beagle.doc

地球模拟器

            SizeDiv | size diversity: (- sum of p * log(p)), where p is the
                      proportion of all adult cells in the soup that fall in
                      a size class.
            AgeSize | average age of sizes: whenever a new size class appears
                      or reappears, its age starts counting at zero.  At each
                      instant of time, the age of all size classes is summed
                      and divided by the number of size classes.
            NumGeno | number of genotypes: total number of distinct genotype
                      classes of adult cells living in the soup.
            GenoDiv | genotype diversity: (- sum of p * log(p)), where p is the
                      proportion of all adult cells in the soup that fall in
                      a genotype class.
            AgeGeno | average age of genotypes: whenever a new genotype class
                      appears or reappears, its age starts counting at zero.
                      At each instant of time, the age of all genotype classes
                      is summed and divided by the number of size classes.

 data file = divdat.1

     This is the name of the file containing the diversity indices
output by the Diverse program.  In long runs, a series of these files may be
produced, with the names divdat.1, divdat.2, divdat.3, ..., divdat.X.  The
Diversity option will read each of them in turn, if you specify the name of
the first one.

 range file = divrange

     This is the name of the file containing the ranges of the diversity
indices, output by the Diverse program.

 shrink factor      = 1

     The axes will normally fill the whole screen, but if you use a shrink
factor of less than 1, the y axis will shrink to fill only part of the screen.
This option was introduced to get the display to fit a device that was
cropping the vertical dimension (when making a video tape).

====== TEMPLATE ============================================================

     This option provides a display of the structure of a genome, as
indicated by the arrangement of instructions using templates.  Since all
instructions that affect the control flow of the program (jump, call) use
templates, this provides a sort of schematic of the program structure.
The Template option will read and display genomes from the genebank.
You will need to know what genome are stored there.  Use the arg t option
to get a list of the genomes stored in any of the .gen files in the genebank:
e.g.:  arg t 0080.gen
will produce a list of the genotypes in the 80 size class in the 0080.gen
file.

     Selecting the Template option generates a window that looks like this:

+templates--------------------------+
| genebank path = c:\tierra\gb      |
| genefile name = 0080.gen          |
| genotype      = aaa               |
| min temp size = 3                 |
+-----------------------------------+

     Within this window, use the cursor key to move to an option, then type
in your choice.  When you have all the options as you want them, use Ctrl-Enter
to activate the Template display.  Use the Escape key to exit from the
Template option.

     An explanation of the Template options follows:

 genebank path = c:\tierra\gb

     This is the path to the genebank, where the files containing the saved
genomes of the creatures are written by the Tierra program (XXXX.gen,
XXXX.tmp, XXXX.mem files).

 genefile name = 0080.gen

     This is the name of the file in the genebank containing the genomes of
the size that you want to examine.

 genotype      = aaa

     This is the actual genotype name of the creature that you want to examine,
of the size indicated by the name of the genefile.

 min temp size = 3

     You might want to ignore templates below a certain size.  There is a
MinTemplSize parameter in the soup_in file used by the Tierra simulator.
Templates below this size are not recognized as templates.  You should set
min temp size to the same value as was set in the soup_in file of the run
that produced the genome you are examining.

     When you run the Template program by hitting Ctrl-Enter, you will get
a window that looks like this (for 0080aaa):

        +-------------------------+
        | locus:   9, adrb  0000  |
        | locus:  16, adrf  0001  |
        | locus:  28, call  0011  |
        | locus:  34,  jmp  0010  |
        | locus:  54,  jmp  0100  |
        | locus:  61,  jmp  0101  |
        +-------------------------+

     The second column (numbers) contains the position in the genome of the
instructions using templates.  The third column contains the names of the
instructions at those positions that use the templates.  The fourth column
contains the actual templates used by the instructions at those positions.

====== PROBE ===============================================================

     This option allows you to compare two genomes by probing the sequence of
one with the sequence of the other.  Probe slides the probe sequence along
the genome sequence and determines the positions of the major alignments.
These alignments are then reported to you, and you may choose how many you
want to recognize.  Then the two genomes are displayed together, in their
alignments, with the differences highlighted.  The Probe program makes a
heroic effort to deal with complications like multiple allignments, insertions
and deletions, and overlaping alignments.  However, it fails miserably for
some of the more complicated cases (the ability to detect insertions or
deletions may not be working).  This program is not mature, but it
provides some help in comparing sequences.

     
     The Probe option will read and display genomes from the genebank.
You will need to know what genome are stored there.  Use the arg t option
to get a list of the genomes stored in any of the .gen files in the genebank:
e.g.:  arg t 0080.gen
e.g.:  arg t 0045.gen
will produce a list of the genotypes in the 80 size class in the 0080.gen
file, and in the 45 size class in the 0045.gen file.

     Selecting the Probe option generates a window that looks like this:

+probe----------------------------+
| genome path = c:\tierra\gb      |
| genome file = 0080.gen          |
| genome      = aaa               |
| probe path = c:\tierra\gb       |
| probe file = 0045.gen           |
| probe      = aaa                |
+---------------------------------+

     Within this window, use the cursor key to move to an option, then type
in your choice.  When you have all the options as you want them, use Ctrl-Enter
to activate the Probe display.  Use the Escape key to exit from the
Probe option.

