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Revision 1.2 - (download) (as text) (annotate)
Wed Dec 7 19:38:22 2005 UTC (13 years, 10 months ago) by golsen
Branch: MAIN
CVS Tags: rast_rel_2014_0912, rast_rel_2008_06_18, rast_rel_2008_06_16, rast_rel_2008_07_21, rast_rel_2010_0928, rast_2008_0924, rast_rel_2008_09_30, caBIG-13Feb06-00, rast_rel_2010_0526, rast_rel_2014_0729, rast_rel_2009_05_18, caBIG-05Apr06-00, rast_rel_2009_0925, rast_rel_2010_1206, rast_rel_2010_0118, rast_rel_2009_02_05, rast_rel_2011_0119, rast_rel_2008_12_18, rast_rel_2008_10_09, rast_release_2008_09_29, rast_rel_2008_04_23, rast_rel_2008_08_07, rast_rel_2009_07_09, rast_rel_2010_0827, myrast_33, rast_rel_2011_0928, rast_rel_2008_09_29, rast_rel_2008_10_29, rast_rel_2009_03_26, rast_rel_2008_11_24, HEAD
Changes since 1.1: +1 -1 lines
Don't mean to be pedantic, but I figured that I might as well add newlines
at the end of text files that lack one.  Identified with a script:

/bin/sh -O extglob -c 'for f in */*.@(c|css|html|js|pl|pm|py|TXT); do perl -e '"'"'while(<>) {$s = ! /\n$/} exit $s'"'"' $f || echo $f; done'

fixed with a script:

for file in _list_; do echo "" >> $file; done

Higher Level Constructs

The Higher Level Constructs table provides a way to define entities
that can be formed from gene products.

For exqample, if a multi-meric enzyme comprises subunits alpha and
beta, we would put two roles in its subsystem, one for each subunit.
Those roles might have one, none, or several genes assigned to them
according to what is present in the organism.

The Higher Level Constructs tool provides a means to express these
constructs.  The tool is a simple table with two columns, "Construct Name"
and "Requires."

In "Construct name" enter the name of the Construct your are defining, e.g., GOGAT_NADPH.
In the "Requires" column, enter a comma separated list of all the things that are
required in order for the construct to be present.  In other words, it is a list that
is AND-ed together.

Each entry in the requirements list can be one of two things.  It can either be the
abbreviation for a functional role or it can be the name of another construct.  For
convenience, you do not need to enter the abbreviation, but can enter the row number
and, when you hit the "Update" button, the row number will be converted to the
abbreviation for you.

A Construct name can  be listed multiple times.  This corresponds to OR's.  For

Constsruct Name		Requires

This table says that GOGAT_NADPH is present when  GOGDP1 AND GOGDP2 are both
present.  These are abbreviations of functional roles in the Ammonia Assimilation
subsystem.  Also, GOGAT is present when either GOGAT_NADPH or GOGATF or GOGATD
are present.  GOGAT_NADPH is the Construct defined in the first line.  The other
two are abbreviations of subsystem roles.


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