BEE-spoke-data/govdocs1-by-extension huggingface dataset:
Accelerator Physics meeting minutes
11/1/2001
Present: J. Wei, J Galambos,M. Doleans, S. Danilov, S. Aleksandrov,
 E. Tanke, S. Kim, D.Jeon, J. Holmes, P. Chu, J. Stovall
S. Henderson is checking the Ring and transfer line magnet power supply
specifications. Some power supplies have specs. > 2 times the requirements
and these are being revisited. There was also a discussion on the need to get
 the effective magnetic length. For each type magnet, it is desireable that
it be measured once, but the presesnt measurement plan allows for use of a
 model supplied number, due to cost concerns.
J. Wei discussed the FRont End Ion Source modeling needs. Presently
PBGun is being used, but it needs to be benchmarked. The model results
(beam distributions) should be compared to the emittance measurements. He
also noted there is a suggestion from LBNL to do beam scraping in the DTL.
Eugene Tanke discussed linac activities: The DTL streeing power supply
procurement package i done, the CCL SCL steerer power supplies are finalized,
the CCL quad pakage is out and the SCL quad package is being finalized.
J. Stovall noted that Accel is building the CCL, and that the delivery schedule
is ~ 22 months, slightly longer than anticipated. Also, the number of and
final positions of the wire scanners needs to be finalized.
There was a discussion on the number of CCL correctors to be
 classified as critical. Presently all are critical, but Stovall questioned this.
The SCL area, a PCR to introduce piezo-compensation of the Lorentz detuning is
being done. Sang-ho is working on the beam dump window stress analysis,
crowbar design for the JLab high power test stand, and analyzing transient
Lorentz  detuning.
In the Ring area, there is focus on the extraction kicker impedance, and the
effect on beam stability. New calculations show the inclusion of chromaticity
increases the threshold by a factor of 2-3.  Also plans are to remeasure the
kicker impedance with no ferrite, do discern its impact. Also a heating test
will be done to
address this concern.
The following is a file prepared partly by Richa Agarwala describing a
simple use of SimIBD on a real data set. I have removed references
to the data set to avoid revealing any research information.
This describes a cookbook usage. 


The reference for SimIBD is:

Davis S, Schroeder M, Goldin LR, Weeks DE (1996) Nonparametric simulation-based
statistics for detecting linkage in general pedigrees. 
Am J Hum Genet 58:867-880.



Running SimIBD
--------------------------------------------------
Summary
------------------------------
Do not use SimIBD version 1.x.y as it has been superseded by version 2.1
(and possibly later versions).
Required input files:
             locusXYZ:LINKAGE/FASTLINK format locus file
             pedigree file: LINKAGE/FASTLINK format pedigree file
One output file is produced.
SimIBD currenlty does only 2-point analysis.
--------------------------------------------------------------------------------

Simplest usage: simibd  <pedigree file> <locus file>


SimIBD produces two output files:
  simibd.out
  simibd.aff.out

Steps:
0. simibd <pedigree file> <locus file>. 
   We are only doing SimIBD computation and not SimAPM or SimKIN.
1. Choose weighting function from
     A : f(p) = 1
     B : f(p) = 1/sqrt(p)
     C : f(p) = 1/p
  Choose option B; this is strongly recommended in the documentation.
2. Specify number of replicates; a recommended value is in brackets,
   but you must specify some number
3. Specify number of BOOTSTRAPS per SIMULATED NULL replicate.
   Again, a number is recommended in brackets.
4. Specify number of SIMULATED NULL DISTRIBUTION replicates total.
   Again a number is recommended in brackets.
5. Trait locus number: 1
   This is the LINKAGE convention.
6. Enter the marker locus number:


This creates simibd.out which summarizes the results of the runs and 
simibd.aff.out which is the full output from affected comparisons.

The important table is simibd.out with headings:

  Family   ZObs    # Aff.  Weight  Weighted ZObs  PValue   Range

This will be followed by 1 row of results for each pedigree in your
data set.

The Weight column here has to do with the number of affected people
in the family, and is unrelated to the allele frequency weight
that you were asked to select.
For this program you should literally look at the "bottom line" and
see if the p-value is small. p-values < 0.05 are considered significant.

