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.

December 26, 2008

Did you know they made amaretto cake?

Filed under: Electronics,Recreational Travel — James @ 4:57 pm

I sure didn’t before we had some for christmas.

Visit was a lot of fun, even if I was half dead the whole time. (Three hour jet lag + red-eye + stress of major holiday = zombie james.)

One moment of terror came when I lost my ability to connect to my server back in the apartment. My fears ranged a roommate who killed the power before she left, to break in attempts, to having the electricity cut off, but fortunately it turned out to be an issue with my ISP which they’ve since resolved. This is the first time I’ve had any sort of outage that was the result of the network rather than my equipment, which makes Time Warner, Qwest and Comcast all look pretty shabby by comparison.

December 10, 2008

Bad Teachers

Filed under: Electronics,Free Stuff,Politics — James @ 12:04 pm

Edit: Upon reflection it is quite possible this woman is excellent at teaching whatever it is she teaches. The more important lesson of this incident should perhaps be the importance of learning to distinguish between where one is actually an expert and one is not. This mistake can be made by anyone, including myself, when we think our knowledge in a particular field translates into knowledge of ALL fields. Just yesterday I was taken to task for my assumption that there are no fundamental differences in complexity between prairie ecosystems and woodland ones. (I’ve never had an ecology class in my life.)

Just today I wrote about building a computer to run BLAST for my whole lab essentially for free (once the lab orders a new graphics card, and I can put mine back in my computer at home, it will have cost a total of $40). There was no piracy involved, all the software running on that computer, specifically the operating system, the web server, and wwwblast, has been made available free of charge. When you can build a computer for $150, buying even the home version of windows adds 60% ($90) to the cost of your computer.

The desktop version of Ubuntu, a kind of linux, provides almost all the, non-gaming, functionality anyone expects from their home windows computer (going up against apple is another matter), doesn’t get viruses, runs fast on cheap or old hardware, and almost never crashes. For free.

I tell you this, not to evangelize about the wonders of Free and Open Source Software in general, or Linux in particular, but so you will understand the outrageousness of what follows:

“…observed one of my students with a group of other children gathered around his laptop. Upon looking at his computer, I saw he was giving a demonstration of some sort. The student was showing the ability of the laptop and handing out Linux disks. After confiscating the disks I called a confrence with the student and that is how I came to discover you and your organization. Mr. Starks, I am sure you strongly believe in what you are doing but I cannot either support your efforts or allow them to happen in my classroom. At this point, I am not sure what you are doing is legal. No software is free and spreading that misconception is harmful. These children look up to adults for guidance and discipline. I will research this as time allows and I want to assure you, if you are doing anything illegal, I will pursue charges as the law allows. Mr. Starks, I along with many others tried Linux during college and I assure you, the claims you make are grossly over-stated and hinge on falsehoods. I admire your attempts in getting computers in the hands of disadvantaged people but putting linux on these machines is holding our kids back.

This is a world where Windows runs on virtually every computer and putting on a carnival show for an operating system is not helping these children at all. I am sure if you contacted Microsoft, they would be more than happy to supply you with copies of an older verison of Windows and that way, your computers would actually be of service to those receiving them…”

Karen xxxxxxxxx
xxxxxxxxx Middle School

The recipient of this e-mail makes a remarkably calm and rational rebuttal here. I’d add only that the argument she makes about all computers running windows would apply equally to giving children apple computers as to giving them linux ones.

We have here a teacher who knows little or nothing about technology, who sees students gathered around a computer excited, not about a game or a video, but an operating system, and her first response to this display of curiosity and excitement is to chew everyone out and “confiscate the disks.”

Speaking from personal experience, running Linux for any length of time is going to spark the development of high level computer skills. Unlike the strong line between a computer programmer and a computer user in windows, Linux has a gradual transition where each new piece of knowledge proves immediately useful to user. If even one of those kids could have grown up to be a programmer or a computational biologist or an IT guy and instead ends up flipping burgers for a living, that child’s suffering is on her head.

