One of the things that falls out of our genomic evaluation system are breeding values for individual chromosomes for each trait evaluated. For the past few days I’ve been thinking about how to compare the genetic covariance matrices that we can calculate for each chromosome. This might help us identify markers that affect groups of traits by changing the correlations among them, but which do not have lerge (QTL-type) effects when compared to other markers. The evolutionary genetics guys have pondered some related issues, and I spent a lot of time reading about Flury’s hierarchy and common principal components and that sort of thing. Today I decided that it was time to write some code so I could do some calculations, and oI (of course) whipped up some Python to do the heavy lifting. The first step was to load the data into a dictionary of dictionaries of dictionaries, although I’m starting to think I should spend some quality time with PyTables. Then I wrote a function that uses NumPy to calculate the mean vector and covariance matrix from the EBV on a given chromsome. And it took about two lines of code to loop over that function to get the means and covariance matrices for all 33 chromosomes plus the whole genome. (I know, cattle have only 30 chromsomes, but we also have to consider the pseudoautosomal region and unassigned markers.) I expect it’ll take a little time Monday to get all of the trait data into a single structure (we currently process our traits in groups), and then I can get on to things like the actual principal components analyses, matrix correlations, etc. How cool is that?

convert this post to pdf.

I was looking through the October 2008 issue of Dairy Herd Management and happened to see myself quoted in an article on strategies for reducing stillbirth in dairy herds:

A new genetic evaluation for stillbirths is part of the Lifetime Net Merit index, and is 3.6 percent of the index’s total emphasis, explains John Cole, research geneticist at the USDA’s Animal Improvement Programs Laboratory in Beltsville, Md.

There’s more in the article for your reading pleasure. Here are a few more links to material I’ve written about the national genetic evaluation for stillbirth in U.S. Holsteins:

• Genetic Evaluation of Stillbirth in United States Holsteins Using a Sire-Maternal Grandsire Threshold Model (J. Dairy Sci. 90:2480-2488)
• 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)
• AIPL Research Report SB1: Genetic Evaluation of Stillbirth
• Interbull Form GE describing the stillbirth evaluation

Now I’m off to play with Flury’s hierarchy for comparing variance-covariance matrices until it’s time for lunch. Mmm…leftover Chinese food…

convert this post to pdf.

The projections show that Barack Obama will be the 44th President of the United States. I just watched John McCain concede the election on PBS! After eight painful years our long national nightmare is over. Someone needs to pinch me to reassure me that I’m not dreaming.

Now the hard part begins. I feel like kind of an outsider because while I voted for Obama, and agree with him on many more issues than I do McCain, I could never let myself believe in him the way many of his supporters have. While he’s a very inspirational politician he’s still a politician, and I have lots of concerns about his economic plans. There’s a lot of work to do over the next four years, and it’s going to be hard, dirty work full of distasteful compromises and unpleasant realizations. If we’re getting the leadership we think we are we’ll be asked to make sacrifices and suffer some tough times, and I hope that we can put aside our divisions and rise to the challenge.

All of us who are parents want to make a better world for our children. Conservatives and liberals may disagree very strongly about the details, but we all agree that things are broken and need to be fixed. Let’s work to make it happen.

convert this post to pdf.

I voted!

convert this post to pdf.

I’m in line at the polling place. Representative democracy rules!

convert this post to pdf.

I’m at a congregational meeting.

convert this post to pdf.

Residents of Prince George’s County may or may not be aware that the county Fire and EMS Department is furloughing firefighters because of budget shortfalls. Tonight crews from Companies 39 and 43 will be furloughed. The same county fire chief who has stated that he wants his legacy to be that he oversaw the elimination of the volunteer fire system in PG County is now turning to the volunteers to make-up the staffing. Citizens of Bowie can rest assured that all three Bowie VFD stations will be staffed at or above county levels, which are far short of NFPA recommendations, as we did Sunday night when two of the career staffers were pulled out of Station 19. The County’s been trying to keep it quiet, but the details on [para]medic furloughs have also been leaked to the press. So what does this mean to the taxpayer? The volunter and career firefighters and EMTs will come to your aid as fast as they can, but due to gross mismanagement at the county level there are fewer people available to provide that help, and it may not come as fast as it once did.

convert this post to pdf.

So I’ve been told.

convert this post to pdf.

Today was fun, but busy. After an early wake-up we had a light breakfast and headed to Wilmington, NC, to the USS North Carolina. (You may have heard of Wilmington because it was the first market in the U.S. to convert to digital TV.) After a thoroughly exhausting climb up, down, and over the ship we had a quick lunch at McDonald’s and came back to Topsail Island, where we spent the afternoon at the beach. We ate dinner at a local deli, and got the kids in bed early. We’re expecting our friends Roger and Zoe (and their son and daughter) in a couple of hours.

I’m also very excited that the debate’s back on. McCain is going to get Kennedy-Nixoned, and I’m going to love every second of it.

convert this post to pdf.

It’s Monday morning, and I’m sure you’re expecting me to talk about LSU football. All in good time. First, here are a couple of patches from the Lake Charles Fire Department that I got back in the spring:

They’re both pretty sharp, the first one with the city seal in it especially. I was born in Lake Charles, too.

If you’re looking at these and thinking, “Why didn’t he convert these to PNGs and use a transparent background, it’s not that hard!” or “It’s really annoying that the bottom of the cross is cut off on the second patch, why was he too lazy to fix it?” I suggest you remember that it’s Monday morning. Have another cup of coffee. Remember that LSU beat Auburn on the Plains Saturday night. Relax.

convert this post to pdf.