Redefinition.

It’s about midnight, I’m writing this in wordpad right now because our internet is all messed up and I’m too cheap to invest in microsoft office so I am using wordpad. Obviously, since you are reading this, we got the internet figured out so I could paste and post…woot woot.

I’m holding it in my hand – a proposal to do a piece of work I believe would truly be an awesome research venture and naively I forget, of course, that I’m not the only one that thinks of these things. Having been scooped several times now in what is actually still considered an ‘early’ career, I should know well that what I think is cool…well others think it’s cool too. Enter https://phys.org seriously – f%@&ing bane to my existence. “Researchers have just discovered…” – I toss the proposal aside, seriously – words that are going to be on my tombstone. “Researchers have just discovered…” Novelty erased, pass Go, do not collect $200, find a new angle or just start again. Continue reading “Redefinition.”

where i hide on occasion…

Now to be fair, this was a particularly hectic week and the ‘busiest’ my desk has been but upon reflection it pretty much sums up my existence as a postdoc…”semi-organized chaos”.

Click on the picture to enlarge.

What you don’t see is the 3 pairs of shoes under the desk along with 2 bags and flat rate mailing boxes. On the cubicle wall out of view are several postcards from friends in Boston, Jackson, WY–now Australia and Great Falls, MT, 3D dengue sequence structures and a post it note to pay bills–the line between normality and nerd is definitely a blurry one.

a typical lunchtime thought process…

Mmmm…hungry time for lunch…
lunch, pork and vegis with sauce and rice
hair in food…
hmmmm…my hair or their hair
*pulls hair from food*
their hair
*flicks hair onto ground, keeps eating*–meh

pause

i wonder how many microbes are on a typical piece of hair
i wonder how many microbes are on my hair
i wash my hair
does she wash her hair
*looks at lady serving food*
maybe

I should culture/test my hair
that’d be interesting
no, not applicable–i need to test a food servers hair
*looks for dropped hair*
its on floor
floor contamination, damnit, can’t test it

someone in the US would wreak havoc if hair was in their food
is it that dangerous?
i should culture hair and see
*eats more food*

coffee sounds good
i should get around to reading Rob Dunn, wildlife of our bodies
he’d know if hair was dangerous
*finishes food, pays*
coffee

i read a lot of science blogs, scientists are getting ‘hotter’ looking
we used to have to hide under rocks
my German friend was surprised after learning i was a microbiologist
i asked why
he said because i’m attractive

i should make a calendar of ‘hot’ scientists
that’d be cool
with links to their publications and blogs
hot.

i should find someones hair and culture it…

Assessing the pathogenic potential of people

So it’s been a good while since I have posted anything as I’ve been attending a conference in Philadelphia, PA put on by the American Society of Tropical Medicine and Hygiene. Following the denouement of the conference I found myself at El Vez restaurant, awesome restaurant by the way, just down from my hotel sipping on a very strong (apparently) pomegranate margarita and going over my notes whilst eating lunch. And for those of you following my blog and know I’m fasting–before you cry foul, this week I’m off it due to a number of reasons but will promptly re-initiate when I return to Bangkok. When one is fasting for a year…actually turns out to be a little longer, I have to allow myself a certain modicum of sanity. Or rather preserve what I have. In anycase, back to matter at hand…

So I’ve been at this conference for the past week and it’s proven very informative though I feel like a small genetic fish swimming in a sea of immunology and epidemiology which is a bit disconcerting, especially since I come from a completely environmental background with minimal medical/clinical knowledge.

Now I am a genetic data cruncher who enjoys population level analysis with some mathematical modelling thrown in for good measure…

I know right? The personal ad practically writes itself. Continue reading “Assessing the pathogenic potential of people”

Power outage kills 34 million state BEAST run, Investigator contemplates Linux homicide

As the title suggests I walked into the office this morning to two computers…both shut off. Now no one touches my desk especially when I have analysis running and we had a huge storm last night with lightening and wind and although Bangkok is a ‘1st’ world entity of itself some days the fact of the matter is, I live in a 3rd world country that is 98% agriculture. The result? 34,510,000 iterations of a BEAST run of 100 million completed and the analysis ends with the power cutting off. My poor linux, diligently plowing away at iteration after iteration, only to be thwarted when its attachment to life power is cut.

CURSES!

A check in tracer reveals that my posterior, prior, likelihood, tree likelihood and coalescent are all at ESS values in the red (under 100) and clock.rate is under 200 (in the yellow). So things have not finished ‘mixing’ and converging altogether.

DOUBLE CURSES!

Thankfully I started the same run on the Oslo Bioportal August 23, 2011 and currently the status is on resource/started. Unfortunately they do not give me an up to the moment snapshot of my analysis and I cannot check using Tracer with it along the way so it will march to 100 million generations until it is done. I was hoping to track my run as it went to see if it exhibited good mixing and convergence prior to 100 million iterations– but alas, I will never know. And if Oslo has a power outage–then the ‘gnomes’ or ‘gremlins’ are up to something … little bastards.

