Below are the 20 most recent journal entries recorded in jay_monger's LiveJournal:

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Saturday, May 3rd, 2008
9:02 pm	Therapeutic Birding Last weekend it was dealing with my 2007 Canadian taxes (they weren't due until April 30th) and the weekend before that was an annotation jamboree with the Phenoscape people - we gathered together with three invited fish morphologists and a couple of observers from other OBO projects (you can read about it on the project blog: http://blog.phenoscape.org/2008/04/18/first-data-jamboree-is-beginning/). So I finally had a semi-free weekend. It's true, I miss field biology. Since I finished my degree, birdwatching is the closest thing to fieldwork I can easily do. I don't regret the path I have taken, but I think being out in the field with free-living animals has become important to me. The next step will probably be getting some new video equipment, even though I've only digitized two of the 60-odd tapes from my Florida fieldwork. I'm sure it will take some practice to even approach the results I got with the jays, they were just so easy to work with. So, I went to two places today: Flint Hills National Wildlife refuge, about 20 miles east of Emporia KS, and the Tallgrass Prairie National Preserve, about 10 miles north of Cottonwood Falls KS. I'd been to Flint Hills NWR before, but that had been earlier in the season and I expected to see some new species. At the Burgess Marsh site I actually saw quite a bit less - still a fair number (25-30) American Coot and a couple of Blue Wing Teal, but the last time there were closer to 100 coots, dozens of Blue Wing and very an uncommon Cinnamon Teal. The Town Site trail did provide some new warblers and the same male Cardinal with the two extra syllables in his song. The Dove Trail was overrun with Boy Scouts, so I passed. Tallgrass Prairie was a new location for me. It was similar but not identical to Kanza Prairie in Manhattan. Since this area is a preserve with actively preserved farm buildings and a school, there isn't any significant ecological manipulation like there is at Kanza. I assume they burn from time to time to keep the trees under control, though. There were lots of meadowlarks, a couple of species of flycatchers that were giving me identification problems and a couple of surprises, such as a Nighthawk call in the middle of the afternoon. All locations had Chickadees (even the Prairie - probably because there was woodland along the side of a creek). They seemed to be of the Black Capped species, though Sibley's range maps suggest I was close to the boundary with the Carolina Chickadee's range. I'd include pictures, but a small Phoebe in a big tree and 7 coots swimming away didn't seem like they were worth sharing. Current Mood: satisfied (Comment on this)
Saturday, April 5th, 2008
10:16 pm	Final 4 madness KU is in the NCAA final and as you might expect, Lawrence is sounding like a cross between New Years and the fourth of July - actually a lot more amateur fireworks then I remember from New Years - of course it's 50F tonight, so a lot more people are milling around outside. I expected this after the late afternoon fireworks last sunday when KU beat Davidison. Current Mood: amused (Comment on this)
Wednesday, February 6th, 2008
9:31 am	Kansas Caucus Kansas Democrats had their caucus meetings last night. We literally had an overflow crowd at my designated site, one of three in Lawrence. They shuffled us a couple of blocks away to a local theater. As in the rest of Kansas, Obama won by a wide margin. This wasn't surprising, Obama visited the state, got the endorsement from Kathleen Sebelius, the governor, and had at least one campaign office in Lawrence. The office was actually on the route I take when I walk to work. I never saw an office for Clinton, though there may have been one somewhere. I caucused for Obama, mostly for electability reasons. Now KU is closed for snow, so I'm at home today. Current Mood: accomplished Current Music: NPR morning edition (Comment on this)
Saturday, October 6th, 2007
2:48 pm	Forgot Mesquite The Maddisons decided to bump Mesquite's version to 2.0. It's been out for a couple of weeks now, and at least some people find the UI considerably improved. I've been working with it so long that it doesn't really affect me that much - unlike, say Office 2007, which I found next to unusable when making last minute slide changes at Animal Behavior last July. Current Mood: satisfied (2 Comments |Comment on this)
