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

January 30, 2009

Firefly Music Server

Filed under: Electronics — James @ 7:46 pm

There are two common problems that a music lover faces in the digital age. (Well a lot more than two.) Keeping access to music across multiple computers, and the fact that music libraries can grow to enormous sizes, which can be problematic when your primary computer is a laptop with limited ability to increase your storage capacity. My solution: Firefly Media Server. I copy all of my music over to the home server (my incredibly energy efficient linux box). It indexes my music and provides it as a shared library over the network using the same interface as an iTunes Shared Library, which means there’s no need for any special configuration on the computers accessing the library. Now I just need to write a script to check my library and copy over new music as I purchase it to keep the central server up to date.

Here’s how it shows up in iTunes:

And here’s the webbased configuration file:

Of course it isn’t a perfect solution:

  • It requires you have an always on computer in your house. Which still isn’t as common as it should be.
  • You lose information like data added, and rating (see the screen capture of iTunes I posted).
  • Out of the box firefly will only work when you’re on your home network.
For all these reasons it’s not a perfect solution and probably won’t replace a music library on a primary computer. But It’s great for:
  • Providing music to secondary computers 
  • Providing music to media extenders designed to work with shared iTunes libraries so you can listen to your music anywhere you have the proper hardware installed. (XBMC works great for this.)
  • Pooling music between members of a household
  • Slimming down an otherwise overflowing iTunes Library on your personal computer without losing easy access to the files at home.

January 26, 2009

Graduate Admissions

Filed under: Uncategorized — James @ 10:12 pm

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.

Vilsack’s First Week

Filed under: Uncategorized — James @ 4:39 pm

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).

Chinese New Year

Filed under: food,Photo Posts — James @ 2:32 pm

Lots of new photos up on Flickr. On Saturday I went down into San Francisco to see Chinatown in the weekend before Chinese New Year (which is today:  新年快乐 ! <– I theorize this means happy new year, given it’s appearance on so many people’s facebook statuses over the past few days) Lots of pictures.

That night we decided we wanted cake, and took advantage of the fact that I keep buying boxes of cake mix, even though I never get around to mixing them. Resulting in so much cake. Just to clarify, there are FOUR pans of cake in this photo:
Four Cakes

Work is going well. Only two weeks left in this rotation and I’m racing to have something to show for my three months of effort.

This is the year of the ox. The second time it’s come around since the year of the ox when I was born (which for those doing the math means I’ll be turning 24 all too soon.)

January 18, 2009


Filed under: Photo Posts,Plants,research stories — James @ 9:57 pm

Jamesandthegiantcorn turned one year old on thursday (and a good friend of mine turned 23 that same day). As it happens this will also be my 100th entry, I’ve averaged about two updates a week over the past year, which is pretty good given my previous experience with blogging. Without further ado, my 100th entry:

Brachypodium? What is it? Well it’s a grass species that looks like this:

 Brachypodium distachyon

I first mentioned it almost a year ago in an entry I posted during my interview weekend at berkeley:

Most “I’m definitely a potential grad student” moment: 


“Um…wait…I can’t remember his name but he works on a species called bracopodia brachypodium.” <– I’m better at remembing the names of new species of grass than of the people I meet who study them.

Obviously while I remembered the name, I did not learn the spelling. But since then I’ve learned a lot more about the species and why people study it. Brachypodium is a tiny temperate grass that is (like so many other species) an “emerging model organism.” That means people think studying brachypodium can teach us more about other species*, and are having brachypodium’s genome sequenced. Part of developing a useful genome is annotating genes, which is something I’ve been working on during my rotation.

*I would say the reasons its considered a good model are first that brachypodium is what arabidopsis (the first plant ever to have it’s genome sequence) would be if arabidopsis were a grass: a small plant with a small genome and a generation time of only six weeks (compared to 3-5 months for corn, or 15-20 years for humans). 2. It’s much more closely related to wheat than any other sequenced plant, and wheat could use better molecular resources.

Of the big five crops, rice, maize and sorghum as all getting their genomes sequenced. The two that aren’t are potato and wheat. Potato is tetraploid (where humans have two versions of every chromosome potatoes have four versions), and wheat is hexaploid (six versions of every chromosome!). Until sequencing and assembly technologies improve, the closest we can come to sequencing these vital crops is a related species with a more tractable genome (tomato for potato and brachypodium for wheat).

PS The new comment posted will be the fiftieth non-spam comment on this blog. A lot of milestones this week.

January 13, 2009

Well That Didn’t Take Long

Filed under: Uncategorized — James @ 10:16 am

The answer to the mystery vegetable:

Well, I thought it was a mysterious vegetable.

January 11, 2009

Vegetables and More

Filed under: Photo Posts,Plants — James @ 7:23 pm

I was originally going to post this yesterday afternoon, but instead I had a crises with my Linux box which I’ve just now resolved. I’m just lucky I bought so many 500 gig hard drives back in undergrad that I had an unused spare on hand when the Operating System drive in my computer suddenly went bad.

Anyway the point of my post was to draw your attention to the new pictures I’ve put up on Flickr of my expeditions into the world of vegetable buying. Be sure to especially check out the purple cauliflower (because that’s intrinsically cool) and the newest entry in the “name that mystery vegetable” contest:

Mystery Vegetable Episode 2

It was actually a lot of fun. I’ve been to the local farmers market a bunch of times. But it’s very expensive, and they’re openly opposed to people like me:

Sad Sign At Berkeley Farmers Market

So on Saturday my roommate took me up to the Monterey Market (which is on Monterey Street, not in the city a couple of hours away) which is just amazing.

Monterey Market

More fruit

My only real disappointment was that I finally found papayas from Hawaii (which is where virus resistant papayas were first introduced as a cure for the papaya ring spot virus that was ravaging the papaya farms) and they were organic. Of course it turns out I could have bought it anyway, as many organic papayas are now “contaminated” with the resistance gene (according to wikipedia) allowing organic cultivation to thrive in areas where the virus would otherwise make it unviable.

January 9, 2009


Filed under: Uncategorized — James @ 9:51 am

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.

January 7, 2009

A day in the life

Filed under: Uncategorized — James @ 9:13 pm

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:
Pipet tower of video

January 4, 2009

More travel

Filed under: Uncategorized — Tags: — James @ 2:45 pm

Apparently a 2 TB hard drive looks very suspicous on an xray machine . Who knew? We’ve just heard that the plane from my flight hasn’t left
Denver yet and is grounded with mechanical problems so they have no idea how long the delay will be.

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