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p2p doc

<h1>Using the Peer-to-peer (p2p) Update Services</h1>
The SEED has been set up to offer p2p update services for
<li>annotations of genes,
<li>assignments of function to genes (the differences between annotations and assignments of
function are described below), and
<li>the collection of rewrite rules that can be used to try to rewrite gene function assignments to 
a single consistent form.
To invoke any of these services, you click on the link provided just below the standard header in the <i>initial
search page</i> you get when you go to http://SERVER/FIG/index.cgi.  This brings you to a page in which you select a
<b>Source</b> and a <b>package</b>.  The <b>source</b> identifies a system that you will ask to send data to your copy of the SEED.
The <b>package</b> describes the type of data you want.
To make this all work properly, you need to actually maintain a table describing who you plan on
visiting to get data.  The file is <b>~fig/FIGdisk/seed_peers.cfg</b>.  This file is a 2-column, tab-separated table.
We allow comment lines that begin with a "#".
The first field in each line is a URL of the form
where "hostname" specifies a host running a version of the SEED.  The second field in each non-comment line should be 
a description of that host.  For example,
# an example seed_peers.cfg file
http://seed-linux-1.mcs.anl.gov/FIG	The ANL Linux MySql SEED
http://seed-linux-2.mcs.anl.gov/FIG	The ANL Linux Postgres SEED
http://seed-mac-1.mcs.anl.gov/FIG	The ANL Postgres G5 running Panther
http://seed-mac-2.mcs.anl.gov/FIG	The ANL Postgres G5 running Janguar
This file is used by our interface to specify the set of systems from which you can
acquire new versions of code and data.  For now, you must edit this file with your 
favorite text editor.  If we get funded, we will put in a GUI to hide some of the gory details.
Our intent is to add software that interrogates a registry to dynamically find spots that have
the data you need, but for now...
<h2>Updating Your Code</h2>
The ability to update your code is critical.  If that works properly, we can get new versions of code
to you.  It might be worth noting that you can report bugs or desires by sending mail to <b>seed-tech@mcs.anl.gov</b>.
The seed developers read this mail and try to offer reasonable responses.  Please keep in mind that, at this point,
we have no funding and these people are working for the joy of it.
So, to actually grab the currently running version of code from someone, you choose a source, choose <i>Lightweight Code</i> as your choice of package, and click on <b>Start Update</b>.  An attempt to update your code will take place, and the results
will be reported to you.  To understand some ofg the messages you might get, you should know that releases of code
are identified with a release ID of the form <i>x.y.z</i>.  You can think of the three positions as specifying
major release, minor release, and revision.  You would normally update to a later release, although you are allowed 
to move to older releases.
You should understand that, once you have acquired a release, you retain it.  You can switch to any release that
is already on your system by typing a Unix command similar to
	switch_to_release 0.0.1   (of course, any release that you have works)

<h2>Updating Annotations of Genes</h2>

There is a distinction between annotations and assignments.  Assignments specify the functions of genes.  Annotations
are essentially free-form comments that are time-stamped and attached to genes.  When you ask for an
annotation update, you are asking for whatever comments people have attached to genes.  You do not
have to worry about "overwriting your values", since all that happens is that the comments are added
to your existing set (and merged in by the exact time-stamp).
So, to actually get someone's annotations, you pick a source and <b>Annotations</b> as the selected package.
When you click <b>Start Update</b> you will get a page asking you to select a set of genomes.  You can specify
<b>all</b>, but this can result in a substantial transfer of data.  If you know exactly what organisms you
really care about (and believe that the source as annotated particularly well), pick the exact set of genomes.
The acquired annotations will be merged with your existing set (eliminating any duplicates).

<h2>Updating Assignments</h2>

Assignments are actual assertions that particular genes implement specific functions.
To actually get someone's assignments, you pick a source and <b>Assignments</b> as the selected package.
When you click <b>Start Update</b> you will get a page asking you to select a number of things.  You specify
the set of genomes you are interested in.  Optionally,you can specify the name of the individual who made the 
assignments (i.e., you can restrict the transfer to assignments made by a specific individual), and optionally 
you can specify a date indicating that you only wish assignments made since that point in time.

<h2>Updating Translation Rules</h2>

Finally, you can update <i>translation rules</i>.  Each user has a set of translation rules that can be used
to rewrite functions in an attempt to create consistent function assignments.  Each user can extend his set and 
acquire rules from others.  However, when importing rules, you need to realize that you may be attempting to
import rules that are inconsistent with your own.  The SEED will block the import of such rules and will
report them by logging message into FIGdisk/FIG/Data/Global/translation.update.results.log.  Eventually,
we will create a GUI to allow you to inspect all added/rejected rules.  For now, pick your favorite text

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