2:14 pm	Life with the fish (ontologies) The last six weeks have really focused on ontologies, job search (for next year), and figuring out what to do for the last year of our multi-year collaborative project. The fish ontology project had a workshop two weeks ago, where we invited some outside people to join us at Nescent, the evolution synthesis center over in North Carolina. This week I'm off to Philadelphia to help kick start the curation process on the anatomy ontology - which started life as a clone of an ontology for zebra fish anatomy. Last week, I posted a mini copy of the taxonomy ontology. It's a little more than just an is_a hierarchy, because we have terms for Linnaean taxonomic levels, and lots of synonyms. Eventually, this will get auto-updated from an Access database for something called the Catalog of Fishes, but that's still coming. Just yesterday, I got my official invite to go back to Nescent the second week in November to talk about ontologies for phylogenetics interchange. I've been working on an ontology to describe models of evolution: everything from the simple Jukes-Cantor model of DNA evolution, to more complicated likelihood and Bayesian models of molecular evolution and of (simple) phenotype evolution (including our recently published BiSSE model). At least at the start, it will be in OWL. It would be interesting to try describing these models, in research Cyc, but that will have to wait until I land that 'real' position I'm searching for. Same goes for behavior. I saw _rck_'s musings on his tenth year with his (ontology-related) employer, where I once worked, and some of the responses of other former co-workers who couldn't say what they were currently doing with ontologies professionally. I am actually happy to be in a position to share the things I've been working on, either at sourceforge, or in our little wiki at Nescent. (OK, we do have a few non-public areas). I'm also happy that _rck_ can share some of his ontologies for history work at sourceforge. It's gotten hot again in Lawrence, but the front that's due tomorrow might actually push us over into autumn. It's about time! Current Mood: hopeful Current Music: My A/C (Comment on this)
Monday, August 20th, 2007
7:44 pm	I've been in Lawrence for 2 weeks now I'm settled in, started work - which means more or less continuing the same things, and started the job search for next year. Actually there are some new things - probably less Mesquite, and more bio-ontology work - I'm being paid 25% to curate an ontology of fish anatomy. First step is building a traditional taxonomy in the OBO format. This gets built from a database with about 20K species listed. Not so hard once we have a copy of the database to play with. At least the weather has cooled of since last week. Current Mood: hopeful Current Music: The neighbor's pipes (Comment on this)
Sunday, July 8th, 2007
8:12 pm	Changes coming As many of you know, I'll be moving to Kansas at the end of the month. I don't know quite what to expect from Lawrence, though I'm sure I'll miss the proximity of the ocean - I can walk to the beach from my current digs. Before then, I have the Animal Behavior Society Meeting to look forward to. Last year I did a poster about an ontology-based behavior scoring tool. Actually I'm trying to get out a new version before the meeting. This version will actually somewhat usable as a behavior scorer - the times will be right and the CSV excel format will be available as an option. In the behavior scoring world, CSV is the lowest common denominator. Sadly, I'm spending more time on programming than ontology design. I had hoped to land some part time curation work next year, but that's looking less likely at this point. This year, it's on to comparative methods for ontologies. I'll be talking and trying to stuff sufficient background into the talk to lay out my three approaches in the 12 minute talk time. I am actually looking forward to this meeting a lot - I had a lot of fun there last year. It would have been nice to have hit AAAI this year, since it is in Vancouver, but it's the same week. I also should have gone to the Evolution meetings (it's plural because they include 3-6 organizations), but they were in New Zealand this year and nice as that would have been, I had neither the time nor money for this trip. They would have been a better venue for the talk. Current Mood: hopeful (Comment on this)
Monday, May 21st, 2007
9:28 pm	Farewell to Berlin I return to (rainy) Vancouver from sunny, hot Berlin tomorrow. It's been a good two months, though not as spectacularly productive as last fall. I don't know when I'll be back, though this is the third long trip to Germany this decade, so who knows. I get to spend a bit of time in Vancouver, then I take two trips in June and then July comes - Animal Behavior Society in July and then the trip to Lawrence Kansas, where my next gig is. Closer to C'dale so I can't complain. It's even closer to Carbondale Kansas, just to add confusion to my life. Current Mood: sad (2 Comments |Comment on this)
Wednesday, April 11th, 2007
10:30 am	Back from Norway, Sweden Got back from Trondheim and our road trip to Ostersund and Lit Sweden. My brother obtained documents showing my maternal grandmother's line lived here back to the 1850's. Unfortunately, although he made multiple copies, no one seems to be able to find them. We had relatives buried here, and perhaps they still are, though the grave was unmarked. Anyway, the church in the picture was certainly part of their lives. It dates back to the 18th century. There are remains of a 12th century stone church nearby. Lit is much larger than I had expected. It seems to have a population of at least a thousand, perhaps two thousand. Nearby Ostersund seems to have at least 20,000, though I haven't looked it up. Trondheim was fun, though it was snowing almost the entire time I was there. It stopped about 2 hours after I left. Current Mood: contemplative (Comment on this)
Sunday, April 1st, 2007
