October 2010 Archives

Learning to Model

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Computational modeling requires a diverse set of skills.  While most aspiring modelers are expected to have solid math skills, many advisors assume that other skills, like writing programs or building complex FORTRAN projects, will be learned on the fly.  These skills form what I call "applied scientific computing" and they can be some of the biggest challenges that rookies and even some veterans face.  For example, we're trying to get an implementation of ROMS running on our lab system.  Like many large models, ROMS comes as a series of FORTRAN files.  These files must be compiled and then linked against a series of external libraries (for example, NetCDF).  Magnanimous developers will often provide a "make" file or build script to make the compiling and linking simpler.  However, my experience is it always takes some digging to get this process to work.  Even if you've had a course on FORTRAN programming, you very likely have no idea what it means to link to an external library.  At one point, it was my mission in life (well, not quite) to fight against the "I had to teach myself this stuff, you should too" mentality.  I developed a series of short courses on doing science with Matlab, FORTRAN programming, and even a course on libraries.  I've created a "Scientific Computing" section of seascapemodeling, and put a couple of the courses on there.  I'll try to get the complete set up shortly.  If this is a topic that's interesting to you, please leave a comment or send me an email.

Nutrients, Whales, and Ancient History

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I'd hoped to do a more extensive posting on Roman and McCarthy's paper on whales and nitrogen cycling, but travel and meetings got in the way. I'm on my way home from the IMBER Imbizo II meeting on the island of Crete in Greece.  The IMBER program brings together scientists with an interest in biogeochemistry (flows of nutrients and chemicals through the ocean) and ecosystem science.  I was participating in a workshop on the role of stratification in marine systems.  Anyway, the whale poop paper is very relevant to the topics of the meeting.  One of the things that the recent whale-nutrient papers and our whale-carbon paper touch on is how differently past ecosystems with abundant fish and lots of whales may have been. It is entirely possible that the ocean pictured in this 5000 year old fresco
from the Minoan palace at Knossus had important feedbacks between the large species and the smallest particles that allowed the ecosystem to support abundant fish and abundant Minoans.  

Seascape modeling on NPR

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Autumn is upon us, and we've been busy at seascapemodeling.org, despite our lack of blog entries.  Here is a link to an NPR story featuring Andy:

Whales help fertilize ocean with floating dung

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