unclebooboo

Over the past 20 years much of my research has involved the development of software for various kinds of optimization problems. I've always made this code available to my fellow researchers, and as "open source software" became a buzzword I started to make my software more formally available under open source licenses. My biggest project, CSDP has been made available through the COIN-OR project.

Another trend that has been accelerated by the internet is easy access to large data sets. I've been particularly impressed by how easily graduate students in the earth sciences can get access to huge datasets of seismological records of earthquakes. Similar advances are being made with scientific data from earth observing satellites, astronomical data, etc.

During the same period, interest has been growing in "open access to scientific research", partially as a result of the crisis faced by academic libraries that have been unable to keep up with the costs of journal subscriptions, but more broadly because researchers want their papers to be more broadly accessible and some members of the public feel that its very important that taxpayer funded research be available to the public. I've been aware of this open access movement through my work on our university's library committee and found in my own research career that papers that I've made freely available on the web are much more widely cited than other papers.

There's an emerging movement to broaden these themes even further into a movement for "Open Science." The short slogan version is "Open Source, Open Data, Open Access, Open Notebook." The first three of these should be clear from what I've written above. The "open notebook" refers to scientists working collaboratively using social networking technologies.

I'm convinced that in the very near future, these trends will combine to really affect the way in which science is done. As one example of this, I'll offer up the new journal Mathematical Programming Computation, which requires authors to submit their code for review along with their paper drafts, and encourages authors to make their code available as open source software. I'm a volunteer technical reviewer for MPC.

I can highly recommend the OpenScience Project Blog for those who are interested in this stuff.

( Long essay behind the cut )

Today was the second race of our fall series. I once again beat my two closest competitors, with a time of 22:19, which is my second fastest 5K time ever, although the course was just a bit short.

( details, including picture and splits, behind the cut )

The gym at our university sponsors a twice a year fun run of 13 miles from campus to the Owl Bar in San Antonio New Mexico. Today was the third time I've done the run. This has become a tradition for us, with Sue taking pictures of me and other runners staggering in to the bar, and then we stay for a dinner of green chile cheeseburgers. Given my recent problems with Plantar Fasciitis I was a bit worried about this run, but it all worked out OK, and I had a good run, and a wonderful dinner afterward.

( details cut for those who are bored by running )

Today was the first 5K race of our fall series. The short summary is that I ran a
fairly hilly course in 23:15 at a relatively low average heart rate of 165. This is a minute slower than my PR, but I haven't been doing speed work recently and trained right through this race, so I was happy with that time, particularly considering that I didn't really go all out, as evidenced by the low heart rate.

I have a number in a Google Docs spreadsheet that changes from day to day. I'd like to have this number appear on my facebook profile page.

From Google Docs, I can get a link for the spreadsheet in question, or I can embed it using an iframe, as in:



Unfortunately, Facebook won't allow iframe's on profile pages.

Does anyone have any suggestions of ways to accomplish this?

Sue and I went up to Albuquerque on Thursday evening for a bit of business (a meeting with our financial planner), and a Suzanne Vega concert at the Kimo theater.

I first heard a solo version of "The Queen and the Soldier" on a monthly sampler record called Fast Folk, sometime around 1984. When Suzanne Vega's first album came out in 1985, it got a bit of airplay on our college radio station, but didn't seem to be a huge commercial success. The 1987 album, "Solitude Standing" included some minor hits, such as "Tom's Diner", "Luka", and "Calypso." I remember quite clearly hearing all of these songs while working a concert at the McNeil room at RPI back in 1987 or 1988 on one of my road trips from Boston to Troy. At this point, she'd added a full band with drums, keyboard, electric guitar, and bass, and the sound was quite a bit more produced. She seemed a bit shy and overwhelmed by her role as the star of the show. Since then, she's release a new album every three to five years, and although I'm always interested to see what she comes up with next, her songwriting has always been interesting and she's tried on a bunch of new styles, none of the newer albums have been quite as successful.

This concert was nominally part of a tour in support of the latest album, "Beauty and Crime", which came out in 2007. Most of the audience wanted to hear the 80's era hits, while I was hoping to hear some new (even newer than Beauty and Crime) material. The set list was well packed with the old favorites, and a sprinkling of songs from the more recent albums, but there was only one really new song. Although I was a bit disappointed by the set list, I was impressed by the guitarist and bass player who were backing her up, and I was very impressed by the way in which she interpreted these 25 year old songs. I think she's a better performer now than she was back in the 80's, even though her song writing creativity may have ebbed.

