BOSC finishes and I weep as I miss it already

BOSC always comes and goes so fast. I am a melancholy kind of guy so whenever things finish up I get a little misty eyed with regrets at the things I could have done and the people I could have met. But it was all so great it makes me smile with the understanding of the entire world. Plus weeping really gets you the women — makes you look quite sensitive. And I am all about sensitivity. But before I got into this mindset, I tried to write down what happened. Read and feel my joy.


You may be wondering what Australia is like. So am I. So far I have been
entirely in the service of you, the faithful reader of BOSC news, and have
been basically a good boy attending conferences and generally getting my
money’s worth. All this science. All in Australia.

But yes, in case you are wondering if I suddenly turned into an
all-contributing hard-core science type who works day and night thinking only
of how I can further increase the general scientific knowledge of the world,
this is not at all true. So last night it was time to explore the wonderful
world of Australian bars. And I’m happy to report on that; if I could remember
any of it.

Okay, I can remember. I’m not all that bad, dontchaknow. My first impressions
of this region of Australia basically center around two points — there are
not a lot of bars around here, and damn these streets are complicated. Sadly,
the first impression is likely due to the second — I am the kind of person
that get readily lost. But no one cares — the point is that we ended up at
the apparently only bar on this side of the river separating our conference
site from the downtown casino part of Brisbane; South Brisbane versus the rest
of Brisbane.

As an amateur sociologist, amongst other things, I am very interested in the
people of Australia. Specifically, I was watching the flight information on
the plane ride from Melbourne to Brisbane and noticed something very
interesting and peculiar. The flight info basically said the same things —
fasten your seatbelt, put on your oxygen mask before helping small children
and invalids around you, blah blah blah. The interesting thing is that even
though it was the exact same information, it was presented in an entirely
different sort of fashion. The language and intonations of the talk was all in
English, but it was Australian English, a factor of living in Australia and
speaking with Australian people. Its more than just different phrases, but a
completely different way of thinking about saying a sentence.

The search for understanding these differences of course proceeded directly to
the bar. Understand the Australian animal in its native environment. Study the
behavior and write it all down in the notebook. I forgot my notebook. Or if I
had one it sunk to the bottom of the Brisbane river when I fell in. But I can
remember what I learned and the key to it all is this — Australians love
karaoke. We ended up in bar featuring karaoke that was so massive that we
actually confused it as being two bars. I talked with several Australian
women, on a purely professional basis of course, and asked extensively about
my in-flight language realizations. I came to the conclusion that an
Australian can’t say what it means to be Australian any more than I can say
what it is like to be an American. You suck up the culture and people and just
become what you become without thinking about it and then you are that region.
In one day, or one week, or one month, I am never going to learn what it’s
like to be Australian. So we all gave up on that quest, drank a lot of beer
(mmm, good beer) and I sang karaoke for no apparent reason. And it sucked.

That last bit of philosophy and thinking was incredibly boring, but of course it is my
mindset for the next few days in Australia. Experience it all, understand it
all, wake up with no memories of the previous night next to eighteen
Australian women on the roof of the conference center wondering what substance
inspired you to get a tattoo of a kangaroo on your forehead. I like wallabies
much better.

And there are talks going on. I am diligent. This is what I heard. It may not
necessarily be what was actually said, but all one can report on is their
perception of reality. Before I degenerate into cheesy Matrix-philosophy
pretending that I actually know something about philosophical thinking further
then watching Kevin Spacey play a philosophy professor in a movie on the
plane, here’s how the talks have been going:

You’re my PAL. Heh. Heh. — Matthew Goode

Let’s say you have to do phylogenies. Lots of us do. I can faithfully say as a
current study of phylogenetic techniques that these analyses might be the
single most complicated thing on this planet. One consequence of all this is
that with all the assumptions and differences in the variety of techniques you
normally want to try multiple analyses on your data. My normal thinking is —
do a lot of trees in various ways. If you can get yourself the same basic tree
using a variety of acceptable methods, then you can probably get yourself to
trust it. So the thing you would like to be able to do is write code that will
run all of these various trees using different methods and assumptions, let it
go all night, wake up in the morning and then evaluate it. If you program in
Java, you are lucky enough to have this fine project to help you with this
goal. This code looks incredible — it has all your favorite algorithms and
substitution models and all those good things. Beautiful. My highest
recommendation. Four stars. I recommend the oyster platter with sea clams in
mint garlic sauce. Tasty.

Generic Model Organisms and their Database — Suzanna Lewis

Continuing on a food theme (damn, when is lunch?), let’s say you take a dash
of collaboration, a pinch of model organisms (geez, these cheesy recipe
metaphors are really painfully bad. I will stop now), and you mix it all up
(oh yeah, I was supposed to stop that. I promise now. Promise.) with some
folks who know how to code and you get out a model organism database. The
history of these types of databases is that each organism had a central type
of database that a research organization worked on. Each organism had it’s own
schemas and tools and people working on it. The more organisms that came
about, the more this development philosophy led into duplication of tools.
Additionally, some databases had nicer tools for certain things,
depending on the expertise of the people in that group, and other organism
databases wanted to use it. Well thanks to the genius of many great people in
the open-source biology world, it was decided to build a generic model
organism database with shared tools. Every lab donated certain tools, they all
began to work together, and the beauty and elegance and greatness (man, I am
feeling really happy-happy this early morning; everyone is beautiful and happy
and time to go frolic in the grass with bunnies and sunflowers and, stay on
task, stay on task) became GMOD. This set of tools has great things for
literature curation, gene expression data, genome organization, laboratory
notebooks, genome analysis — basically everything you’d like to have for
your organism. So, yeah, I’ve got this whole plan for job searching — find a
job working on an organism that needs a database and get the job setting up
the database. Use GMOD, forget to mention that you just used all this free
open source, code, and then take six months off traveling around the world on
a sailboat you built yourself when you are “working” on developing this
database. I think I’m gonna sail my boat to Puerto Rico.