     An explanation of the Probe options follows:

 genome path = c:\tierra\gb

     This is the path to the genebank, where the files containing the saved
genomes of the creatures are written by the Tierra program (XXXX.gen,
XXXX.tmp, XXXX.mem files).

 genome file = 0080.gen

     This is the name of the file in the genebank containing the genomes of
the size that you want to examine.

 genome      = aaa

     This is the actual genotype name of the creature that you want to compare
to the probe, of the size indicated by the name of the genome file.

 probe path = c:\tierra\gb

     This is the path to the genebank, where the files containing the saved
genomes of the creatures are written by the Tierra program (XXXX.gen,
XXXX.tmp, XXXX.mem files).

 probe file = 0080.gen

     This is the name of the file in the genebank containing the genomes of
the size that you want to examine.

 probe      = aaa

     This is the actual genotype name of the probe that you want to slide
along the genome indicated by the first three options, (size indicated by the
name of the probe file).

     When you run the Probe program by hitting Ctrl-Enter, you will get
a window that looks like this (for 0080aaa and 0045aaa):

        +----------------------------------------------+
        | position:  0   fit: 44   diff: 0   idpos: 0  |
        | position: -1   fit: 16   diff: 0   idpos: 0  |
        | position:  1   fit: 14   diff: 0   idpos: 0  |
        | position: 25   fit: 13   diff: 0   idpos: 0  |
        | position: 23   fit: 12   diff: 0   idpos: 0  |
        | position:  7   fit: 11   diff: 0   idpos: 0  |
        +----------------------------------------------+

     The first pair of columns (positon) contains the relative position of the
alignments of the two genomes.  0 indicates that the alignment occurred with
the first instruction of the two genomes together, -1 indicates that the first
instruction of the genome is aligned with the second instructions of the probe,
1 indicates that the first instruction of the probe is aligned with the
second instruction of the genome.

     The second pair of columns (fit) contains the goodness of fit, as the
number of instructions that matched between the genome and probe in that
alignment.  In this example, the probe is 45 instructions long, so a match
of 44 indicates that only one instruction is diferent between the probe and
genome.  

     The third pair of columns (diff) indicates a difference in length
resulting from an insertion (positive) or deletion (negative).

     The fourth pair of columns (idpos) indicates the position of the
insertion of deletion.

     When this window appears, you examine the alignments to decide how many
you want to use.  In this case, there is only one really good alignment, so
we will use one.  Now hit Esc, and another window will appear that looks
like this:
                                           +number of matches to use-----+
                                           | number of matches = 1       |
                                           +-----------------------------+

     You either accept the suggested value (1) or change it, the hit
Ctrl-Enter, and the alignments will be displayed in two windows that look
like this:

+instruction list--------------------------------------------------------------+
|   0:nop_0  1:nop_1  2:or1    3:shl    4:zero   5:if_cz  6:sub_ab 7:sub_ac    |
|   8:inc_a  9:inc_b  a:dec_c  b:inc_c  c:pushax d:pushbx e:pushcx f:pushdx    |
|   g:pop_ax h:pop_bx i:pop_cx j:pop_dx k:jmp    l:jmpb   m:call   n:ret       |
|   o:mov_cd p:mov_ab q:moviab r:adr    s:adrb   t:adrf   u:mal    v:divide    |
+------------------------------------------------------------------------------+
+genome-to-probe match:  genome (top) - 0080aaa    probe - 0045aaa ------------+
| 11114233os00007pt0001861101um0011vk001051100cde1010qa5k010089k010151011ihgn1 |
| 11114233os00007pt0001861101um0011vk001051110c                                |
|                                                                              |
| 1105                                                                         |
|                                                                              |
+------------------------------------------------------------------------------+

     The highlighting is not indicated above, but it indicates where the two
genomes do not match.

====== PREPARE - FRAGMENT ===================================================

     If you want to display a portion of a long run, you may edit the long
run using the "Prepare - Fragment" option from the Beagle menu, or the
stand-alone fragment utility.  This will produce an output file which may
be read by itself, or you may produce several fragments, and then concatenate
them together in order to produce an edited version of a longer run.  The
edited fragment(s) resulting from this process MUST be used as the input file
operated on by the "Prepare - Run Info" option to produce the run_info files
read by the Bars and Trace displays.  Beware that if the fragments begin or
end at the same time that the "update" attempts to create a new list, very bad
interactions can result.  Just be sure you don't try to fragment and update at
the same time (if you use the default update frequency of 100, don't break
your fragments at 100 million marks).

   select the Prepare option
   then select the Fragment option

     Selecting the "Prepare - Fragment" option will produce a window that
looks like this:

+fragment----------------------------------+
| directory    = c:\tierra\td              |
| input file   = break.1                   |
| output file  = fragment.run              |
| start time   = 0                         |
| stop time    = 1                         |
+------------------------------------------+

     Within this window, use the cursor key to move to an option, then type
in your choice.  When you have all the options as you want them, use Ctrl-Enter
to activate the "Prepare - Fragment" process.  Use the Escape key to exit from
the window.

     An explanation of these "Prepare - Fragment" options follows:

 directory  = c:\tierra\td

     This is the path to the file containing the birth and death records
output by the Tierra program (the break.X files).

 input file = break.1

     This is the name of the file containing the birth and death records
output by the Tierra program.  In long runs, a series of these files may be
produced, with the names break.1, break.2, break.3, ..., break.X.  The
Prepare - Fragment program will read each of them in turn, if you specify the
name of the first one.

 output file  = fragment.run

     This is the name of the fragmentary output file that will be produced.

 start time   = 0

     This is the start time of the fragment that you wish to produce, in
millions of instructions.

 stop time    = 1

     This is the stop time of the fragment that you wish to produce, in
millions of instructions.  Be sure the start and stop times do not coincide
with update times.  The stop time must be greater than the start time.

     The "Prepare - Fragment" option uses a lot of memory.  On long runs,
it may run out of memory.  If this happens, you should use the stand-alone
fragment tool.  It takes the same input parameters, but by not being bundled
with the rest of the Beagle tools, it has a lot more memory to spare.  Just
type fragment the DOS prompt.