This weekend, Sue and I attended a yoga retreat at the Hurd-Wyeth ranch near Ruidoso NM.

The ranch is the family estate of the Hurd-Wyeth family (Henrietta, N.C.'s Wyeth's grandaughter, married into the Hurd family, and her husband and son went on to become well known artists in their own right.) It's now a fancy art gallery/bed and breakfast/small time conference center.

Ruidoso is located in the mountains of southern New Mexico, about two hours from Socorro in Lincoln county. You've probably heard of Lincoln county because of the history of Billy the Kid and "The Lincoln County War." The original Smokey the Bear (a wild bear cub) was rescued from a forest fire in the Lincoln national forest back in the 1950's.

The area around Ruidoso is sort of like the Adirondacks of west Texas- there are some ski resorts, casino's, and a horse racing track (Ruidoso Downs is the most important track in the specialized world of quarter horse racing.) There are also lots of chainsaw carved wooden bears (we picked up a small one to add to our growning collection-his name is "shorty"), 50's style motels, and other kitsch. Our favorite find was a pizza joint called "Cafe Rio", which has the best pizza we've ever had in New Mexico, and the first pizza with linguica that I've been able to find here.

There were nine participants in the retreat, including myself and Sue, an older couple from Albuquerque, a couple of women who take classes at our local studio, an "off the grid" guy from Lincoln county, and another couple who were friends of one of the teachers. Our experience level ranged from "first time" to "have taken yoga for several years." Our ages ranged from 30's to 60's. This was by no means an advanced workshop, but it was pretty intense. We did four yoga classes and two meditation sessions between Friday night and Sunday morning, and after driving back home on Sunday afternoon, I did my regular Sunday evening class at the studio.

Yoga classes with two teachers for nine students meant that we got quite a bit more attention than usual. Sue and I have taken classes with one of the teachers for the last several years, but we'd only done one class before with the other teacher, so it was a bit of a learning experience for both of us. I'm a bit of a strange student, since I'm strong enough that some things are very easy for me, while inflexible enough that other things are extremely difficult. Our regular teacher Marisa is familiar with this and typically has figured out in advance what modifications I should do. She was also familiar with almost all of the other students. I was impressed with how quickly the other teacher, Halli, figured us all out.

I hadn't tried any serious sitting meditation in over 20 years- when I'd tried back then, I'd found that I simply couldn't handle it physically- sitting still for half an hour at a time (especially sitting cross legged on the floor) was simply too demanding. The postures in yoga were actually developed in part to help prepare people for the physical demands of this kind of meditation. I was pleased to discover that I can now sit still with my legs crossed and spine straight for half an hour of meditation. Many of the mental strategies that I've been taught in yoga were also very applicable. For me this was one of the best parts of the weekend.

I feel pretty good after the weekend- not at all tired or sore. We'll see how running and yoga go tomorrow.

One of the participants was a professional photographer who was hired to take publicity shots for the two instructors. Sue and I (and almost everyone else) signed model releases and took part in a photo shoot, so we might appear on advertising brochures in the future. I've been told that I can get copies of any pictures of us that come out good- we'll see.

Today was my second running of the Magdalena to Kelly race. This is a short (only 6K) race from the village of Magdalena up to the old ghost town of Kelly. What makes the race interesting is that it starts at 6,500 feet and climbs up to 7,400 feet, with the course getting steeper with each mile. You can see a map of the course here.

I started off a bit too fast, and then faded on the steeper sections later in the course and even had to take a couple of walking breaks. I finished in 37:38, which was 1:28 slower than last year, partially because of my poor strategy and partially because it was quite warm today. Even so, I managed to grab second in my age group. I really wanted to improve on my time from last year, so I'm a bit disappointed with this result.

A recent collection of articles on self tracking from Wired magazine left me wanting to be unify the ways in which I track various data about myself.

On a daily or nearly daily basis, I weigh myself, record my blood glucose, check my blood pressure and resting pulse, and keep track of my weight lifting, running, and other forms of exercise. For the last year or so, I've been keeping hand written records of blood glucose, BP, and pulse, while logging my runs on the mapmyrun.com web site.