8:14 pm	Back in Berlin Last fall I got to spend a month in Berlin because W, the guy I'm working for, is doing a sabatical at the Wissenschaftskolleg zu Berlin, though most people refer to it as Wiko or the Institute. It's spread out over a couple of converted houses in a residential area of southwest Berlin, near the Halensee and Grunewald. Well, I'm back for another two months. The biggest news otherwise is that two papers I contributed to went to proofs on the same day, so I was rather busy last weekend. One was on comparative methods, the other on applying an ontology of spider anatomy to retrieving images from a database. Now if I can just get another behavior paper out. Meanwhile, another paper is in review that came from the work we did on my last trip here. It's a paper on estimating parameters in a extended birth-death model applied to evolutionary trees. I hope to get a second paper out of this model while I'm here. This weekend has been focussed on debugging an improved version of the tree simulator we use to test our model. I think I've figured out where the problems are coming from, but I don't have a fix yet. I did get to play tourist a bit yesterday, exploring the Kreuzberg area on foot. Current Mood: drained (2 Comments |Comment on this)
Monday, February 12th, 2007
8:15 pm	Happy Darwin Day I noted the day by attending a screening of Flock of Dodos and reading about the guy who got his PhD in paleontology from U Rhode Island and is off to teach at Liberty University. In the past couple of hours my reaction has moderated from, they probably can't revoke the degree, to something like the degree shows only that he is capable of doing science, not that he will necessarily do it in the future. I liked the film's treatment of God in the gaps theology - bad science, bad theology, don't go there. Finally, Darwin seems, from all I've read of him, a very decent guy, as well as one of the high points of Western Civilization. I'm happy to think kind thoughts of him and his work on this, his 198th birthday. Current Mood: relaxed (Comment on this)
Tuesday, February 6th, 2007
10:17 pm	Life in Vancouver It's the start of my second year living here in Vancouver, with J still at her job in Illinois. Of course since she has the "permanent" job, and I'm on soft money, that's probably the best way to deal with it. I have done some applying for real jobs, but I'm hoping that the flush of recent papers - 2 accepted and another submitted during the last 3 months of '06 promises better in the future. I'm in the middle of putting together what will probably be my job talk in the coming year. I ran it past a Chinese woman in the lab here, because she's off to Argentina for 4 months of spider morphology with one of the best. I'll be back to Illinois for a month, including giving the afore mentioned talk as a department seminar and then back to Berlin for another 2 months. November and December were pretty tough up here, but we may already be seeing the end of winter. It was colder in Illinois this week than here. Current Mood: content (Comment on this)
Sunday, May 21st, 2006
12:35 pm	Good week for Biology software Well, the new Mesquite (1.1) was released at around midnight Friday. The brothers M are quite pleased with both what was added and how the build process has been smoothed out with the transition to Eclipse and Ant. I'm partially responsible for the former, though not much for the later. If you are familiar with Pagel's program Discrete, Mesquite now has a module that does essentially the same test. Thursday evening was also a good time for OwlWatcher. I've been working, on and off, on getting Quicktime to play in a panel in a JFrame. Until Thursday evening, it would not display, play the sound track for a few seconds then crash hard (an exception generated in Quicktime itself which Java wasn't able to do anything with). That's gone and I can now watch a very distorted clip of spider courtship from within OwlWatcher. Still looking for the ideal owl shot for the splash screen. With any luck maybe some owl behavior to fill out the demo package. Now I need to get back to the juvenile scrub jay learning paper. Looks like I may have a room rate for the Animal Behavior Meeting in August. I expect this will be a lot of fun. Current Mood: optimistic (Comment on this)
Saturday, March 18th, 2006
5:03 pm	Ethotools Still up here in BC, plugging away on Mesquite and my ontology projects. On the Mesquite side, it's implementing Pagel's test for correlated evolution of discrete characters. The matrix algebra is done, I just need to get the optimizer to behave better. The boss has some suggestions for how to turn this into a paper. As for behavior ontologies, the Cornell ABO project is, I assume, progressing. I shipped an editted version to the Cornell people about two weeks ago and it sounds like they're still reworking the site. I'll link to it when it works. I've also been putting a reasonable amount into my ontology tools project. Since Mesquite went with SVN for its source repository, I waited for source forge to support SVN before I moved my code there. Now all my important source is off this poor old laptop. Weather here is nice, apparently better than in Carbondale this weekend. I suppose I should add that J was here over last weekend. A throughly enjoyable 70 hours. The Stellar's jays are fun to watch - similar to, but not quite like the eastern Blue Jays. I'm hoping to find some owls to photograph for the splash window for one of my tools. My brother came into Los Angeles from Trondheim yesterday. Talked to him, seems to be fine. (Comment on this)
