iCal support means that Kathy can subscribe to the calendars and still make pretty printouts with our calendar data from iCal.
• Remember the Milk: (web) Absolutely rockin’ to-do list manager. Lets you keep multiple to-do lists, has hooks into SMS and IM services to remind you when things come due, integrates with Google Calendar, lets you share individual items or whole lists with other people, and has a very rich and flexible recurrence model so that I can set “Pay Bills” for the first of every month, but can set “Change Air Filters” for 60 days after whenever I happened to get around to doing it last. For web app nerds, it also has the best implementation of “Undo” that I’ve seen in a web application.
• Bloglines: (web) A fine online RSS aggregator which integrates nicely with websites, mobile phones, etc. The “Weblogs” sidebar on my weblog is driven by Bloglines.
• Flickr: (web) If you are into photography, you probably already know about Flickr. Photo hosting site that has great community features and data interchange support. It powers the “Recent Photos” sidebar on my weblog.
• Netflix: (web) Great selection, good prices, and eliminates all of that tedious “interacting with real people” that you have to do at the video store. Add ratings, an excellent recommendations service, data export and some community features, and you have a winner. Powers the “What I’m Watching” sidebar on my weblog.
• Grand Central: (web) Provides you with one phone number you can give out to people, which will then ring all of your phones, or only certain ones (or none!) depending on who’s calling. Has actually diminished my hatred for talking on the phone. See David Pogue’s fake ad for more details on this groovy service. (Now if they’d only get some numbers in San Marcos…) Powers this very tasteful button you can use to call me:

• Gizmo: (Mac/PC) A VOIP program for your computer. I never got much into Skype, which does much the same thing as Gizmo, but when GrandCentral added Gizmo integration, I was suddenly able to make calls, local or long distance, to normal phones from my computer for free. (This may change once GC emerges from beta.) If I didn’t have a family, I’d have cancelled my regular phone line by now. As it is, having what effectively amounts to another phone line in a house with a teenager has proven useful.
• Adium: (Mac) Very nice multiprotocol messaging client. Has a ton of power-user features, and integrates nicely with…
• Growl: (Mac) A unified notification manager for Mac OS X. Lets applications that support it give you notification via a variety of popup window types. My main Mac pops up a little bar across the bottom of the screen with pertinent details whenever someone IMs me, when iTunes cues up a new song, when I get a new email, when Democracy Player finishes downloading a video, when iStumbler detects a new wireless network nearby, and more…
• Comic Life: (Mac) Lets you make comics from photos or using your newer Mac’s built-in iSight camera. Immensely fun.
• Democracy Player: (Mac/PC/Linux) Wraps up an RSS client, BitTorrent, and VLC into one nifty bundle. Part of the Participatory Culture Foundation’s suite of software that creates a complete end-to-end alternative video distribution channel through the Internet.
• Firefox: (Mac/PC/Linux) The best, most flexible web browser available. And it’s free. Put IE behind you, slaves of Bill Gates!
• Plaxo: (web/Mac/PC) After .Mac tried to eat my Address Book data for the 6th time, I went looking for alternative ways to keep that data in sync across various machines. Plaxo provided what I needed for free and added in some nice additional data management options. (You could, for example, use it to sync address book data across Macs and PCs.)
• Google Earth: (Mac/PC) It’s like a virtual globe in your computer, but with all of the data-mining power of the internet behind it. Educational and fun.
• Google Sketchup: (Mac/PC) 3D modeling for the rest of us. Easiest modeling program I’ve every used — handy for designing houses, furniture, modeling where the sun will fall on your property, creating building models to share in Google Earth, etc.
• OmniGraffle: (Mac) What Microsoft Visio wants to be when it grows up and gets good taste. Superb package for visual communication.
• Quicksilver: (Mac) The first thing I install on any new Mac. App launcher, data manager, and much more. I keep discovering new things it does. I’m pretty sure it makes french fries and gives backrubs.
• Wesabe: (web) Online financial management program. Kicks Quicken to the curb with Web 2.0 flair, and has shaved about 30% off of my bill-paying time.
• Bibliofile: (web) Well, yes, I wrote it, but I still find it useful. Keep track of your reading.
• Pandora: (web) Lets you create your own radio stations with just the music you’d like. If only they’d get it working on the Wii’s web browser…

For programmers:

• Trac: Combines a Wiki, a ticketing system, and a front-end to a SCM system (subversion, to wit). Each of the tools is nice individually, and together they make a bang-up addition for small to medium teams.
• Subversion: Great source code management system. Has several important advantages over CVS, and is well-supported across a variety of platforms.
• Eclipse: Really nice IDE, originally for Java development but now with plugins for all kinds of languages.
• Magnolia: A CMS that emphasizes functionality and ease-of-use. We switched to this from Vignette, and my quality of life improved markedly. Great bunch of people, too.
• Ruby on Rails: Outstanding framework for building database-backed web apps.