Biopython — me

This was the worst talk I’ve ever seen. This speaker is complete bollocks. I
would have walked out if I wasn’t up there giving the talk.

Lightning Talks — lots of people

Come on these go every five minutes. The only good way to describe them is
with stream of consciousness. Plus I’ve been reading lots of Joyce, so what
are you gonna do. Spreadsheets. Those are all about biologists. We love
spreadsheets. Well not me, but let me tell you that the folks who write Excel
should hire several people in my lab as stress testers for new version of
Excel. They wouldn’t even have to pay them. But the point is that getting your
data and programs to be easily integrable with spreadsheets is incredibly
smart.

Java beans. Web Services. These are very good things and putting them together
is even better. This is the kind of thing that could make you famously famous.
Like the famous Amos. That is my favorite episode of Taxi ever, if you haven’t
seen it. If you believe, they put a man on the moon.

Lightning talks are flying by and where am I where is the pointer not in my
pocket maybe up on the stage I couldn’t have lost it could I have that would
be terrible. Three lightning talks in a row. That is serious. I get lost with
a single talk to give. Of course, my brain is small. Buzzwords are really in
the house right now. After the beans, after the java. Now XML. UML. JML, HML,
RNA, DNA, WWW, WWF, RDF. Networks. All those terms and good words about
Biopython. Associate in your mind — Biopython, buzzword, Biopython, buzzword,
Biopython, buzzword. You know you want to. Hold on a second, I am writing a
blog. I am writing a story, and the talk is about weblogs. Cosmic occurrence.
Integrated with this kind of ridiculous rambling (well, he might have better
rambling then I can manage) are PubMed entries. So you are actually bringing
in science with your rambling and potentially contributing to a quality
discussion about research articles. The only bad thing is that words like
BioPHP pop up. What happened to Biopython. Dueling it out PHP versus Python.
Whoah, this is really degenerating. I need a better filter on my brain.

Microarray data from all over. Philosphically, all these organisms must fit
together somehow, especially in the wonderful land of Louisiana where they’re
eating cajun food. Somehow all of the microarrays come together in my head.
Normalization. C++. BASE. Microarray databases. Work-flow for open source
microarray analysis. Honestly, I wish I was getting into the world of
microarrays at the current time — exploring these types of open-source
projects and all the active development in the area really makes me incredibly
excited and interested. Which shows you exactly the kind of dork I am.

Population genetics. Wow. Not seen very often in the ol’ bioinformatics
circles. Very nice to see, I know several people in my lab who would be
salivating right now. I am also salivating along with them as it’s written in
Python. PyPop. Nice. It uses dataflows and goes back and forth with Excel.
Once again, we know what it’s like to work with laboratory biologists
completely in love with Excel. Here’s the URL for those of you who would be
searching just like me:

http://allele5.biol.berkeley.edu/pypop/


The really nice thing about BOSC this year is that there is lots of room for
people to make contributions “on-the-fly.” A really nice example of this type
of interactive talk is from Andrew, who is talking about his experiences
contributing to BioPerl right now. Honestly, this is really one of the great
things about BOSC in my mind — getting people interested in and contributing
to projects. I am back into my the world is beautiful and lets frolic with
bunnies and bikini babes mindset.

The other great thing about BOSC is exemplified in this next talk (and for me
in the PyPop talk) — learning about software that might do something you need
to know. Right now we are looking at pretty pictures of sequences and picking
out problems with sequences; very nice visualization tools for looking at
tons of sequences that come off a sequencer (quality values, sequence
features). This is incredibly useful for finding problems with the sequencer,
with the assembly, with the quality of sequences.

Two messages for five minutes. I have to disagree with Richard, who doesn’t
feel that crops are sexy. I find Sorghum incredibly sexy, but purely in a
platonic sort of way. Again — learning about useful tools. Do you need to
track genealogies and matings for your crosses in the field? Talk with
Richard, he has got your software.

Social policy bonds is what we are hearing about right now. The basic question
is whether companies or governments (closed versus open, basically) are better
at producing useful things for society. This is economics, and honestly I
don’t know anything about economics other than a single (but enlightening)
agricultural economics class I took back in my senior year to fulfill some
graduation requirements (but also ’cause I was interested, of course). However,
stretching your mind is extremely important to continue to keep yourself an
intelligent contributing member of society (or in my case, to pretend). The
idea is to fund open-source by putting a “reward” on getting something done,
and then paying the reward to the first group or person who accomplishes it.
This gets at the question of who is most efficient at producing a useful
software product, and the benefit is in supporting software “freelancers” as
opposed to building research institutes or the like to produce the things you
would like. My immediate concerns would be — who determines what makes a
“good” software product that does something. This could build a niche for
software junk-bond type traders who could churn out patched together code that
did something but wasn’t extensible or potentially good for everyone.
Interesting ideas, all the way.

Sadly, the evil that is computer battery time is now eating away at my ability
to record further events. Surely this will bring cheers and tears of happiness
from those folks who were wondering exactly when I would stop all this damn
rambling. Well now is the time as the battery dies and the lack of appropriate
power converters leaves me with no other choices but declare myself finished
for the day. Plus my fingers hurt.

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