The announcement is a bit late, but after beating Texas, Bama has won the 2009 Calix Cari.

See below for the complete results of 2009.

We’ve been having network issues for the last week. (The network setup in general is not reliable.) Nothing is wrong with what I have control over, but I’m kind of stuck with the connection that I’ve been given.

My apologies to everyone this affects.

With the conference championship games complete my Calix Cari rankings once again agree with the pollsters: its Texas versus Alabama for the title.

Surprisingly, despite Tebow crying after visiting the wood-shed in Atlanta Florida still ranks #3, ahead of undefeated teams TCU, Cincinnati, and Boise State. Two loss Oregon comes in at #4, based on its strong showings against Cal, USC, Arizona, and Oregon State. Boise State produced the second best victory of the year (against Oregon) but couldn’t overcome a week conference schedule to rise higher than #9.

The Pac-10 placed 6 teams in the top 25, followed by Big 12 at 4, SEC, Big East, ACC, and Big 10 at 3, MWC at 2, and WAC at 1. Clearly the Pac-10’s 8-4 logjam was seen more highly than the SEC’s 7-5 logjam.

It’s snowing right now in Houston. I’m not sure if it will stick.

It’s be a few weeks since I’ve calculated my rankings for collage football, but with Uga VII passing away, I figure I’d post something in honor of him.

Today sucks. Uga VII has died.

This is my first poll of the season, and Alabama is ranked #1, followed by Iowa and Florida. What’s interesting is that a quick look through the results reveals that Boise State’s victory of Oregon is considered the best win of any team of the year.

I need to head home early today to clean up my otaku pad.

I have a girl coming over for a sleep over.

We’ve hired a master’s student to be my minion in the lab. Bwahaha…

We’re having network issues which explains why this machine has been off the net since yesterday. It’s working now. Hopefully it will stay that way.

Well I’ve moved to Houston and my server is back online.

I’m moving to Houston this weekend. Expect this website and other I administer to have limited functionality for about a week.

I’m moving to Houston next month, and I’m working furiously to finish up about 4 papers before I leave. Yesterday was a good day because two things worked absolutely perfectly.

I’m calculating the likelihoods of some of our observations and I wrote a specific routine to do it for a first-order model. I then wrote a generic routine to calculated likelihoods for higher-order models. When I used the generic routine to calculate the likelihood for a first-order model, I got the same result as my specialized routine. Yatah!

From previous analysis using partial autocorrelations, we determined that a third-order model should explain our data the best. When I compared our models to see which one was most parsimonious (using AIC), the third-order model again came out on top. Yatah²!

After a while of testing, I’ve released new versions of Xomment and MT-Dispatch.

Information and download links can be found in the documentation liked to in the sidebar

Air New Zealand’s new safety video: Bare essentials of safety from Air New Zealand. (If you are not a fan of realistic body painting, you shouldn’t view the videos.)

And their new ad:

A while back Six Apart made much of their Movable Type blogging software open source. Many people hoped that this would make MT a community driven software project and allow Six Apart to focus on providing support for enterprise blogging solutions. Sadly, Movable Type is still developed basically as a closed source system, with roadmaps and feature sets kept internal to the company.

It is nearly impossible for someone on the outside to contribute to the project. And if you don’t serve MT using Apache, good luck getting support or getting them to fix non-apache bugs in their software. I filed a bug with Six Apart over a year ago, which pertained to how certain plugins interacted with my MT-Dispatch system.—MT-Dispatch is the only way to run MT on some webservers, like Nginx, and provides advanced FastCGI support on all webservers.—In this bug report I provided a one-line patch to MT, which ensures that all plugin types behave the same way and work with MT-Dispatch. It wasn’t even a new line of code I just copied some logic from one plugin type to another.

However, Six Apart had no interest in including this simple patch in their software because MT-Dispatch and non-Apache webservers were not supported by their company. Its is a stupid policy if they are trying to get community involvement in their open source system. They finally committed my patch this month, after they discovered that Mod-Perl was affected by the same problem as MT-Dispatch. If they would have just listed to me in the first place, they would have fixed the Mod-Perl bug sooner.

But’s that’s all history because a group of influential Movable Type consultants and developers have forked MTOS and are producing Melody, which will be an actual open source, community driven project.