I have a rule about using any of these advertising supported web sites that I will always keep backup copies of my data, and I also try to arrange things so that I can get my data out of the web site in a standard format. For example, I keep regular backups of my livejournal and Google mail accounts. I have a Google "My Library" with over 1300 books from my professional library- I keep a backup copy of this data in .xml form, and I've written XSLT code to translate it into a plain text file. With respect to my running records, I've got .gpx files of every single run that I've done since February of 2008- these files could be used to recreate my running log.

Using a web based system like mapmyrun.com has the advantage that it's easy to access the data from home or the office (or some Wifi hotspot at a coffee house on the road), and makes it possible to export the data to my facebook page, blog, or whatever. Another advantage of using the mapmyrun.com web site is that I can easily produce maps of my running routes from GPS data.

However, the mapmyrun site isn't setup for logging all of the health related data that I'm interested in. Moreover, the company that runs the mapmyrun.com web site keeps changing their terms of service, and over time the web page has become encrusted with more and more advertising. The last straw was that they've now made it impossible to access logs from more than 3 months ago unless you're a paying customer.

So, it's time to adopt a new approach to self tracking. I've decided to setup a spreadsheet on Google Docs. This will be accessible from all of my computers, and I can easily download it in .xls format so that I have a version that I could run entirely on my own. Furthermore, this gives me the flexibility to add columns for all of the weird data (BG, BP, RHR, etc.) that I'm tracking. About the only disadvantage of this is that I'll having to deal separately with mapping my runs on Google Maps- I'll keep my mapmyrun.com account going just for that purpose.

Are any of you using a similar approach?

Now that we've been back for a couple of days, and I've caught up on my email and sleep, it's time for a report on our trip to Amsterdam.

( report (including pictures) behind the cut )

When you've got 9 hours on a transatlantic flight, there's plenty of time to watch a movie or read a book, and I managed to do both yesterday.

First, I took advantage of the opportunity to view the movie adaptation of Bernhard Schlink's novel, The Reader.

I had read the novel (in an English translation) a few years ago, so I already knew the plot (the movie is very true to the novel.) In places the novel was a bit slow for my taste, spending too much time delving into the thoughts of the protagonist. In comparison, the movie lets us just watch what happens and reach our own conclusions about what the protagonist is thinking. Although I liked them both, I found the movie to be even better than the novel.

The movie begins in the 1950's with an affair between a teenaged boy and an older woman. The woman Hannah seems oddly cold and unemotional, while the boy Michael is deeply in love. Hannah (for reasons that become obvious later) has a strange fetish- she likes to be read to. After a few months, Hannah suddenly leaves, and Michael is left emotionally scarred. In the second act, about 10 years later, Michael is a law student. As part of a special seminar on the legal aspects of the holocaust, he attends the trial of six women who had worked as concentration camp guards, and is shocked to find that Hannah is one of the defendants. Without giving away the rest of the plot, I'll just say that the movie delves into themes of guilt and innocence, with an interesting parallelism between Hannah's actions during the war and her relationship with Michael. The movie leaves lots of questions to be answered by the viewer.

The acting, (particular Kate Winslet's role as an "innocent monster"), directing, cinematography, and sound track are all excellent. This movie is really worth seeing.

I went on to read The Calculus Wars by Jason Bardi. This is popular account of the independent invention of calculus by Newton and Leibniz, and the fight for credit that ensued after Newton finally published his work, years after the appearance of Leibniz's work. It's now well established that the two had developed what we know as the differential and integral calculus independently, and that Newton invented it first but didn't publish until later, while Leibniz published first and developed a simpler notation. Thus they both deserve credit as being the "inventors" of the calculus. The book does a wonderful job of describing their careers and their development of the calculus. When it came to the actual dispute between the two, the book becomes quite dull. I could easily have skipped the lsat few chapters.

For fans of Neal Stephenson's Quicksilver series, the biography of Leibniz will be particularly interesting- Stephenson took many of the events in his novels from Leibniz's real life.

Delta is now offering in flight internet service for the low-low price of $12.99 per flight. This was my first opportunity to use the internet from on-board an airplane. It's interesting that the beat up old MD-80 that we're flying on has the service, while the shiny new A330 that we crossed the Atlantic on didn't have it. Then again, we had an in-flight entertainment system for the flight across the Atlantic...