Monday, February 13th, 2006
9:20 pm	More As I was saying... I'm up here at UBC, doing more Java work with the guy I postdoc'ed with in Arizona. I've gotten to meet some heavyweights in the phylogenetics world as well, there was an all hands meetings meeting of the project that's paying me to be here. It was back in Austin of all places. I spent today reviewing matrix algebra (eigenvectors and singular value decomposition, etc.) because I'm trying to get a maximum likelihood calculation to work for this stochastic model of evolution. Yeah, that's what I'm up to here at UBC. I am also doing some behavior ontology stuff. The guy at Cornell who organized the two Animal Behavior metadata workshops said he needs to submit a final report to the NSF by the end of next month - so we probably ought to get something posted soon. Of course my interest is getting something to start with. I am planning to do a poster with two OWL aware tools for behavior this summer. Even if they aren't running, it would be good to have something to show. The code (java) will probably get checked into Sourceforge as soon as they open SVN to us peons. All for now, jay_monger Current Mood: tired (Comment on this)
9:17 pm	I'm in Vancouver Hi, Don't know if anyone is looking at this, but I am up in Vancouver, (Comment on this)
Monday, October 3rd, 2005
1:31 pm	Novel feeding in Downey Woodpecker? I was about 30 feet from my front door, which has brickwork on both sides, with about a 2cm gap for mortar between the bricks. The gap is about 2cm deep as well. As I was approaching, about 5 minutes ago, a Downey woodpecker flew in and starting climbing down and then up along the left inside of my doorframe. She (didn't see a red patch), was poking her beak into the gaps, and several times made multiple pokes before moving on. She repeated this pattern on the right side of our frame, and moved over to our neighbor's door (15-20 cm to the right) where she inspected the right side before flying off. She didn't spend much time with the brickword facing forward between the doors. Considering the amount of insect and spider detritus around the doors, she may well have found something edible, though probably not much that was actually alive. Current Mood: contemplative Current Music: Some random backgroundy stuff (Comment on this)
Tuesday, August 30th, 2005
4:13 pm	Running, ontology, birthday So Saturday we (J and I) did another Marathon training run. We are up to 3 hours and 10 minutes. We are assuming a 10 minute pace, which is a pretty good match for our previous runs. We will probably be running Memphis in December. Up here in Carbondale we got a little bit of rain from Katrina, but the best news was that the temperatures have dropped to highs in the 70's. Much better for running. Finally got to working on my ontology-based comparative methods tools on Sunday afternoon. Actually, I spent more time updating the Habronattus ontologies and making sure they loaded into the tool. On Monday I went back to working Mesquite. The weekend after next is the second ontologies for animal behavior workshop. Monday was my birthday. J gave me an XM receiver and activated it. It is a dual use home/car unit, so we'll have some more listening options for the weekend trip to Richmond VA. (Comment on this)
Friday, August 26th, 2005
6:05 pm	Another Cache River The Ivory Bill Woodpecker has provided publicity for the Cache River of Arkansas, but there is another Cache River in Illinois and that is where I spent my morning. It's a little less than an hour south of Carbondale, though I had my closest encounter with a deer while driving down there. Didn't hit it, but I came as close as I ever have. The network of preserves and natural areas include 11 state record trees and some nice cypress swamps. Well, with the drought we've been having, only one swamp was fully flooded. One of the boardwalks went past an American Elm. I thought Dutch Elm disease had just about finished them off, but there seem to be a few large ones that are hanging on according to the volunteer at the visitor center. Birding wasn't great: great blue heron, cattle egrets, as well as chickadees and nuthatches, and a black-throated green warbler. After I got home I finished and released a new PDAP update. Current Mood: satisfied (Comment on this)
Thursday, August 25th, 2005
12:04 pm	Ivory Bill Woodpecker The NPR coverage over the past year or so has been good. I knew John Fitzpatrick, head of the Cornell lab, back when he was director of Archbold Biological Station, where I did my jay project. I liked the demonstration where they played back the 1935 recording in the area where the recent putative calls were recorded - I've heard of doing similar things to better understand the acoustic properties of particular environments. Of course if the playbacks had actually called in a resident Ivory Bill, the consequences, both legally and for the bird would be decidedly mixed Current Mood: okay Current Music: My refrigerator (2 Comments |Comment on this)