My company is actually looking for two sorts of people. The first is that hourly type that I mentioned earlier. Yes, I would actually pay a generous wage for that, for the right person. The second is another “principal investigator,” kinda like me. Here’s the scoop. If you’re interested in this one, this could be a wild ride for all of us.

BioTeam Inc. is a Boston-based consulting and software development
company specializing in the applied use of information technology for
scientific research.

Here’s the first sentence from my first post of each month this year.

Jan 1, 2:10am: “Help…”
Feb 1, 1:10am: “Good times watching the state of the union address.”
Mar 1, 3:59pm: “** bleary ** Is it the weekend yet?”
Apr 1, 7:51am: “I was watering the seedlings this morning when Jen called out to me from the dining room.” she had seen the first goldfinch of the year
May 2, 8:11pm: “Been a while since I talked about karate.”
June 1, 4:51pm: “We took our “stroll” to see some of the friends of the guest house today” while in Haiti…
July 1, 4:32am: “On the train, back from Boston.” actually written on the train around 12:30pm, after that long and crazy night at Jake Ivory’s
August 1, 9:08pm: “The Hurricane Hunters found much stronger winds than expected in Chris this afternoon.”
September 1, 8:32am: “On the left side of this page is the most creative music video I’ve seen in ages”
October 1, 10:11am: “I plan to do this today, in the small, with my work environment. “Trash bag cleanup” might be a better term. I’m sick of mess.”
November 1, 9:49am: “I appear to be wracked by the same disease that’s afflicting everyone else in the country.”
December 1, 6:24pm: “The Kurzweil trifecta is complete. I have now shaken his hand and directly asked him a question.”

Every few years I try to organize my library. On Tuesday, I tried to explain it to technolope and capital_l as a test to see if I’m enlightened yet. It seems to me that an enlightened human being would, at least as a start, have a decent organizational scheme for his library.

Last time I did this, I settled on sorting the books by height, to optimize shelf use. While this was effective, it left me a little cold intellectually.

Fully wary of my tendancy to pull an _earthshine_ and overthink things, I just plunged into the task and started carving out subsets of the problem.

1. What did you do in 2005 that you’d never done before? Made a budget.

FARK is an alternative news source, with funny headlines for stories that he finds online. This one stood out for me:

Spanish judge wants to question U.S. troops. In other news, people in hell want refreshing Mike’s Hard Lemonade

Also in the news, Monks can meditate better than you

In other news, I spent my day fighting with OS X. Found one decent sized bug in their NFS server (confirmed with other folks). Basically, they screwed up Unix group ownerships. This is bad. Can’t believe they let the software get out the door with something like this in place.

I was going to write more, much more. Instead, I’m going to bed.

I’m at a speech by J. Craig Venter. My heart is filled with envy, because he’s so damn smart. How smart? Well, he’s making scientific history by sailing the world (in his tax deductible yacht). He takes environmental samples (from the Sargasso sea, for example) and sequences all the DNA he finds. It’s changing our understanding of genomic biology. Now he’s giving a keynote using his travel pictures as slides. He’s very quotable:

“Back at the beginning, we had this idea that we had if we couldn’t make a single large machine to sequence the entire genome, we had failed.”

“Once we did drosophila, the rest was really just cranking through it.”

Here’s one of me, with two Apple guys, in front of the India Gate.

Below are the first sentences from the first post of each month in 2004 (except for Jan and Feb, in which I did not have a journal). This idea was stolen from too many people to count.

It seems to me that art has two fundamental components.
Why not? Why not do these stoooopid quizes. Let’s all do the quiz thing and then we’ll all be COOL!
I’ve been captured on the web.
I’m on a train, heading in to Boston for my job interview.
First day at the new job. For those who haven’t gotten the memo, I’ve joined the BioTeam.
Enough lollygagging: It’s presidential physical phitness time.
Done with the gig. Day two went much better than day one.
Just finished all the campaigns in my most recent game purchase: Halo.
Given the amount of energy we’ve seen around this election, I wonder what plans y’all have for election night.
I love this state.

For the pathologically interested, here’s about 40 mega-bytes of the powerpoint slides I created for various training sessions available in two PDF documents:

• Intro to genomic biology and bioinformatics
• Intro to high performance computing and clustering

In this week’s Science, there’s a decent milestone in where we’re at in terms of integrating our molecular biology knowledge into classical genetics. If you subscribe, a summary is available here. Otherwise, use the “free sample issue” link.

Basically, this group of scientists went back to the Galapagos and studied Darwin’s finches. They isolated the protein that causes the beaks to be different, and manually turned it up and down, resulting in different shaped beaks. They then located the regulatory regions (governing said protien) as markers on the genome, and waved their hands at them.

The cool part about this is not its terrifying utility (it’s not), nor how close it is to being broadly applicable (it’s not). The cool part is that there does not seem to be a quantum / macro disconnect in biology like we have in physics. We can trace smoothly all the way up and down the continuum, and it’s just experimental details and unobserved mechanisms.

More geekage.

I’m writing a web service interface to my company’s tools. The idea of web services is to provide a way of remotely invoking methods that can be transparently streamed through any wire protocol you want to use. This idea is far from new, but the infrastructure is finally in place to make it really simple and obvious how to do it.

The goal is this: I have objects (data with attitude, or sometimes functions with associated data structures) that I would like to make available to other people. The traditional, and in many cases still the simplest, thing to do is to pick up the source code which implements those objects, haul it over to the machine on which I want to make it available, build it, and be done. People who want to use my objects must then link against them or include them (depending on the language).

A more painful, but also well accepted method is to write an interface to every aspect of the objects that I want to share, and put that interface online via either a web page or a special and magical protocol made up just for these objects. If I’m really infected with the “not invented here” bug, I might choose to re-implement the “fork and listen” protocol instead of just using one of the zillion open source solutions to that particular problem. Users must, instead of just calling the functions, write code that speaks my language.

The web services solution is a happy middle ground. We agree on a way to serialize objects (SOAP, the Simple Object Access Protocol, which is a special case of XML). Then, we agree on a way to move around these serialized objects. In this case, we’re going to use HTTP, passing through a web server. Then (and here’s the dark magic) the server makes the objects available to clients and nobody is the wiser about where the code really lives.

For example, a PERL client might look like:

use SOAP::LITE;
my $server = SOAP::Lite -> uri(“http://chris.dwan.org/”);
my %results = $server->do_that_funky_dance();

Benefit: We have been saved the anguish of installing the code for “do_that_funky_dance” on the client side.
Drawback: We had to install and use a SOAP client.

I actually think this is a pretty cool set of technologies. Have any of the rest of you used it / got an opinion?