I've recently read two novels by Portland area writer Jay Lake. Mainspring and Escapement are loosely connected novels (a few characters in common and some events in Mainspring are referred to in Escapement) that you'd probably want to read in order, but each novel is actually OK as a standalone book.

These novels are alternate history steampunk, in a version of earth where the northern hemisphere is separated from the southern hemisphere by a mountainous wall many miles high. The first two novels are set in the northern hemisphere, whith the southern hemisphere shrouded in mystery. The British and Chinese empires dominate the world, while two secrete societies struggle with each other over powerful magic that controls the fate of the world. Some reviewers have compared Lake's writing to Gene Wolfes. I wouldn't go quite that far, but these novels are certainly like Wolfe's in the scope of the world building and the quality of the story telling. The magical element makes this not proper science fiction in my opinion, but rather fantasy. In any case, I've decided that I like Lake's characters, story telling, and philosophical musings enough that I'll stick with the series.

Yesterday, I ran a five mile race in Omaha, the Nebraska Five Mile Championship. The short version is that I came in 31/84 in a very competitive field, and got second in my age group.

( More behind the cut )

A little known feature of Google Books is My Library. You can basically do a Google Books search on a set of books that you've identified in advance (typically the books in your own library.)

Since I had already inventoried my work library of over 1,000 books, it didn't take long to cut and paste the list of ISBN's into Google Books. I can now do a search on my library and find (for example) all of the books on my shelves that discuss "Zorn's Lemma" and what pages that discussion occurs on.

I wanted to make sure that I could get my data back out of Google Books too. There's an "Export My Library" function that produces a .xml file, but I wanted a 1970's awk/grep style plain text file. So, I spent this evening learning enough about XML and XSLT to produce a .xsl template for transforming my .xml file into a plain text file. It works great.

Now, all that I have to do is enter another couple of hundred books for which there are no ISBN's (because the books predate the introduction of ISBN's in 1971.) I've got Library of Congress Control Numbers (LCCN's) for most of these books, but there doesn't appear to be a way to give Google books a list of LCCN's to add to my library, so I may have to do these one at a time.

Charles Stross: The Merchant Princes series.

This is a series of 5 (so far, but number 6 is coming out soon) science fiction novels. As with most such series these days, the individual volumes do not stand alone- you need to read these books in order. I've read the first four books in the series over the past few weeks. I'll read book five when it comes out in paperback. Book 6 is expected in 2010. Stross starts with an interesting premise- there's a family of genetic mutants who can "walk" between worlds with alternate histories. The protagonist was born into the family but grew up in our 20th century world without knowing of her unique talent. There is some speculation about how a group of world walkers could take advantage of their talent. There is also a very convoluted thriller plot. I think Stross has done a pretty good job of holding the plot together through the first four volumes, but I find that the books are becoming less interesting as the series progresses- the twisty-turny plot has taken over the novel and Stross hasn't followed through on the science fictional speculation about what would be possible in his universe. I prefer some of Stross's other books, particularly Accelerando and Halting State.

Keith Devlin: The Unfinished Game: Pascal, Fermat, and the Seventeenth-Century Letter that Made the World Modern.

This is an account of the development of probability theory, starting with the famous correspondance between Pascal and Fermat about the "problem of points." After giving biographies of Pascal and Fermat, Devlin goes through the famous letter from Pascal to Fermat and discusses the philsophical issues that Pascal and other early thinkers about probability had to overcome. This is followed by several chapters that discuss later developments in probability theory. Although the book was well written and a fairly easy read, the author didn't dive very deeply into the history, philosophy, or mathematical aspects of his story. As with most other popular books on the history of mathematics, I was ultimately dissapointed by the lack of depth.

So I'm sitting in my office slaving away over a hot computer and listening to "The Hazards of Love" by The Decemberists. Except for the much better recording, this could easily pass for a Fairport Convention or Pentangle album. I like it a lot.

Today was the annual "Run For The Zoo" 10K race in Albuquerque. The short summary is that I ran the 10K in a new PR of 47:41 (almost 3 minutes faster than last year), and enjoyed my run, even though I wasn't quite as fast as I'd hoped.

( pictures and telemetry behind the cut )

Today was the "Run For Your Life" 5K race. The short tweet is that I set a new PR (22:17), and came in first in my age group, seventh out of over 40 runners overall. I actually beat everyone over the age of 29.

( Details behind the cut )