SimIBD can be run in parallel. Contact tran@helix.nih.gov for
more information.
#!/depot/path/expect -f
# Script to solve Jim Bonfield's game that won the 1991 Obfuscated C contest.
# Originally written by Don Libes, NIST, 1/3/91, later rewritten using
# John Tromp's highly optimized set of moves

# If you want to play part of the game, just put in an "interact;exit"
# anywhere and expect will do the first part, leaving the rest for you!
# (That was how I solved the game in the first place - by pushing the
# interact further and further back as I figured things out.)

proc do {moves} {send $moves; expect *}

trap exit SIGINT
set timeout 1000;# need a long timeout because expect can get far enough
		 # ahead of the game that by the final expect, we have to
		 # wait quite a bit for the I/O to complete!
spawn puzzle

# In the opening scene, we don't know exactly what to watch for (a lota #s?),
# so just wait for a 1000 or so characters to go by!
set count 0
while {$count<1000} {
	expect -re .+
	incr count [llength [split $expect_out(buffer) ""]]
}

# opening
do kkklllllljjlll;	# to key room
do kkllljjhjkhhhhh;	# make gems, push left-key-1 into door
do lllllkkll;		# to key room & pick up gems in upper-right-hand corner
do jjjhjjjjhkhkhhk;	# take remaining gems, push up-key free
do jllk;		# push boulder up as long as we're here
do jjllkkhkkkhhjjl; 	# manipulate left-key-2 and boulder
do hhhhhhh;		# push up-key into door-room
do jhkkllllll;		# unlock door and go back to key room
do jjllklkhhhhhhhh;	# get behind left-key-2 and push into door room
do lllkkhhhhjj;		# leave left-key-2 next to door
do lllllllkkhjljhhhhhh;	# go back to key-room, return with down-key
do jhhhhkkklljjkkhhjjjllklj;	# unlock two remaining doors
   # retrieve boulder from key room and smash into boulder at bottom
do llllllkklljjkklljjjhhljjhhkklkhhhhhhhhlllkkhhhhjjkkhhjjjllkljjjjjjjj
do hkkkkhhhllkk;	# go back up, making/picking up gems along the way
do hhhhkhkkkhjjjjlllll;	# make/collect gems from upper-left-hand corner
do kljjjjjjhjhllll;	# move remaining boulder down, pick up remaining gems
do hkkllkkkkjjj;	# make/pick up gems from central chute
do ljjhkkkk;		# move uncompressible into shute
do ljjjhjlll;		# move boulder out of shute, make/pickup gems on bottom
do klljllkhhhhhlll
do lljlllhkhhhhhhjhkkk;	# move another unc into shute
do jjlllllllljlkklkkkhjhjljjhhkljl;	# get beneath boulder, prepare to lift
do kkkkkklkhkl;		# pick up lots of gems
do kkhjjjjjljhkhjjlj;	# get behind key, prepare to move to door
do hhhhhhhhjhklkhhhhhhhhhk;		# unlock door, enter & pick up a gem
do hkhljjjjh;# pick up remaining gems
do jllkhklllllllkljhjlllllllllll;	# move last boulders together
# send final command by hand to wait for congrat message
send l
expect -re "Well done!"
"Minority report and motion to adjourn &#034;sine die.&#034; Speech of Isidor Bush, of Saint Louis, delivered in the Missouri State Convention, June 29, 1863.","","03600","0001.gif","1","1","","0001.tif"
"Minority report and motion to adjourn &#034;sine die.&#034; Speech of Isidor Bush, of Saint Louis, delivered in the Missouri State Convention, June 29, 1863.","","03600","0002.gif","2","2","","0002.tif"
"Minority report and motion to adjourn &#034;sine die.&#034; Speech of Isidor Bush, of Saint Louis, delivered in the Missouri State Convention, June 29, 1863.","","03600","0003.gif","3","3","","0003.tif"
"Minority report and motion to adjourn &#034;sine die.&#034; Speech of Isidor Bush, of Saint Louis, delivered in the Missouri State Convention, June 29, 1863.","","03600","0004.gif","4","4","","0004.tif"
"Minority report and motion to adjourn &#034;sine die.&#034; Speech of Isidor Bush, of Saint Louis, delivered in the Missouri State Convention, June 29, 1863.","","03600","0005.gif","5","5","","0005.tif"
"Minority report and motion to adjourn &#034;sine die.&#034; Speech of Isidor Bush, of Saint Louis, delivered in the Missouri State Convention, June 29, 1863.","","03600","0006.gif","6","6","","0006.tif"
"Minority report and motion to adjourn &#034;sine die.&#034; Speech of Isidor Bush, of Saint Louis, delivered in the Missouri State Convention, June 29, 1863.","","03600","0007.gif","7","7","","0007.tif"