There’s something comforting about watching status lines flip by on an analysis, lets you know the computer is hammering away at the brick wall of analysis trying to find that one loose brick. That’s why I always like to run things on the terminal although I have to say the GUI for the program is quite pretty. Yes, I just called the GUI for a Bayesian analysis program ‘pretty’– sometimes I indulge in superficial scientific vanity.

So I’m torn on whether to restart the analysis from iteration 0 or wait for Oslo to cough up my results. Without status lines to watch much of my previous list of things to do while BEAST runs gets nullified… I guess the ‘analyst’ will have to actually go outside… see the sun… get some fresh ‘non-circulated’ air… engage in social behavior with others perhaps also affected, having lost analysis down the black hole of power outages and now venturing forth confused from their cave like offices into the bright heat of Bangkok… or I need to find a new program with status lines that takes a long time to run!

~cheers.

Call for Nominations: MacGyver of [Insert Your Field]

So I can’t claim complete originality of this idea, I was inspired by a facebook post from a colleague of mine Dr. Jennifer Biddle who consequently is my personal nomination (see below). In the resource strapped world of research in general and in fields that bounce routinely between NIH and NSF funding, like my field: Infectious Disease Ecology (is it ecology? is it medical? is it ecology? is it medical?) innovation is key! But lets not snub the other fields of science where innovation is key! I simply address this field because it’s my field. Any nominations are welcome! Also for those working in the developing world where money can be even scarcer it pays to ‘figure shit out–old school’.

Remember the days when grandpa would walk to school, uphill in the snow both ways and amused himself for hours with nothing but a stick and a string? Where we learned how to ‘make life happen’ with nothing but a few coins in our pockets…things have gotten expensive nowadays! Then the 1980’s came a long and who should present himself but MacGyver…my fiance currently owns every episode of MacGyver created. Then man who could set off bombs with bubble gum, attack and defeat countless terrorists and other assorted bad guys with baking soda and a swiss army knife. The man was scientific ‘magic’ if you will.

So in honor of the world of money strapped scientific research I’d like to open nominations for who you believe to be the MacGyver of your field and why with links to their professional profiles if you so desire. Let’s laud the achievements of our innovative colleagues and strive for their ingenuity borne out of sheer force of will and desperation–“do I buy food or that sequencing kit…” Yes I am guilty of placing a sequencing kit above food at times…but I drew the line at mouth pipeting and just bought some damn pipets!

Continue reading “Call for Nominations: MacGyver of [Insert Your Field]”

Witches Broom in Vietnam…

I decided to repost this from ProMed because I thought it was interesting…who comes up with these disease names!? When I saw it in my inbox of course I had visions of cult activities involving longan fruit in the jungles of Vietnam…yes I have an active imagination.

Witch’s broom gets its name from a deformity in a woody plant, typically a tree, where the natural structure of the plant is changed. A dense mass of shoots grows from a single point, with the resulting structure resembling a broom or a bird’s nest. [Source]

A quick shout out to ProMed which is a great resource for hearing about disease outbreaks of known or unknown etiology around the world…check it out!

But really, Longan fruit is quite prevalent in Thailand as well and it is quite delicious. So, fantastical imagination aside, see below, feel free to read the culti-c disease activities plaguing Longan in Vietnam!

Continue reading “Witches Broom in Vietnam…”

Things to do while BEAST runs

So in the world of molecular evolution one of the cu-de-gras-de-analysis programs would have to be BEAST. A power-packed bayesian analysis software that makes phylogenetic trees, calculates the time to the most recent common ancestor (tMRCA) and substitution rates, geographic partitioning, can handle copious amounts of data and pretty much squeezes blood from a turnip…walks on water…heals your mother, in short, it’s cool.

Sound awesome? It is. For a more technical in depth discussion and introduction to BEAST software I suggest reading the Wiki and attacking the tutorials with full force as well as reading some awesome books on phylogenetic inference such as The Phylogenetic Handbook. If you are super impatient and channeling your inner terrible twos about phylogenetic analysis then read Phylogenetic Trees Made Easy. It has a nice introduction and literal button for button how tos on different software packages including Bayesian ones. When you’ve finished your tantrum, enter the adult world and read Felsenstein or the phylogenetic handbook mentioned above. Now that you’ve been introduced to phylogenetic inference and genetic analysis with forays into evolution over time…jump into BEAST. Although the BEAST wiki and manual are still navigate-able without that background but you’ll be scratching your head a bit and heading to google for answers.

Continue reading “Things to do while BEAST runs”

Modeling…What???….

I found this note in my facebook archives and thought I would reshare it on this blog. It was following a trip to Imperial College, London where I took a Mathematical Modeling course. Posted: Sep 18, 2009.

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So I’ve been at a course at Imperial College in London for the past 2 weeks attempting to turn myself into somewhat of a mathematical modeler (please keep your uncontained laughter to a dull roar). It’s been quite intense and very enjoyable and frustrating, all in all doing exactly what it promised to do.
Continue reading “Modeling…What???….”