We need more teachers in this country, but new teachers cost more money and the quality of education in this country would also be improved by getting rid of the substantial fraction of teachers who do more harm than good. I know I would have happily traded sitting in a classroom of 60 students instead of 25-30 to learn from a competent teacher, or at the least a kind-hearted one…

November 17, 2008

A Good Day

Filed under: Campus Life,Electronics,research stories — James @ 9:16 pm

I got up at 7 am this morning and got to work by eight.

I wore real shoes (not flip-flops) for one of the first times since I moved to Berkeley.

I work in a goverment building, with sign in sheets, and ID badges, and filters on the internet.

I didn’t even get the chance to talk to my new PI today, but I had the e-mail he’d sent me about my rotation project, so rather than sit around and waste time I started to work on it.

Did you know FT has 13 homologs in rice? And I found even more homologs in maize and mapped them on to the tree of rice genes using reciprical blasting.

The other people in this lab are really nice too. Two post-docs and one other grad student.

When I got home I realized I was babbling at my roommate about my exciting first day. We tend to be introverted around the apartment most of the time. I hope she doesn’t think I’m going insane.

To celebrate I cooked delicious pseudo-monty burgers (two plain patties left over from stuffed burgers on saturday, fried in a pan with a whole lot of extra spices.)

I also got an internet server working on my low power linux computer! It required a bit of tinkering to get around using the standard http port (most ISPs block connections on this port for residential costumers to discourage people from hosting web pages at home (like I just did!)). The page itself is just a proof of concept… I still haven’t figured out what I want to host at home (rather than using the hosting account I use for this blog) but it’s another advantage of an always on computer.

And for the record…I was able to bypass the filters at work. There’s no reason to, since I really don’t need access to facebook at work, but the point is, I can. And apparently people there have been trying to for over a year. (Some people really need their facebook.)

October 18, 2008

Upgrade complete

Filed under: Electronics,Fun With Numbers — James @ 4:09 pm

You might recognize this computer:
Then again you might not. After all a black box isn’t very distinctive. Regardless, this is the central server of my home network. It stores 3.25 terabytes of data between internal and external hard drives, can serve video to any computer in the house, and is accessible via VNC or ssh anywhere in the world (that I can get internet access), and draws less electricity than the average lightbulb. And now, after the arrival of a gift and less than an hour’s work it’s more useful than ever.

As I outlined before, the main bottleneck I faced was processor speed. With the arrival of the components I’d talked about that bottleneck no longer exists! Everything happens blazingly fast. I can’t wait to try out WUBLAST on this new and improved machine. I want to build a private database of the rice, sorghum, maize, and brachypodium genomes (and platypus genome, why not?) all in one location.

The wonderful thing about doing bioinformatics, is that if you just feel like messing around and seeing what there is to find, it doesn’t take hundreds of dollars of reagents in a controlled lab environment with super expensive pieces of equipment.

But applications later, for now I just want to enjoy how cool it is!


October 6, 2008

Potential Upgrade

Filed under: Electronics — James @ 9:36 pm

As I recorded here, this past summer I constructed an energy efficient PC for 24/7 use.

This $150 dollar computer has succeeded beyond my wildest expectations. As the result of an unfortunate BCK error my venerable modded xbox was rendered non-functional shortly after my arrival in Berkeley. (BCK stands for between chair and keyboard, it means I did something stupid.) Fortunately at the same time I was bricking my xbox, the people who wrote XBMC were porting to program to run elsewhere: windows, mac, and ubuntu linux computers.

So now it sits under the TV in the living room, doing the job formerly done by the xbox, at the same time serving video (some of it in high-def) to any-and-every other computer in the apartment since they are all capable of running XBMC (although for macs I recommend Plex, a fork XBMC maintained by apple enthusiasts.)

The end result of all this being that between pretending to be an xbox, file serving, and other processes I have running in the background, my poor $150 computer is buckling under the strain of keeping up. On top of that I’m contemplating installing a BLAST server to help with my research/show off to my fellow students.

Which brings me to the contemplation of a system upgrade less than three months into the twenty-five it’ll take for electricity savings to pay off. (Although the experience I’ve gained with Linux and the command like have already been more than worth the expense.) 


Current: 1.8 Ghz single core. 35W maximum power draw. 

Proposed: 2.5 Ghz Dual Core. A lot more horsepower, but also a higher maximum power draw (65 watts). This may be somewhat offset by higher efficiency since the processor is manufactured on the new 45nm process and the smaller processors are, the less energy they take to run.


Current: 1 Gig

Proposed: 3 Gigs, the current 1, plus a 2 gig chip. I’m not sure if my current set up is RAM limited to begin with, but an extra two gigs isn’t going to substantially impact electrical usage.

I’m going to take a while to think on this (and save) before I place any orders so I’d be interested in any suggestions on more efficient/effective upgrades I could make to improve performance on what is rapidly becoming the nerve center of my apartments electronic ecosystem.

August 3, 2008

Finished In Iowa

Filed under: Campus Life,Electronics,Recreational Travel — Tags: , , , , — James @ 9:58 pm

I made my final presentation for my summer position on Thursday. Here’s a graphic showing the distribution of sequences of interest over the rice chromosomes:

With that presentation, and the following day of creating readmes for my folders full of blast results, sequences data, and perl scripts, my summer project was wrapped up. My time as a visiting scientist/scholar has come to an end. (Though I still have the ID card to prove it.) Next weekend I’ll be driving down I-80 towards fame, fortune … and San Francisco. Looking over the route on google maps I noticed the giant salt flats I’ll be driving through in Utah. Hopefully I’ll have the willpower to stop to take pictures of that and other spectacular natural scenery (Nevada, Utah, Wyoming are all going to be totally new for me.)

The total drive is looking at around 26 hours, which I’m very tempted to split into two thirteen-hour drives to save on paying for an extra night in a hotel.

Whenever I do make it to my new apartment, there’ll be internet waiting for me there. I decided to go with AT&T’s U-verse DSL. Mostly I picked them because my alternative was Comcast, the company that’s been in the news lately for interfering with user’s internet connections, but it turns out there’s discount involved if I were to ever get an AT&T cell phone, a consideration my current envy of Monty’s new iPhone.

July 12, 2008

The New PC

Filed under: Electronics — Tags: , , , — James @ 10:49 pm

As a computer geek I need a computer that’s online 24/7. This uses a lot of electricity which A. costs money B. Makes the environmentalists in my life hate me.

Now I could choose between my computerized lifestyle and ever dating another environmentalist (GMO issue aside). Or I could cut my power usage by building a second (super efficient) PC so I can turn off the powerful, power hungry, machine I use for the computational heavy lifting whenever I don’t need it. Guess which option I chose? 😉

Now for the second challenge, my budget for my entire energy efficient computer: $150 (Note that the cheapest computer listed on the best buy website as of this writing is $280.)

  • Processor: Celeron 430L 1.8GHz – Maximum power usage of 35 watts. A standard CPU draws 90 watts, enthusiast CPUs 125 watts or more.
  • Motherboard:MSI P6NGM-FD – On-motherboard graphics save energy vs. a discrete graphics card, and I’ll barely ever even connect a monitor.
  • Memory: 1 Gig G.Skill DDR2 800 – not much to say here, it’s the right speed, it’s cheap.
  • Case: Rosewill R102-P-BK – MicroATX case, cheap, enough room for my hard drives.
  • Operating system: Ubuntu Linux – It’s free, and on this budget I need that.
  • Hard drive: I can use my current hard drives
  • Power Supply: Left over from a system upgrade. Aftermarket power supplies are more efficient. Cheap ones have conversion efficiencies as low as 60-70%

All the components arrived from new egg the middle of last week. Initially set up goes well:
Linux Box Step 2
But then problems arise. Ubuntu is on a DVD. The only DVD drive I own is already installed in my current PC and I can’t remember how to get it out. The solution? Siamese computers!
Computer Life Support
By flipping the new computer upside down and running IDE and power cables between the two I can manage the linux installation!
And now, a mere 72 hours later, I have a working computer!

Ubuntu has many positive qualities. User customization (without spending hours on google and the absolute beginners ubuntu forums) is not one of them.

Anyway the end result: The computer I used to run 24/7 drew 110-120 watts idle. The new one just under 50. For $150 I’ve reduced power consumption by 43-50 kilowatt hours a month. At an electricity rate of 12 cents a kW/h, bringing this new computer online will save 70 bucks a year in electricity and pay for itself in 25 months.

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