[Dart-announce] DART news: RNA multiple alignment, gcc 3.3.* compatibility, logging, 2004 bug hunt...

[Ian H. <ih...@bd...>]

Hi all,

I promised this would be a low-volume mailing list, but two messages per
year might be a bit slack... so to compensate, here is a newsletter.

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GCC 3.4 compatibility

Release 0.2 of Dart is on its way, but I haven't yet found time to make a
tarball (or update the tutorial), and I keep adding little things.

The code currently in the repository works with the latest version of gcc
(3.4.1) and also is backward-compatible with gcc 3.3.* (as used in the
pseudo-parallel universe of Mac OS X).

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RNA multiple alignment

More excitingly, stemloc does RNA multiple alignment! how cool is that?
As you, discerning User, have come to expect, the code is blindingly fast.
It errs on the side of speed (& low memory) versus sensitivity. You can
make it more sensitive by playing with the "-nf" switch. HOWEVER:

It's quite easy to max out the memory on your machine. This means you need
MORE RAM! There may be cooler hackier ways to constrain the Sankoff
algorithm than the ones DART currently knows about. But, ultimately, none
of us can shirk the duty of buying a 64-bit box ;-)

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Today's DART top tip - logging

One quick-and-dirty way to get more info about what's going on inside DART
is to access the built-in logging diagnostics -- pretty much every
debugging output method I've ever written is accessible by using the right
"-log ..." directive. Type "xrate -logtags" or "xrate -logtaginfo" to get
a list (substitute e.g. "stemloc" for "xrate" depending on what program
you're using).

As an example, the relevant logtags for "xrate" begin with "RATE_EM"  &
you can grep for them in the file

	dart/src/hsm/em_matrix.cc

e.g.  "-log RATE_EM_STATS" should give you the alignment log-likelihood,
and also the statistics $u_{ij}$ and $w_i$ estimated during the E-step.

The output is to stderr or a logfile, in a sort of dismal apology for XML.

Just "-log N" where N is a number will give you a bunch of log messages
about everything. The default N is 9; set N to lower for more info (9 is
the most Unix-y, i.e. minimal output; I usually run at about 6 for
standard usage, or 3 or lower for debugging.)

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Current top 5 on the DART wishlist

* Telegraph (machine-readable format for stochastic grammars, plus compiler)
* Irreversible substitution matrices in "xrate" (and other programs)
* Importance-sampling for "tkfalign" (i.e. using TKF as proposal function)
* Generic "Evolutionary HMMs" (as described in Holmes, ISMB 2003)
* Simple "Evolutionary SCFGs" (as described by e.g. Knudsen & Hein)

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DART bug hunt

The 2004 DART bug hunt is a late starter but it is ON! The best bug mailed
to me before 12:01am on January 1, 2005 will win a DART-related prize that
will *astound your friends*! It could be a dart rifle. It could be a Dart
Blaster pen. It could be my 1966 Dodge Dart, resurrected from its dusty
junkshop grave in Coalinga, halfway down the California Interstate 5. What
is certain is that it will KNOCK YOUR SOCKS OFF. Current best contender is
the weird "xrate" normalization behaviour observed by Carolin Kosiol at
the EBI. But YOU CAN FIND SOMETHING WEIRDER! Come on, do you really think
*I* would write something bug-free? Have you SEEN how long Dart takes to
compile? There must be bugs the size of Microsoft Word in that thing!
Entries on a postcard or email.

(The excellent third-party software "newmat" (Robert Davies) & "weighbor"
(Bill Bruno), distributed with DART, is defined to be bug-free for the
purposes of this contest.)

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Ian Holmes
Dept of Bioengineering
465 Evans Hall, UC Berkeley
(510) 643-2393
ih...@be...

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Contributions to DART always welcome. Email me for CVS developer access...
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