Why is this exciting? Because I’ve recently been through the horror of trying to build Numpy and it’s dependencies form source on our new server. That should be easy, right? Well, it’s been a real pain in the neck. Mostly because I’ve had all kinds of problems getting the right versions of libraries linked in to Numpy. There are the system libraries. And the libraries that came with the Absoft Fortran 95 compiler. And the versions that I built in my account. And I can never seem to get the arguments to setup.py quite right. But now I don’t have to. I can’t wait to get to work tomorrow!

Anyway, here’s what I did this last year:

• Appuhamy, J.A.D.R.N, Cassell, B.G., DeChow, C.D., and Cole, J.B. 2007. Phenotypic relationships of common health disorders in dairy cows to lactation persistency estimated from daily milk weights. J. Dairy Sci. 90:4424-4434.
• Cole, J.B., and Null, D.J. 2007. Genetic evaluation of lactation persistency for Ayrshire, Brown Swiss, Guernsey, Jersey, and Milking Shorthorn dairy cattle. J. Dairy Sci, (submitted)
• Cole, J.B., Null, D.J., and VanRaden, P.M. 2007. Best prediction of yields for long lactations. J. Dairy Sci, (submitted)
• Norman, H.D., Wright, J.R., Kuhn, M.T., Hubbard, S.M., Cole, J.B., and VanRaden, P.M. 2007. Genetic and environmental factors that affect gestation length. J. Dairy Sci, (submitted)
• Wiggans, G.R., Cole, J.B., and Thornton, L.L.M. 2007. Multitrait evaluation for calving ease and stillbirth with separate genetic effects by parity. J. Dairy Sci, (submitted)
• Cole, J.B., and VanRaden, P.M. 2007. A Manual for Use of BESTPRED: A Program for Estimation of Lactation Yield and Persistency Using Best Prediction. Available: http://aipl.arsusda.gov/software/bestpred/.

Not included in the publication list is the CSREES National Research Initiative grant on which a co-Principal Investigator, and some work that my support scientist and I are working on. We anticipate that some material transfer agreements [Wikipedia] that will allow us to receive producer-recorded health event data will be signed this year, enabling some interesting work on health traits in dairy cattle. Not that we’d be the first to look at using those data, but getting them into a national database is a big deal.

Hopefully I can get away after lunch to do a little sightseeing. I think I’m going to go down to the USS Midway museum, and then maybe over to Fire Station 1 to try and get a look at their canteen unit. If I can do this I plan to take the light rail since there’s a station right behind the conference center hosting the PAG meeting.

The Journal of Animal Science has added Open Access publishing…

To address scientists’ needs for open access (OA) publication, the Journal of Animal Science (JAS) has added an OA option for authors. OA means that articles published under this option are completely free online (http://jas.fass.org) to every person and every library from the date of publication.

This is great, and I’m excited that the journal management committee for Journal of Dairy Science is also looking into open access [Wikipedia]. I’m pretty sure that my RL won’t be thrilled by the idea of higher page charges, and it may be sort-of a moot point because, as Federal employees, we cannot assign the copyright for our work to a publisher. Because we cannot assign the copyright we’re free to post a copy of the manuscript on our website, although we sometimes have to post the accepted-but-not-typeset version, depending on the publisher. Journal of Dairy Science has been great about allowing us to post their typeset PDFs on our site, but for-profit publishers, not so much. The easier (and cheaper) it is for people to access science the better. For the love of Pete, we live in a country in which only 13% of those polled in a recent Newsweek survey agreed that evolution alone is the best explanation of the origins of the human race. Science, that’s what you’re all getting for Christmas!

I’m going to go with the Metafilter crowd and agree that “Skywalkers in Korea cross Han solo” is one of the most clever headlines I’ve ever read.

Kool-Aid pickles, you say? Ellery’ll love ‘em.

Ubuntu and Kubuntu users, learn how to set G-Mail as your default e-mail client. It’ll even open in a new Firefox tab if that’s what you want (and I do).

• VanRaden, P. M., M. E. Tooker, J. B. Cole, G. R. Wiggans, and J. H. Megonigal, Jr. 2007. Genetic Evaluations for Mixed-Breed Populations. J. Dairy Sci. 90:2434-2441.
• Cole, J. B., G. R. Wiggans, and P. M. VanRaden. 2007. Genetic Evaluation of Stillbirth in United States Holsteins Using a Sire-Maternal Grandsire Threshold Model. J. Dairy Sci. 90:2480-2488.
• Cole, J. B., G. R. Wiggans, P. M. VanRaden, and R. H. Miller. 2007. Stillbirth (Co)Variance Components for a Sire-Maternal Grandsire Threshold Model and Development of a Calving Ability Index for Sire Selection. J. Dairy Sci. 90:2489-2496.

