Monday, February 28, 2005
Sunday, February 27, 2005
wow, a blast from the past: the hitchhikers guide to the galaxy game. like on the apple ][. neato!
the game
and
the walkthrough.
the game
and
the walkthrough.
Saturday, February 26, 2005
the grand sofitel demure amsterdam. take my advice, only stay in the presidential suite, you'll thank me later. great neighbourhood as well, right by the dam.
for discriminating guests, you'll want to stay in the maria di medici presidential suite. check the safe for a false bottom, and you'll find a little gift from me.
ok kids, ready for this? a bunch of perl+xml links for you (and me!):
The Source page:
Perl and XML
more Perl and XML
xml and sax machines part one and part two
schematron - Web Content Validation with XML::Schematron
XML and modern CGI applications.
XML::LibXML - An XML::Parser Alternative
Transforming XML With SAX Filters.
Writing SAX drivers for non-XML stuff. interesting.
The Source page:
Perl and XML
more Perl and XML
xml and sax machines part one and part two
schematron - Web Content Validation with XML::Schematron
XML and modern CGI applications.
XML::LibXML - An XML::Parser Alternative
Transforming XML With SAX Filters.
Writing SAX drivers for non-XML stuff. interesting.
linkfest
gnuplot slides (in pdf).
xmlsh - a shell for interacting with xml
a hack to get barcharts in gnuplot.
why oh why isn't there a free plotting program out there that does graphics worthy of Tufte? Tell me!
gnuplot slides (in pdf).
xmlsh - a shell for interacting with xml
a hack to get barcharts in gnuplot.
why oh why isn't there a free plotting program out there that does graphics worthy of Tufte? Tell me!
Friday, February 25, 2005
Position dependence of non-polar amino acid intrinsic helical propensities1
Michael Petukhov, 1, Victor Muñoz1, Noboru Yumoto2, Susumu Yoshikawa2 and Luis Serrano1
We have interpreted the results from these experiments with the model of the helix/coil transition (AGADIR), that indicates that the intrinsic helical propensity is position dependent. Gly, Val and Ile are more favorable at the first turn than in the middle of the -helix, while for Leu and Met we observe the opposite behavior.
Thursday, February 24, 2005
Wednesday, February 23, 2005
5.1. nm command
The nm(1) command can report the list of symbols in a given library. It works on both static and shared
libraries. For a given library nm(1) can list the symbol names defined, each symbol's value, and the symbol's
type. It can also identify where the symbol was defined in the source code (by filename and line number), if
that information is available in the library (see the -l option).
The nm(1) command can report the list of symbols in a given library. It works on both static and shared
libraries. For a given library nm(1) can list the symbol names defined, each symbol's value, and the symbol's
type. It can also identify where the symbol was defined in the source code (by filename and line number), if
that information is available in the library (see the -l option).
LD_LIBARARY_PATH and LD_PRELOAD
If you want to run a program that needs a different library:
1) ldd programname
This lists the dynamic libary dependencies of the program
2) Copy all those libraries to a directory
3) setenv LD_LIBRARY_PATH /path/to/directory/with/libs
LD_PRELOAD lets you load a different function instead of a libc library call
like if you wanted to make your own testing version of open().
So, so far, I can't override the GLIBC_2.3. If anyone has an idea
email me, please.
If you want to run a program that needs a different library:
1) ldd programname
This lists the dynamic libary dependencies of the program
2) Copy all those libraries to a directory
3) setenv LD_LIBRARY_PATH /path/to/directory/with/libs
LD_PRELOAD lets you load a different function instead of a libc library call
like if you wanted to make your own testing version of open().
So, so far, I can't override the GLIBC_2.3. If anyone has an idea
email me, please.
Saturday, February 19, 2005
This command line goes through 5gb of files and pulls out the number
of matched residues and atoms from the model building part of Crank.
and the next one:
and the synthesis:
of matched residues and atoms from the model building part of Crank.
find . -maxdepth 3 -name 'log' -exec grep -m1 "atoms.*residues" generated/*/log \; | less
and the next one:
find . -maxdepth 3 -name 'log' -exec sh -c "echo -n {} ; grep Rfree {} | tail -1" \; | less
and the synthesis:
find . -maxdepth 3 -name 'log' -exec sh -c "echo -n {} ; grep Rfree {} | tail -1 ; grep -m1 'atoms.*residues' {}" \; | less
Friday, February 18, 2005
Thursday, February 17, 2005
Tuesday, February 15, 2005
Monday, February 14, 2005
Sunday, February 13, 2005
more funky unix command lines:
the first one did what i needed it to do. it got me the lines
that said
out of a 18k line logfile. nice.
