Science can answer moral questions

Listened to this on my iPod yesterday. Watched it on YouTube today. Very powerful if you let it sink in.

Science can answer moral questions

I like this piece a lot more than when he spends most of his energy attacking religion. I already agree with him on most of that material, so it's far less interesting to me and too aggressive for my comfort.

Far better to focus on positive changes in science rather than "that over there is patently stupid."

Gratuitous Moosey ego stroking

The Godfather of Moose gave me mad shout-outs on his blog for some minor tweaking I did to the Moose website.

Later I expressed some of my recent concern about academia, and he offered this sage advice:

11:37 <@stevan> jhannah: go into their lab, climb up on one of the work benches and yell "ANY OF YOU NANCY BITCHES STEAL MY CODE AND I WILL CUT YOU INTO LITTLE PIECES"
11:37 <@stevan> then kick over a few bunson burners and walk out
11:37 <@stevan> they wont bother you in the lunch room anymore
11:38 <@perigrin> stevan did something like this in Art School
11:38 <@perigrin> 'cept s/bunson burners/cerulean blue/
11:38 <@stevan> I offcentered their pots on the wheel

Firefly shot me 51 days into the future

I feel pretty good about my project this weekend. I used the University of Nebraska Firefly Cluster for a real project for the first time, completing 51.6 DAYS worth of data crunching while I slept between 3am and 9:30am this morning. The code I ran is my fork + branch of a bunch of Perl from Harvard against the latest human genome from UCSC. Masochists can read all the gory details (username: guest password: guest) and suggest improvements.

Computers are pretty cool sometimes. :)

Pipeline evolution - again!

It evolved again! This too, shall pass. :)

Pipeline evolution

Over the last couple of weeks I've been writing and changing a bunch of software trying to answer some research questions. I find the visual evolution of this pipeline interesting. Maybe you will too.

Sneak peak of the first chart:

GraphViz prettyness

My first mapping of bioinformatics alignment score to how dark a GraphViz line should appear, and switching colors based on other criteria... Perl++ GraphViz++

I don't think it's very informative, but there's no denying it's pretty. :)

Chiselling chunks off of BioPerl

There's been renewed conversation about breaking BioPerl up into smaller distributions. I'm trying to help, citing the Catalyst development model as an example of how the world could be better.

For some values of 'better'. -grin-

Tweak the Perl regex engine: assign to pos()

OK, Perl is way too cool.

I was minding my own business, searching for every occurrence of 'CCAGC' in E-coli, when I hit a snag. Several hundred of my known locations weren't showing up.

Why? Because the Perl regular expression engine, by default, starts searching for the next occurrence of something after the end of the occurrence it just found. This is what most humans want. But you may notice that in the string 'CCAGCCAGC' the thing I'm searching for ('CCAGC') overlaps itself, so the regex engine doesn't see the second one.

"Crap," I thought.

But this is Perl -- maybe there's a way? 30 seconds in the documentation (perldoc -f pos) and it said I could assign to pos(). Really? Sweet! Problem solved!

#!/usr/bin/perl

use strict;

open (IN, "E_coli.seq");
my $seq = <IN>;
chomp $seq;
close IN;

my $find_this = 'CCAGC';
while ($seq =~ /$find_this/g) { 
   my $start = pos($seq) - length( $find_this ) + 1;
   my $stop  = pos($seq);
   pos($seq) = $start;
   print "   Found $find_this at [$start..$stop]\n";
}

Swirly bacteria

Spent yesterday drawing pretty pictures of bacterial genomes with Perl, BioPerl, and R. Given the genetic sequence of different bugs (ACCTGTCGATGCTA...) we're looking for fingerprints in the composition of those sequences. Pick out the 200 most frequest 5-letter "words" (oligos), sort and plot those, and maybe we can see the fingerprint of each bug.

It seems to work. The black line is E. coli., which is very different from Staph. aur. (red and green) and Staph. epi. (blue). You'll also notice that the 2 Staph aur. lines are very close to each other, since they're almost identical; they're very similar to yet distinct from Staph. epi; and distant from E. coli.

Cool, huh? The details (username: guest, password: guest)

SICI (Search for IntraCellular Intelligence)

Much like SETI (Search for Extra-Terrestrial Intelligence), I spent all day yesterday searching protein sequences for periodicity using chemical property filters, entropy, Fourier transformations, and R.

None of the ~80 graphs I generated looked like an old dude with a beard...

Genome center information management

Awesome.

