A week's worth of data

9 ii 2012
0632- sleeping
1002- getting my motorcycle loaded
1521- driving
2000- driving
Random Fact- when tying down a bike, you want the front shocks compressed about 1/3 the way down- enough when it bounces there isn't slack, but not so much you screw your bike up.
 
Lunch/dinner- tortillas and bluebell 

Markus and I met up shortly before 10 and got my bike loaded and strapped down.  Checked my email and found out I needed to be back by 1125, not 1500... I ran a couple of errands and headed north.  I left a bit before noon, and by the time I got to Tyler found out Mikey was leaving Austin today also.  The weather was great, no rain and some sun.  About 1900 I got a text from Mikey saying he missed his plane so we coordinated to meet up in St. Louis about 0100 Friday.

10 ii 2012
0847- sleeping
1233- at Bird Lab
1410- waiting for Drew to get done talking to the admissions committee
1724- at the PEEC mixer
Random Fact- Carotenoids cannot be synthesized by animals, so are thought to be an honest marker where as animals can produce melanin so its possible for them to "cheat" and be more attractive then they really are.

Lunch- pizza  at Bird Lab
Dinner- shiner and random finger foods at the mixer  then nachos at Murphys

Today was incredibly long- I picked Mikey up, and then we took turns driving the rest of the way to Urbana, finally getting in a bit after 0500.  Unloaded and got a few hours of sleep before I had to walk a prospective student between meetings on campus.  The afternoon got complicated as recruit schedules kept changing but the recruit I was helping with was pretty cool so it worked out ok.  The highlight of the recruiting things today though was the free Shiner at the mixer (I wasn't excited about mixing so only talked to people I knew).  I also found out Chris took my data comment to heart- while we were talking about my DDIG he made a comment about the fact I'm only interested in the data.

11 ii 2012
0505- sleeping
0747- sleeping
1904- home playing WoW
2220- playing WoW
 
Random Fact- Male three spined sticklebacks provide all parental care including fanning the eggs to provide fresh oxygenated water and guarding the eggs and young.

Lunch- McDonalds 
Dinner- pizza (sausage, peperoni, extra cheese, and tomatoes) and beer (ordered an Anchor Steam, but mikey didn’t like his beer so we traded casue I'm nice like that) at Jupiter's  

As part of the recruiting weekend there is a research symposium where grad students present their work and then a mixer afterwards.  As usual, I didn't present anything so enjoyed sleeping until almost 11 at which time I figured I should attend.  Caught a couple presentations then met up with Mikey and Massimo for lunch after giving up waiting for the recruiting people to get their act together.  After lunch I sat through another 3 hrs of presentations, then to the mixer/poster session.  I was way over my limit on crowds, talking to people, and socialization in general so when KJ told me I looked bored I took that as a sign it was time to go home.

12 ii 2012
0433- sleeping
0743- sleeping
1917- Skyping with Eddie trying to fix my Nexus conversion program
2138- playing WoW

Random Fact- Unix and dos use different protocols for dealing with the ends of lines.  My brother and I spent 3 hours trying to make something work before realizing that was the problem...

Lunch- eggs at IHOP 
Dinner- fish sticks  

I had big plans of PCRing today, but instead spent a big part of the day skying with Eddie trying to get a program he wrote for me to work.  Taxonomy programs all want slightly different files, so he made me something to convert files from the alignment program I use to the nexus files.  It worked fine for him, but wasn't working for me.  After 3+ hours he realized it was the conversion issue mentioned above so that problem was solved.  Now I get to actually do the data analysis on the sequences I got last week.

13 ii 2012
0043- playing online
0720- sleeping
1641- reading the paper for biogeography discussion
2318- home playing WoW
Random Fact- Excluding captive bred animals, 2008 was the first time in over 200 years a Tuatara successfully bred on mainland New Zealand.
 
Lunch- corned beef 
Dinner- lingcod and rice  

Ran a bunch of PCRs today, and did some purification.  Assuming everything goes well I can submit my plate tomorrow- mostly 28s, but some 12s and Histone too. I added a bunch of outgroups from Jamie's extractions, so hopefully this will help with the kinda weird trees I've been getting.  I also sent Chris a new copy of my DDIG- not sure if it was better or worse than the old one but it was different (he said it was better).  The highlight though was free hot chocolate- my reward for keeping the recruit from getting too lost on Friday.

14 ii 2012
0555- sleeping
1027- purifying sequencing reactions
1411- tea time
2211- talking online

Random fact- In some species female parrotfish can become male if the male leading the harem dies.

Lunch- lingcod and rice 
Dinner- Mas Amigas  

Submitting a plate is never easy, pipetting 96 reactions is enough to fry anyone's brain.  Couple that with having to purify a bunch of reactions before you even start and it's no surprise I had a bruised hand by the time I was done.  It took so long we even had to push lab meeting back an hour so I could get the SEQ reaction started by 1400 (the cut off for submission to the Keck Center since they close at 1700).  Looks like I'll be getting a new office- I'm not sure where yet but there is going to be a bunch of shifting around in the NRB and our office is way to crowded with 3 people.  Hopefully I'll get the one on the 3rd floor, its got sloped ceiling and a nice view...

15 ii 2012
1024- sleeping
1559- PEEC seminar on grass vs corn decomposition
1714- back at the lab clearing specimens
2102- at home reading a paper

Tundra peregrines often won't molt primaries 8-10 until sometime in January, when they are on the wintering grounds. 

Lunch- salami 
Dinner- salami and honey nut Cheerios  

At my biogeography discussion group I think I traumatized some first year grad students by telling them primers don't always work even, in fact, even when they work for closely related things they still may not work.  Oh to be young and full of hope for easy sequencing...  I also got the comments fixed on my DDIG and sent it back, so hopefully this round will be the last (excluding the preliminary results since I'm waiting for the sequences from yesterday's plate still).  I tried convincing Chris to send me to Australia but then he started finding the leafhoppers I needed so there went that plan.  He claims I need to work in the lab sometime, life can't only be field work, although I disagree.  Speaking of field work apparently I didn't tell KJ I was going to the Philippines, so now he's jealous- its 4th on his list (they have endemic families of birds), yeah the life of a grad student is amazing.

16 ii 2012
0257- playing World of Warcraft
1726- getting extractions set up
2016- eatting dinner
2359- working on the alignments

Random Fact-  AIC favors overparameterization of models.

Lunch- salami 
Dinner- cheesy cheddar steak burger  
I almost had a heart attack today since the first group of sequences I looked at were not the right lengths for the genes they should have been.  After BLASTing to discover they were in fact leafhoppers I figured out they were the sequences from my old plate and redownloaded the data (correct this time).  Overall they look fine, although the alignments are a bit strange on the Caliscelidae.  Systematics Discussion group was pretty good (once we got in the room, no climbing through the ceiling required), with plenty of laughter and random arguments about models (that's not a model, that's reality).  I also started some extractions of 10 leafhoppers from Australia- the last of the continents I needed represented.