UC Riverside's wireless network uses WPA-EAP for the encrypted network. [The unencrypted network does a https based browser capture.] Unfortunately, none of the default wicd encryption templates support the precise brand of WPA that the network does, so you have to make your own template. Luckily, wicd makes this fairly simple:

Create a new template, say, /etc/wicd/encryption/templates/eap-only, with appropriate contents.

 name = EAP
 author = Don Armstrong
 version = 1
 require identity *Identity passwd *Password 

 -----
 ctrl_interface=/var/run/wpa_supplicant
 network={
    ssid="$_ESSID"
    key_mgmt=WPA-EAP
    identity="$_IDENTITY"
    password="$_PASSWD"
 }

Then tell wicd about this new template by editing /etc/wicd/encryption/templates/active and adding eap-only to the existing list of templates, and restart wicd /etc/init.d/wicd restart. [I'm not sure if restarting wicd is necessary, but it shouldn't hurt.]

Finally, configure the network using the appropriate wicd interface as usual.

Trying to do some work for the Mystery Hunt which starts on Friday at noon, and the wireless at MIT keeps deauthenticating me for reason 1. (Which apparently is the dreaded "unknown reason for deauthentication".) Reassociating makes everything work again. Fast, hack solution:

 while sleep 1s; do
  if iwconfig wireless |grep -q "ESSID:off"; then
    iwconfig wireless essid "MIT GUEST";
    echo "reset wireless";
  fi;
 done;

and I'm back at work with relatively continuous network connectivity.

This year has been fairly good for our lab; a few years ago we found an association of rs17849502 with SLE. Finally, after significant work by our collaborators, we managed to demonstrate a functional significance of this SNP with possible importance for SLE. Changing H389 to Q reduces the function of the NADPH oxidase complex by 50% in Vav dependent Fcγ response.

You can read the paper "Lupus-associated causal mutation in neutrophil cytosolic factor 2 (NCF2) brings unique insights to the structure and function of NADPH oxidase." (pmid: 22203994)

If you're doing genetics and use SNP, you've probably often wanted to extract information from dbSNP. A long time ago, I wrote some scripts to scrape their webpages for information. Now that I'm dealing with millions of SNPs, that's no longer possible. I needed my own mirror of dbSNP. I did this as of build 132, and since they've now released build 135, I wrote up what to do, and shared the git repository which has the utilities and schemas I used.

Updating the bios on my X200 Tablet was surprisingly simple in Debian. Often, updating bios requires some sort of Windows or Dos boot disk and all kinds of machinations to make that happen. Lenovo provides an iso image to update the bios which alleviates some of these problems, but as the X series don't have built-in CDROM drives (and I don't have an ultrabay),

All you have to do is download the iso, install syslinux aptitude install syslinux, and configure grub to start memdisk and boot off of the iso. You can do this by copying the iso to your boot partition (cp 7wuj43uc.iso /boot/;), copying memdisk to the boot partition (cp /usr/lib/syslinux/memdisk /boot/;) and adding an entry to your grub.cfg like the following (putting it in /etc/grub.d/40_custom is probably the most reasonable):

menuentry "Thinkpad x200 BIOS Upgrade to 3.19" {
       insmod part_msdos
       insmod ext2
       set root='(hd0,msdos1)'
       linux16 /memdisk iso
       initrd16 /7wuj43uc.iso
}

Note that your configuration will be slightly different depending on whether you have a separate /boot partition (I do) or not.

Then you just need to boot the laptop, select the bios upgrade option in grub, and tell the program that you really do want to upgrade the bios and that you really do have a full battery and the laptop plugged into an AC adapter.

The major idea for this method came from ThinkWiki's entry.

My lab's aging LaserJet 1200 recently started failing in an interesting fashion. It would print a page nicely, but then attempt to feed a second page before the first had finished, leading to a jam. Some googling lead me to this page which indicated that the feed solenoid was sticking. After a failed attempt to clean gunk off of the feed solenoid arm (and failing to find anything else wrong, I wrapped the feed solenoid arm in scotch tape and attempted again. Viola, a printer working once again.

In October, a few of my friends and I took a trip to Mehrten Meadows near Lodgepole in SeKi. Over a nice two day drip, we ran across a few bear tracks, about three deer, and a small handful of humans. All in a backdrop of recently fallen snow which had just melted enough to allow for easy walking.

Switching my website to use ikiwiki; hopefully I'll manage to actually modify it now.

I've been in school as a student for almost all of my life up till now. While that's a relatively normal thing for younger people, the older you get, the rarer and rarer it is.

Finally, on Monday I went through the ceremony which marked the end of my tenure as a student who is actually enrolled in school, and the beginning of my tenure as a student who happens to also contribute to and convey knowledge. That's right, I've finally managed to finish my PhD in Cell, Molecular, and Developmental Biology. It's been a while getting here, but with my dissertation completed and accepted by graduate division, my defence completed, and finally being hooded by my major professor, I'm done!

Getting my PhD has resolved a few fundamental dilemas that I've always had. First, I now know what to put in that pesky "Mr/Mrs/Ms/Miss/Dr" field. Before, Ms. was technically correct, but no one apparently knows that means Master and confuses it with an abbreviation for Miss. Now I just put Dr., and no more confusion. Second, dealing with pretentious people and physicians who insist on being called Doctor becomes easier. I can now ignore their silly titles with impunity. [And yes, those of you who haven't spent an eternity in the ivory tower should just call me Don anyway.] Next, I now have the covetous union card that enables me to teach at instutitions of higher learning.

Unfortunatly, that also means that I no longer qualify for student discounts anywhere. Of course, I must admit that lately the people at movie theaters have been looking at me askance when I ask for a student discount. I'll have to wait 36 more years until I qualify for the senior discount.

Mark and I took a trip to Joshua Tree over the previous weekend. We hiked in towards Pine City on Friday night and set up the tent near the edge of the day use area. It took us about 10 minutes of wandering in the dark with head lamps to find an area that was far enough off the trail and appeared to be flat and rock-free enough to set up a tent. Mark happened to find a miniature cholla cactus in the dark and of course managed to stab himself with it, which added to the excitement of setting up the tent.

When the sun came up the next day, we were finally able to see where we had actually set up camp. A series of amazing bolders were to the south east of our campsite, and we spent some time in the morning exploring them as we finished off our slightly smushed pop tarts.

We then packed up the tent and our bags and took off to see Pine City itself (which is in the day use area). It appears to be called that because of a few ancient conifers which have managed to survive in the desert, though I'm only guessing based on what I saw.

From Pine City, we took off cross country heading north-west towards Queen Mountain, where we wandered around through a ton of gullies and dry washes. (Note of caution: be very careful in areas like this during the rainy season. Rain miles away can cause flash floods.) Eventually we found a neat place to camp around noon a bit south east of Queen Mountain.

We set up the tent, dropped off the packs and then went wandering around to boulder some of the neat rock formations and lollygag about looking at the neat scenery. During this entire time, the only evidence of humans we had seen were a few footprints on the trail into Pine City, a couple balloons in advanced decomposition, and a single glint off a car windshield more than 10 miles in the distance.

The next day, we hiked back to the car, and drove back into civiliation. It's been a while since I've been to Joshua Tree, but I've remembered now why I like the place. It's really hard to beat for getting away from human presence into a relatively pristine environment. [The closer to summer you go, the harder it is to handle, and consequently, the fewer people you're going to see.]