however, it got both test cases, and the second was a redundant
error checking test case where the wrong hand was run through
ARP/wARP. like this:
which wasn't really so bad. however, i wanted just the first match. the second attempt
didn't work, i leave it as an exercise to the reader to figure out why. the third, though
worked great:
just what i needed. please note for these that i didn't fix the rms calculation yet,
so please disregard it.
grep atoms generated*/gilu/log | grep residues
to
grep -m 1 atoms generated*/gilu/log | grep residues
to
grep -m1 "atoms.*residues" generated*/gilu/log
the first one did what i needed it to do. it got me the lines
that said
3375/3152 atoms 323/323.0/341/353 rms=0.402232675761 residues
out of a 18k line logfile. nice.
however, it got both test cases, and the second was a redundant
error checking test case where the wrong hand was run through
ARP/wARP. like this:
mistress 9 [~/cranktestdata] % grep atoms generated*/gilu/log | grep residues
generated-feb0205/gilu/log:3884/3665 atoms 257/257.0/257/387 rms=0.00495389765562 residues
generated-feb0405/gilu/log:3646/3665 atoms 151/151.0/151/387 rms=0.00698162302107 residues
generated-feb0405/gilu/log:3592/3665 atoms 9/9.0/97/387 rms=0.239588154743 residues
generated-feb0504/gilu/log:4023/3665 atoms 380/380.0/380/387 rms=0.00345315304147 residues
generated-feb0504/gilu/log:4639/3665 atoms 9/9.0/141/387 rms=0.248391814632 residues
generated-feb0805/gilu/log:4167/3665 atoms 382/382.0/383/387 rms=0.0697324167629 residues
generated-feb0805/gilu/log:4129/3665 atoms 19/19.0/306/387 rms=0.708511969219 residues
generated/gilu/log:4291/3665 atoms 381/381.0/381/387 rms=0.0807934893814 residues
generated/gilu/log:4142/3665 atoms 18/18.0/313/387 rms=0.713575518255 residues
which wasn't really so bad. however, i wanted just the first match. the second attempt
didn't work, i leave it as an exercise to the reader to figure out why. the third, though
worked great:
mistress 10 [~/cranktestdata] % grep -m1 "atoms.*residues" generated*/gilu/log
generated-feb0205/gilu/log:3884/3665 atoms 257/257.0/257/387 rms=0.00495389765562 residues
generated-feb0405/gilu/log:3646/3665 atoms 151/151.0/151/387 rms=0.00698162302107 residues
generated-feb0504/gilu/log:4023/3665 atoms 380/380.0/380/387 rms=0.00345315304147 residues
generated-feb0805/gilu/log:4167/3665 atoms 382/382.0/383/387 rms=0.0697324167629 residues
generated/gilu/log:4291/3665 atoms 381/381.0/381/387 rms=0.0807934893814 residues
just what i needed. please note for these that i didn't fix the rms calculation yet,
so please disregard it.
Saturday, February 12, 2005
Tuesday, February 08, 2005
permutations and combinations. A program to generate all of these. I didn't use the program, but found the math on this page useful.
Monday, February 07, 2005
Sunday, February 06, 2005
Friday, February 04, 2005
I had a bunch of run scripts that had line in them "for n in caufd dna360" etc. I wanted to see which ones I had forgotten. Here's what I came up with:
ll generated | cut -c "57-" | cut -f 1 -d "/" | sort > 1
grep for run-all* | awk '{for(i=4;i>=NF;i++){print $i}}' | sort > 2
cat 1 2 | sort | uniq -c | less | grep 1
Thursday, February 03, 2005
mistress 17 [~/cranktestdata/generated] % qstat -n | grep node | fold -w 1 | sort | uniq -c
102
51 -
51 /
18 +
46 0
46 1
23 2
7 3
6 4
5 5
6 6
5 7
5 8
4 9
51 d
51 e
51 g
51 n
51 o
mistress 18 [~/cranktestdata/generated] % qstat -n | tail -10
node-g16/1
27174.mistress. terry dque NaAlH4-2-1 21198 6 1 15gb -- R 03:31
node-g26/1+node-g26/0+node-g24/1+node-g24/0+node-g23/1+node-g23/0+node-g22/1
+node-g22/0+node-g21/1+node-g21/0+node-g02/1+node-g02/0
27218.mistress. terry dque Li-Pnma 18297 1 1 8gb -- R 00:58
node-g28/1+node-g28/0
27227.mistress. girts dque res.pbs 30134 1 1 1gb -- R 00:45
node-g03/1
27228.mistress. terry dque Li-Pnma 28895 1 1 8gb -- R 00:43
node-g27/1+node-g27/0
Wednesday, February 02, 2005
Tuesday, February 01, 2005
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