Newsgroup: it.comp.os.dibattiti
Titolo: Linux su Nature

Homegrown computer roots out phylogenetic networks
HENRY GEE
[LONDON] If Ward Wheeler and Dan Janies suffer any computer glitches,
they won't need to rely on the IT helpline. These two systematic
biologists, based at the American Museum of Natural History (AMNH) in
New York, should know exactly how to fix their powerful parallel
computing system they built it themselves from scratch.
Their machine is a testament to what can be achieved with some
imagination, a 'can do' attitude, and a truckload of parts from your
local Radio Shack. And it is already being used to slash the time needed
to find the most likely phylogeny describing the evolutionary
relationships between groups of organisms, or taxa.
Systematists like Wheeler and Janies view phylogenies as 'unrooted'
networks. 'Rooting' the network to a putative common ancestor, producing
the familiar textbook evolutionary tree, comes later.
Identifying the most plausible unrooted network can present a formidable
computational challenge. There is just one unrooted network that
expresses the relationship among three taxa. But after that, the numbers
go up rapidly: with four taxa, there are three possible solutions; with
five taxa, there are 15; with 10 taxa, there are 2,027,025, and with 20
there are around 2.2110 20.
Rather than test every possible permutation, systematists use algorithms
that select the ones that look most likely and ignore the majority  a
compromise, perhaps, but one that produces solutions in less than a
human lifetime. But even so, you need a powerful computer to crack
difficult phylogenetic problems in hours, rather than years.
Wheeler and Janies have given themselves a state-of-the-art computer for
a fraction of the usual price. The secret is a massively parallel
design, using off-the-shelf components, a freeware operating system, and
homegrown phylogenetic software. The hardware is a stack of 129 boxes
each fitted with a hard drive, a pair of 500-MHz Pentium III processors
and 512 Mb of RAM, connected over a 100-Mbit switched network. One
machine acts as the master that controls all the others.
"We made the thing from bare bones," says Wheeler. When they placed the
order for the parts, he says, the incredulous electronics supplier
thought that Wheeler and Janies ran their own computer shop. Bolting the
bits together took a week and a half.
Fitting out a suitable room with air conditioning and switching cost
US$300,000; the hardware came to another US$300,000. The operating
system was free  the machine uses Linux, a freeware system similar to
Unix. Funds came from NASA, the AMNH and the City of New York.
Wheeler is currently using the system to crunch through a 130-taxon
insect database that combines data on morphology and molecular biology.
There are 10154 possible networks for a data set this size. But the new
system allows unprecedentedly fast and aggressive search strategies. "We
found better solutions in hours than we had found in months of searching
before," says Wheeler.
The system can be accessed remotely, and is being used by an increasing
roster of collaborators working on a variety of problems. The homegrown
parallel-processing software used by Wheeler and his colleagues can be
downloaded from the Internet, at 
ftp.amnh.org/pub/molecular/poy
 and at
ftp.amnh.org/pub/molecular.malign
.
-- 
Ciao, Carlo Fusco

US$300,000; the hardware came to another US$300,000.
Seicento milioni per la stanza? Cavolo! 8-|
Leonardo
Microsoft Outlook: cosa vuoi postare postare postare oggi?


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-- 
Ciao, Carlo Fusco
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