I am hoping to see my MT-Dispatch and Xomment technology (or some derivative of them) committed to Melody’s core. But I lack the time to do such development, so I’m hoping to interest another developer to do it. Time will tell if anyone is interested enough to put the work in.

This month I’m going to two conferences: SMBE and Evolution.

At SMBE, I’ll be giving a poster in poster session #2 on Friday, June 5^th. Drop by between 8–9pm and take your picture with Prof. Steve Steve.

At Evolution, I’ll be giving my talk on Tuesday, June 16^th at 11am, in the “Population Genetic Modeling” section.

In my previous post, I mention that I will email you a reprint of a paper, if you send an email to [Enable javascript to see this email address.]. I actually do nothing. The reprint is handled automatically using my Procmail. In this post I will explain how I got it to work.

The first thing to note is that my email supports sub-addressing. This means that in the above email address, the mail is delivered to “reed” with argument “2009b”. I use this argument to determine that the sender is looking for a PDF reprint of my recent paper.

Next I had to modify my .procmailrc to copy 2009b requests to a specific folder and reply to them with the paper. Here is my solution, which is based somewhat on the solution for vacation notice emails with Procmail.

PLUS=$1 #copy the sub-address into variable PLUS

[snip]

:0c:
* PLUS ?? ^2009b$
* !^FROM_DAEMON
* !^X-Loop: reed+2009b@[snip]
* !^X-Spam-Status: Yes
"Requests"

   :0 A
   | (formail -r -A"From: reed@[snip]" -A"X-Loop: reed+2009b@[snip]" \
        -I"MIME-Version: 1.0" \
        -I"Content-Type: multipart/mixed; boundary=\"------------070504020300020208040609\""; \
      cat $HOME/papers/2009b.msg ) | $SENDMAIL -oi -t

This solution will copy and auto-reply to the incoming email if it matches the +2009b argument, is not from an email list, has not already been auto-replied to, and is not spam.

To send the reply, I use the formail tool that comes with Procmail to construct the reply. This involves using flags to specifying some email header variables, followed by catting a prespecified email body that contains the encoded attachment. I generated the body by sending myself the email and attachments that I wanted to send out to people, and then copying the body of the message to a text file, 2009b.msg. I just had to copy the boundary header used by my email program to the formail recipe above.

This rule can be expanded to autorespond to multiple requests and to handle formail or sendmail errors.

The final chapter of my dissertation has finally been published in Molecular Ecology. This is the project that got me involved with the software SPAGeDi. Although, none of that work remains in the final version of the paper, I have successfully collaborated with the authors of SPAGeDi to make it portable to Linux and OS X. The portable version will soon be made public.

Anyway, the citation of my paper is

Cartwright RA (2009) Antagonism between local dispersal and self-incompatibility systems in a continuous plant population. Molecular Ecology 18:2327-2336. [doi:10.1111/j.1365-294X.2009.04180.x]

Unfortunately, there is not a free version available yet online. The research was partially funded by NIH, so a copy should show up in pubmed in several months. Until then, you can email me at [Enable javascript to see this email address.] (NB this is not my usual address), and I’ll send you a reprint.

Abstract: Many self-incompatible plant species exist in continuous populations in which individuals disperse locally. Local dispersal of pollen and seeds facilitates inbreeding because pollen pools are likely to contain relatives. Self-incompatibility promotes outbreeding because relatives are likely to carry incompatible alleles. Therefore, populations can experience an antagonism between these forces. In this study, a novel computational model is used to explore the effects of this antagonism on gene flow, allelic diversity, neighborhood sizes, and identity-by-descent. I confirm that this antagonism is sensitive to dispersal levels and linkage. However, the results suggest that there is little to no difference between the effects of gametophytic and sporophytic SI on unlinked loci. More importantly both GSI and SSI affect unlinked loci in a manner similar to obligate outcrossing without mating types. This suggests that the primary evolutionary impact of self-incompatibility systems may be to prevent selfing, and prevention of biparental inbreeding might be a beneficial side effect.

I haven’t blogged here in a while, but I do have some recent posts on Panda’s Thumb.

I’ve been busy recently. I’ve flown to Oxford and Montreal for postdoc interviews. I’m also preparing a poster for SMBE in Iowa and a talk for Evolution in Idaho.

I’m currently on vacation. We went snorkeling in Florida: Wakulla Springs, Ginnie Springs, Santa Fe River, Ichetucknee River, and Rainbow Springs.