If that’s enough action-packed Science-with-a-capital-S for you then head on over to the USDA Office of Communications Video Releases page and check out Genetic Evaluations Help Breed Better Bossies (Windows Media Player format).

John’s WTF for today is this: I’m supposed to fly up to Chicago tomorrow for a meeting. I got an automated call from United telling me that my Wednesday morning flight was cancelled, and that I was re-booked on an earlier flight Thursday morning. Um…seriously? I phoned the travel agency and I’m on a 9:00 AM flight tomorrow. I’m not sure just what quirk of human/computer logic led to that little scheduling gem, but it needs fix.

Experts in the field have carefully reviewed your manuscript and I am happy to report that they recommended only minor revisions of your paper before it can be accepted for publication.

How cool is that? Maybe the wait was worth it!

• I must have this Discworld cake — seriously;
• A link for Misty on making cyanotype quilts;
• Some interesting work on visualizing document history using Wikipedia as an example;
• The winner’s of Science magazine’s Science and Engineering Visualization Challenge 2006.

You can now search source code using Google. For example, you can search the PyPedal source. Apparently someone once did a Darwin port.

Tomorrow evening I am going to ride in an evening parade with the fire department. As a former New Orleanian I’m well-versed in parade watching. I’m pretty sure that sitting on my duff and waving out the window of the special events ambulance is something that I can master in a hurry. I’ve Ellery’s even got a hefty supply of beads to be thrown. I better ask if that’s okay, though. Northerners aren’t like us Southerners. They might view throws as a sign of hostility or something. I’ll try and get a few photos.

Did I mention that the airline we’re supposed to fly within Brasil has gone bankrupt and been acquired? Who knows if I’ll ever make it to Belo…

Attached is an announcement for a symposium entitled ‘National Carcass Disposal Symposium-2006, Connecting Research, Regulations, and Response’ being held on the University of Maryland campus.

Registration materials will soon be available online. You can’t make this stuff up. Oh, wait. Up this stuff you can’t make. Or something. Crud. Anyway, topics at this exciting event include:

• Research and public policy on carcass disposal in response to routine mortalities; natural disasters; and disease outbreaks
• New & emerging carcass disposal technologies
• Carcass treatment options
• Final product disposition
• Public policy on disposal of wildlife; marine mammals; and agricultural mortalities
• State and agency response and training experiences

I think that I may have to e-mail Dave Barry about “Public policy on disposal of…marine mammals”. Two-and-a-half days of this stuff could kmess with your head, that’s for sure. I know that this is a serious issue for professionals in both animal agriculture and disaster relief/recovery, but it also reads like an item in “The Onion”. I’m not sure if FEMA will have representatives at the symposium or not; they’re very close-mouthed about that kind of thing. Maybe it’s best if I don’t say anything about the pre-conference workshop:

Pre-Conference Workshop – Euthanasia & Decontamination
December 4th at USDA-ARS, Beltsville, MD

I feel very Upton Sinclair [Wikipedia] and I haven’t even raked any muck.

Okay, I couldn’t resist. I forwarded the PDF of the symposium announcement to Dave Barry with this message:

Dear Dave-

I felt that this scientific symposium might be of interest to you given your well-known passion for proper disposal of marine mammals.

Regards,

John.

I’m just doing my part to spread science to the masses.

This article has been cited by other articles: (Search Google Scholar for Other Citing Articles)

				B. J. Heins, L. B. Hansen, and A. J. Seykora Calving Difficulty and Stillbirths of Pure Holsteins versus Crossbreds of Holstein with Normande, Montbeliarde, and Scandinavian Red J Dairy Sci, July 1, 2006; 89(7): 2805 – 2810. [Abstract] [Full Text] [PDF]

				C. Maltecca, H. Khatib, V. R. Schutzkus, P. C. Hoffman, and K. A. Weigel Changes in Conception Rate, Calving Performance, and Calf Health and Survival From the Use of Crossbred Jersey x Holstein Sires as Mates for Holstein Dams J Dairy Sci, July 1, 2006; 89(7): 2747 – 2754. [Abstract] [Full Text] [PDF]

V. Adamec, B. G. Cassell, E. P. Smith, and R. E. Pearson Effects of Inbreeding in the Dam on Dystocia and Stillbirths in US Holsteins J Dairy Sci, January 1, 2006; 89(1): 307 – 314. [Abstract] [Full Text] [PDF]

How snazzy is that?

But it gets better! I’m currently preparing two papers to go in to the Journal any day now. Here is the comment I received from one of my co-authors who is extremely meticulous and has high standards with respect to what he’ll put his name on: “Not muich overlap between the two papers, so I relinquish my right to comment furhter on the first one. Good job!” I’ve been working my fingers to nubs on these papers the last couple of weeks, and it’s very gratifying to receive praise from one’s peers.