More awesome: I actually understand what he's talking about and why nowadays. I've come so far. :)

A carbon atom and four hydrogen atoms

Spent all of Sunday tying DNA methylation data into my JCVI project. Another classic battle inside my brain:

I'm fascinated by everything we (humanity) knows about this process, and the fact that sitting in Omaha, NE on my laptop, my mentor and I can harness that information, creating millions of data points in a database of my design using software I wrote. What a wondrous time we live in, flush with opportunity to explore the universe.

I'm repulsed by the ambiguity of the datasets we work with. How can we not know what's actually happening? What's the point of me gathering a million possibilities? How is drowning in maybes helpful? My brain panics! Call me when we can know something!

Science seems to be about spotting and exploring trends in noisy data. My computer programmer brain likes on and off, black and white. Trends are tough for me to swallow. This recurring theme convinces me that I make a good scientist's side-kick, and a lousy scientist. :)

Reinventing the wheel for fun and profit

I was all proud of myself last week and impressed the other kids when I wrote an amino acid property converter in about 15 minutes.

$ perl properties.pl TLPDILHASGPPGPPGQPEQPGAGR
               small 1011000111111111010011110
            aromatic 0000001000000000000000000
           non_polar 0100111101001001000001110
                tiny 1000000111001001000001110
             charged 0001001000000000001000001
           aliphatic 0100110000000000000000000
            positive 0000001000000000000000001
               polar 1001001010000000101100001

Little did I know that mine was inferior to Bio::Tools::OddCodes, which I could have downloaded for free in about 1 minute.

But, in my defense, not knowing that tool existed it would have taken me longer to find it (not knowing what I was searching for) than to write my own from scratch.

And as a programmer, it's far more fun and satisfying to spend 15 minutes solving a problem and impressing people than to spend 15 minutes searching the Internet for something you may never find.

So perhaps reinventing the wheel is good for morale sometimes. Trivial wheels, at least. :)

Cloth physics, genetics research

peterthomas introduced me to this interactive cloth physics demonstration via Twitter. It's awesome. Click it!

This is what I was hoping my bionerdary would reveal. Perhaps the rules of biology are very complex, but as you discover them useful patterns emerge, systems are revealed, and eventually you can actually do useful things.

I'm not quitting, but I think I've lost hope that genetics research will reveal itself in the useful way cloth physics does in my lifetime. Perhaps biology is too complex for my feeble mind. Perhaps it is too complex for the collective efforts of all of humanity to encapsulate effectively. Or perhaps, long after I'm dead, our children will pull up little "curing cancer" simulators on their computers and wonder what took us so long.

In any event, my desire to witness tangible progress arising from my daily/monthly work seems a poor fit for the current state of the art in mankind's attempts to grok biology via computers.

Hidden Markov Models

Great quote from Cryptogenomicon:

David Lipman commented that the only thing that made HMMs interesting was their name - there’s something’s hidden, and a Russian is involved.

Read more about HMMs.

Not only is that hilarious, but his 95-page HMMER Users Guide includes such indispensable sections as "How to avoid reading this manual" and "How to avoid using this software (links to similar software)".

As scientists go, you gotta love this guy. :)

Dream job? Pass.

I don't understand me.

17 months after starting my part-time adventures in genetics research (showing up at the medical center 3 days a week), I am now trying to find someone else with my skill set to take this job on, full time. I'm not leaving, but apparently I don't really want this gig full time either.

I think it's the money. Plus the current lack of some big, computationally extensive pipeline for me to wrestle every day and be the expert on. I like knowing big balls of code inside and out, and having people need me for high powered data nerd ninja action. Plus the lack of other people like me sitting here. Lack of coworkers is depressing.

Or maybe it's just the money.

A year in the life?

-ponder- I guess this "Integration Candidates" page I just made is sort of a list of possibly general use tools I've worked on over the last year... : BioCMS (RT username: guest, password: guest)

Grassius debugus

Helped a guy at Grassius use -link and Bio/Graphics/FeatureFile.pm link_pattern() today. Yay me! :)

Glyph::dna, Kiva props

My jays.net ISP went "poof," so I made an ungraceful migration to a new one. Between that and my lappie hard drive dying it's been a tough month in the personal computing front. :)

I added how to add a DNA track to the BioPerl wiki. BioPerl is so cool. :)

It's been a month since we made our first loans on Kiva.com, and now our first round of re-payments have arrived! mwoohahaha! Oh, and did you know about Kivafriends and Kivapedia?

Yay! I *is* smart!

Sweetness. I'm starting to understand this bioinformatics stuff enough to submit patches to minor problems in the work of Harvard grad students. :)

Evidence this week: Corrected arrows in (1) Denaturation, another PCR glitch.

(Last semester I found a few glitches in professor's slides and even two in my textbook. Yee ha. -grin- ... Come to think of it, there was a typo in my Chem answers book this semester too. That one made me scream. -frown-)