James and the Giant Corn Genetics: Studying the Source Code of Nature

It’s good to be such a tech geek sometimes. On Friday the lab’s servers came under a DDOS attack from east asia. The professional computer guys are still formulating a response, but until then I can’t access the servers. And since right now my project requires hours and hours of computing time to narrow down the the tens of thousands of genes found in a plant genome to a handful of good candidates for genes that are bound by an important transcription factor, it was looking like I might have to take the whole weekend off from work, falling days behind schedule.

What the DDOS types didn’t count on was the strength of my personal computational resources. (Actually I’m pretty sure they don’t even know what we do in the lab, random attacks are just part of the risk of being on the public internet.) Two 2.5 Ghz cores and 2 gigs of ram might not look like much compared to four servers containing eight cores and 16 gigs of ram each, but I can tie my own linux box up indefinitely without stepping on the toes of other people’s research. My roommate and I have had to make due without anywhere in the apartment streaming high quality video for a weekend, but I’m already running my second set of comparisons between the gene sets of rice and sorghum (each one should be a little faster as I narrow down the characteristics of real binding sites) and generating my own ad-hoc list of rice-sorghum-brachy gene pairs.

And on top of that I’ve got a great (if completely inaccurate) hacker vibe going, spending all day today and most of last night splitting my attention between two computers (three counting the linux box in the other room being controlled by command-line and VNC connections), rocking out to trance, and troubleshooting perl scripts at my L-desk with dirty plates and glasses accumulating around me as cryptic updates scroll by in terminal windows.

The weather out here continues to be amazing.

However I’ve recieved word of over 70 degree weather back home in the midwest, so I don’t get to gloat about this nearly as much as I did in January.

Since my last real post, I’ve started a new rotation and the rainy season has started out here in the bay area.

This new rotation as been … a lot of work. I went from a first rotation in a traditional genetics lab, to a second rotation doing molecular biology with a little gene annotation thrown in on the side, and now I find myself working on a purely computational project, and I spend half my time teaching myself all the thing I would have learned about Perl if I’d ever had the time to take a formal class in it or reinventing the well because I haven’t realized someone already found a solution to the problem. I feel like I’m learning quickly, but since I was starting essentially from zero, I’m making a lot of newbie mistakes and then have to work twice as hard to catch up.

I’m four weeks in to my current rotation and have yet to so much as pick up a pipetter or run a PCR reaction. In fact the only laboratory chemical I’ve had any interaction with is Isopropanol and that was just because I was helping one of the techs in the lab upgrade the processors in one of our servers and isopropanol works great at cleaning the thermal paste off of processors.

Getting the chance to assist with the upgrade process was fascinating in its own right, the labs servers are co-located in the primary hosting facility for UC-Berkeley. To get access we had to call up and have them send an elevator down and show ID once we got up to the central command chamber for the facility. Walking through the rows of actual server racks, one is buffeted by alternating blasts of hot and cold air (heat exhaust from the servers and the outlet vents of the enormous air conditioning system respectively), and the process of actually pulling, upgrading and reassembling of the server was coordinated by pantomime and shouts half hear over the roar of the assembled equipment and the mandatory earplugs.

Pictures from two and a half weeks ago.

I’m one of eight graduate students Berkeley admitted to their plant biology program last year. We come from a range of schools with a range of strengths and interests. But lets say you wanted to squash all that down to a couple of numbers. One approach is to look solely at what undergraduate schools we graduated from. This is incredibly inaccurate. For example, my roommate and I both attended the same school for undergrad, but we’re not interchangable. I know her GPA was way higher than mine, our GRE scores no doubt also vary, and we had very different sets of undergraduate research experience. Still the appeal of this method is that it doesn’t rely on having access to any remotely confidential information (like GRE stores or GPA) making it very easy to make comparisons between my class, and the set of students invited to interview for next year’s class.

My cohort’s undergrad schools:

• Average rank: 29
• Median rank: 21.

Interviewee’s undergrad schools:

• Average rank: 12
• Median rank: 4

This was not an easy year to be applying to graduate schools.

My old governor is my new boss (at least for two more weeks). There’s an interesting summary over at La Vida Locavore. To me it sounds like he’s doing everything right, and it appears the organic/local food/etc movement can get behind every action he’s taken as well (even if they dreamed of a secretary of agriculture that would do other things as well).

The answer to the mystery vegetable:

Well, I thought it was a mysterious vegetable.

I’m not sure if I’ll be able to figure out a way to fly a flag from my apartment, but I’d urge any of you who are able to, to display an American flag on the 20th. I’ll be attending the screening of the inauguration that UC Berkeley will be hosting Sproul Plaza, a block from where we gathered to celebrate on election night. Patriotism shouldn’t belong solely to one half a fraction of the country:

 Spontaneous patriotism was the reaction to Obama’s victory for many in neighborhoods where displays of Tibetan nationalism had been more common than its American equivalent.

Many people ask me what it is I do in grad school. Well a few people anyway. I never have a good answer. Without further introduction…

When I was home for new years, my dad was really excited about this group he’d found online where people would film their day and edit it into a 90 second clip. So 40+ minutes of film, some odd camera arrangements and two hours of editing later, this clip was born.

Sorry about the poor sound quality, when I had to replace a big piece of my digital camera after making the mistake of packing it in a suitcase that was gate checked last year the replacement I ordered off ebay came with a damaged mic. Normally I don’t take video and therefor don’t notice.

My days aren’t that exciting. But it was a lot of fun learning iMovie again. And filming myself at work called for some odd arrangements: