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

February 16, 2010

Newer Tighter CoGe-MaizeGDB demo

Filed under: Computers and Coding,research stories — Tags: , , — James @ 1:08 am

I invested in a new video capture program that lets me record voice overs in real time. There are a few more ums and uhhs but my voice and the action on screen are in much better sync, and I don’t find myself rushing to keep up with the movements of my own mouse or trying to fill apparently dead time while nothing happens on screen. The new video is also two minutes and fifteen seconds shorter, dropping below the psychologically important 5 minute barrier, above which watching a video starts to feel a lot more like work, and I get to show off two new features (visually flagged tandems, and predictions of where a gene would have been before it was lost) that we’re still in the process of rolling out.

Sorry to harp on the same topic a second time, this video is just SO MUCH BETTER than the previous one and I needed to show it off. 😉

February 9, 2010

MaizeGDB and CoGe: A Beautiful Friendship

Editor’s note: I have a new shorter, better, tutorial, here.

One of the earliest fruits of my work to define relationships between syntenic genes* was a list of sorghum genes and corn genes in one or both of the two related regions of the corn genome (each region in sorghum corresponds to two in corn because the ancestors of corn completely doubled their genome in the time after the ancestors of corn and sorghum went their separate ways.)

But this is not the post where I explain my research projects. That post would be confusing and densely written at the best of times, which two AM in the morning certainly isn’t. Tonight my goal is simply to introduce the embedded video below, which explains how any researchers who want to can check out the relationships I’ve identified between genes in the two duplicate regions of maize, and the genes of the sorghum genome can do so using the MaizeGDB genome browser, and CoGe’s own GenomeViewer application. Video below. If you’re going to watch, I recommend selecting the highest resolution youtube offers you. (more…)

December 1, 2009

One of the Joys of Comparative Genomics

Filed under: Computers and Coding,research stories — Tags: , — James @ 1:26 pm

I was originally scheduled to fly home yesterday, but was forced to extend my stay by unfortunate chain of events that (among other things) has resulted with me swearing off contact lenses for the foreseeable future.

If I worked with arabidopsis or brachypodium, I’d probably have plants flowering this week that I’d be missing. Without the chance to make the crosses I needed to continue my research I might be set back a month or more while I waiting for new plants to grow. If I was mostly doing wet lab work, I wouldn’t fall as far behind assuming I’d gotten all my projects properly refrigerated or frozen before leaving for Thanksgiving, but the whole week I was gone would still be a complete loss.

Fortunately, I now study comparative genomics, which means, while I won’t get as much done this week as I normally would have, I’m definitely going to continue working. I’ve already shown off my workstation in the lab.

And here is where I’ll be working most of this week.


I’ve been advised, by people who’ve been doing a lot longer than I have, that working on a laptop long-term is a great way to burn out your hands (carpel tunnel), but for a week it’s no big deal. I can get more work done from here, thousands of miles away, than from an apartment a few blocked from the job, because the faster internet connection means I’m better able to access my own workstation (the first computer pictured), two of the my lab’s servers, and even a Linux box I left running in my apartment, all of which was using for different parts on my work on Monday.

If you look closely you’ll also notice one other difference between the permanent and temporary digs. Just for this week, I have a window!

November 9, 2009

We’re Back

Filed under: Computers and Coding — Tags: , — James @ 4:15 pm

I apologize for the downtime today. This morning the server this site is hosted on apparently came under DDoS attack.* And just as my hosting provider was able to compensate, the bank of servers providing mySQL support went down (presumably from the strain inflicted by the DDoS attack, two unrelated failures in the same day from a service that’s normally pretty reliable seems unlikely).

So that’s why Jamesandthegiantcorn has been either unreachable or returning database errors all day, and I really am sorry.

In case you missed them while the site was down:

Last night there was a post on how some, but not all, corn uses chemical signals to attract nematodes when its roots are attacked by insect larva that the nematodes eat, and how that functionality can be restored in lines of corn that don’t normally have it with a signal transgene (with the presumption that introgressing the native corn gene would also work).

This morning the first in my series of profiles of genetically engineered plants that are commercially available, Canola, went up.

And orignally scheduled to go up around noon (in the middle of the outage), was an explanation of how I’m going to handle creating a resource on crops that have actually been genetically modified, since writing one long post was clearly something I was going to keep putting off indefinately.

Anyway, such attacks are just a part of life on the modern internet. Sometimes they come at random, sometimes they’re a way of shutting down sites the attacker doesn’t like. Since I share my server with a bunch of other people, we’ll probably never know why (if there even was a reason) we were attacked.

*DDoS stands for Distributed Denial of Service. An attacker uses hundreds or even thousands of compromised computers across the world to attempt to access a site at once. The huge load swamps the host server to the point where it can’t respond to legitimate requests, and since the traffic is coming from lots of different computers with different addresses it’s hard to block it without also blocking the real people trying to access a site. And that doesn’t even take into account what happens when routers are so overwhelmed the datacenter personel can’t log into them to alter their settings. (Monty, if you’re reading this can you give an expert prespective on these attacks?)

November 2, 2009

Spam Problems

Filed under: Computers and Coding — James @ 11:59 pm

My spam filter has become drunk with power and is attacking innocent comments while allowing obvious spam to pass unchallenged. I’ve disabled it at least temporarily, I’m sorry if your comments have been disappearing without a trace. If you run into any other problems with the site drop an e-mail to jcs98@(this website’s URL here).

October 29, 2009

Try Ubuntu

Filed under: Computers and Coding — Tags: , , , — James @ 5:48 pm
Screen grab of Nymph my at-home Ubuntu Box. Click for fullsize.

Screen grab of Nymph my at-home Ubuntu Box. Click for fullsize.

With the latest release of Ubuntu (a flavor of Linux) open source operating systems have never been more user friendly. It’s still not for everyone, but how are you going to know whether it is for you or not if you don’t try? And trying Linux is so easy these days. After burning a CD or DVUD with the disk image downloaded from the Ubuntu website, simple restart your computer and you should be given the option to either install the OS to boot direct into Ubuntu’s version of the Linux desktop. Trying out the desktop without installing it doesn’t affect anything installed on your hard drive, your computer has just booted up from the CD. (The downsides are that reading data from external media can be slower than from the hard drive, and since the CD is read only, nothing you do in this test mode will be remembered after a restart.) But starting up your computer this way isn’t a long term solution, it’s just a way to find out whether Linux is something you’d be interested in installing and learning to use. If you do, the CD will walk you through installing Linux next to your existing OS so you’ll have the option to start your computer into either one.

Why should you try Ubuntu? There are all sorts of philosophical big picture arguments people make about open source software (software than can be freely redistributed or modified by anyone), and another set of pragmatic ones about never having to pay for another version of Windows or Mac OS X, let alone Microsoft Office, and Ubuntu’s safty from viruses and spyware. There’s even a third set based on personal hatred of Microsoft and everything it represents. I can get behind all of those, but for me, there’s a single compelling reason to spend at least part of every day using Ubuntu or another version of Linux.

On a window’s computer the gap between being a computer user and a computer programmer is a vast and gapping chasm. Trying to jump from a person who uses computer programs to someone who writes them takes a lot of knowledge, and it takes a long time before what you learn about programming actually helps you accomplish useful tasks. On Macs the gap is narrower, and that’s where I first started writing code. In Linux the gap is the smallest of all. People can even drift across it accidentially. And the code you start writing is immediately useful for things like data analysis.

Linux breeds superusers. People who don’t just use programs others have written, but when confronted with a question no one else has ever asked, or a problem no one else has ever addressed, can still get their computers to do what they want. Two guys who came in the same year as me started using linux this past summer for the first time for a two week python course (only one week of which was useful, I was there). Now one of them is writing C++ code for his phylogenetics project, and the other programs his lab’s liquid handling robot. Both are getting things down in weeks or months that without the ability to write their own code would take a big part of their entire doctoral research (or just wouldn’t even have been considered feasible in the first place.) As in any field, once you know enough to get results, learning begins to snowball and before you know it you’re doing things you never thought you’d be able. (more…)

October 12, 2009

Internet Scale Data

Filed under: Computers and Coding — James @ 9:12 am

I’m pretty proud of my eight core* workstation. But then I picked up the New York Times this morning** and found out I’m in fact behind the times:

For the most part, university students have used rather modest computing systems to support their studies. They are learning to collect and manipulate information on personal computers or what are known as clusters, where computer servers are cabled together to form a larger computer. But even these machines fail to churn through enough data to really challenge and train a young mind meant to ponder the mega-scale problems of tomorrow.

“If they imprint on these small systems, that becomes their frame of reference and what they’re always thinking about.”

Analyzing huge data sets is only going to get more important in the future, especially in biology. (more…)

October 1, 2009

September Stats

Filed under: Computers and Coding — James @ 12:01 am

Helped by a huge final day, September is now my second highest traffic month on record.* Coming after a record low in August. And almost all this month’s traffic came in the past two weeks.

I’ve also managed to keep up an update rate of at least one per day for fourteen days now**, (though I’m not sure how much longer I can keep it up). Adding further weight to the idea that readership and frequency of updates are positively correlated (who’d have guessed?). And this while getting zero search engine traffic. I’m still waiting for their indexes to purge the data on my link-contaminated hacked pages.

Thank you to all my readers, keep doing what you’re doing, and I’ll try to keep updating.

*First place goes to January of this year, which was helped by dating a girl at the time who was using this site as her main way to check my twitter feed throughout the day. I was so excited at the upward trend until I figured out what was going on.

**Not counting this post, but I already have one written for later in the morning.

September 25, 2009

Still Very Irritated

Filed under: Computers and Coding — James @ 7:54 pm

Turns out I declared mission accomplished too soon before. I’ve now done a clean install of wordpress itself, which unfortunately includes a new theme (plus side, rotating pictures in the header). Unless the corruption worked its way into the mySQL database itself*, this should have killed it.

*Is that even possible? Databases are right after objects on my list of coding relating things I should learn about since I know practically nothing about.

September 22, 2009

Very Irritated

Filed under: Computers and Coding — James @ 1:04 am

I noticed a major drop off in traffic back in July (on the order of 50%). Since that coincided with a substantial drop off in my updates over the summer I didn’t think much of it. Recently I got suspicious and checked out the top keywords on my site using google webmaster tools. Corn doesn’t even show up until #13, all the spots above it were taken up with drug names and even less savory words.


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