To celebrate Spring Break last week, we decided a family camping trip to Inks Lake State Park was in order. We all piled into the car Tuesday morning as soon as Maggie was back from a tearful visit to the doctor (where she got a couple vaccinations and the assurance that she wouldn’t have to be punctured again until she is 11 years old) and headed north.

We arrived in time to set up tents and unload the canoe from the top of the car, where I had lashed it with several miles of overcautious not-boy-scout-approved knots, before the sky opened and the rain started in earnest. We rode the worst of it out by loudly reading The Chronicles of Narnia in the tent before taking off for a sodden hike to the Devil’s Waterhole. (I looked, but saw nobody of particularly diabolical mien swimming there.)

I had no memory of having been to Inks Lake before, and wasn’t terrifically impressed with the photos I saw of the place on the Internet, so was delighted to find the lake and its environs absolutely beautiful. Our campsite was mere feet from the edge of the water, and an easy walk from some of the rocky falls and grottos that marked a nearby river’s ingress to the lake. The park was well-appointed, with lots of playgrounds, a general store, and even boat rentals. (My only disappointment in that regard was that the website promised Surfbike rentals, which looked like an excellent reason to sign a liability waiver, but they were nowhere to be found.)

We spent a couple of days paddling around the lake, doing a bit of geocaching, taking hikes, wandering around the campground, roasting anything that came to hand over the campfire, reading, exploring nearby Marble Falls, etc. Sadly, a mere 6 photos into the trip, our camera decided that the world should be considerably more purple and smeary than it actually is, so we weren’t able to take much in the way of useful pictures. In spite of that setback, it was a nice vacation, loudly and repeatedly proclaimed by several of the kids as “the best camping trip ever!”

For the first time, I want a PS3.

UPDATE: Here’s the editor in action as well. Very nice indeed.

Last weekend, thanks to Kathy’s willingness to hold the fort, I was able to make my way up to Waco for Baylor’s All-University Sing, a huge show that fraternities, sororities, and other student organizations put on every year and for which my good friends Jason and Barry arrange nearly all the music, in addition to playing in the pit band and building some of the props. Kathy and I went for the first time last year and had a superb time of it, so I was understandably keen to get back. (As I told my boss, “You haven’t lived until you’ve been in a room with thousands of baptists hopped up on sugar and adrenaline seeing their friends go crazy Broadway style!”)

I took off work a bit early to get up there in time, and had to sweet-talk my way past one of the door-guards to get in and find Jason. (“See that guy in the orchestra with a cell phone in his ear? He has my ticket!”) We connected up about 15 minutes before the show began, and he introduced me to Matt, with whom I’d be sitting and who had kindly offered to give me a place to sleep that night. Before long, the lights dimmed, Jason sprinted for the pit, and Matt and I settled in to enjoy the spectacular show.

Matt, as it turns out, is working on his PhD in physics, with a focus on String Theory and Quantum Physics. Our conversation quickly took a technical turn as we talk about his research and programming and simulation concepts. During one of the 6 minute lulls between acts, we had this conversation:

Sean

I wonder how many calories were just expended on that stage.

Matt

I’ll bet we could figure it out.

Sean

Oh, totally. There were, what, about 80 people on stage?

Matt

That sounds about right. And at a good exercise heart rate — say 150 beats per minute or so — people expend about 900 calories an hour.

Sean

Good, so since the acts are about 9 minutes long, we’ll call it 100 calories/person over the course of the act for easy math, so about 8,000 calories per act.

Matt

And for 19 acts, the total would be…ummm…152,000 calories per night, not counting the orchestra or the stage crew.

Sean

That sounds just about right. Excellent!

Sean & Matt

[Satisfied pause]

Matt

We are really big nerds.

Sean

Oh yeah. Totally. [beat] And the next stage, of course, is to figure out how much arable land would be required to meet the caloric needs of the show…

After the performance wrapped up, we went to Cricket’s for some chow and a debrief of the show. We told Jason and Barry which acts we liked the best, laughed together about some of the little musical tricks and jokes they’d worked into the arrangements, and recounted highs and horrors of years past. Between the brilliant company and the good food and brew, this was the best part of the evening for me. We then retired to Matt’s house where we talked and banged through a bit of Shadow of the Colossus, a beautiful Playstation game, before falling exhaustedly to sleep. It was a superb time, and left me grateful for such engaged and hospitable friends.

Jason’s blurb on this year’s sing is here.

I’m booked to go to Portland for RailsConf in May. Though I wasn’t able to arrange to travel by train, which would have made it that much better (both because I enjoy traveling behind a locomotive and for the silly pun), I am looking forward immensely to the opportunity to meet a couple of people who I have known only through the Internet: Mark, with whom I’ve sparred, corresponded, and cultivated a friendship over the past half decade, and Seth, for whom I used to work at Macrobyte Resources and with whom I’ve also enjoyed a long, varied and fruitful correspondence over a similar span.

If any of the rest of you are going to be in Portland or know of anything I should make a point of not missing while I’m there, please drop a note!