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revision 1.7, Wed Jul 28 21:21:59 2004 UTC revision 1.8, Wed Jul 28 22:42:21 2004 UTC
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1  <h1>SEED Administration</h1>  <h1>SEED Administration</h1>
2  <p>This tutorial discusses a number of issues that you will need to know about  
3    in order to install, share, and maintain your SEED installation.</p>  <p>
4  <h2>Backing Up Your Data</h2>  This tutorial discusses a number of issues that you will need to know about
5    in order to install, share, and maintain your SEED installation.
6    It is organized as follows:
7    </p>
8    
9    <ul>
10    <li><A HREF="#backups">
11         Backing Up Your Data
12    </A>
13    
14    <li><A HREF="#copying">
15         Copying a Version of the SEED
16    </A>
17    
18    <li><A HREF="#multiple_copies">
19         Running Multiple Copies of the SEED
20    </A>
21    
22    <li><A HREF="#adding_genomes">
23    Adding a New Genome to an Existing SEED
24    </A>
25    
26    <li><A HREF="#sims">
27        Computing Similarities
28    </A>
29    
30    <li><A HREF="#deleting_genomes">
31        Deleting Genomes from a Version of the SEED
32    </A>
33    
34    <li><A HREF="#reintegrate_sims">
35        Periodic Reintegration of Similarities
36    </A>
37    
38    <li><A HREF="#pins_and_clusters">
39        Computing "Pins" and "Clusters"
40    </A>
41    
42    </ul>
43    
44    
45    <h2 id="backups">Backing Up Your Data</h2>
46  The data and code stored within the SEED are organized as follows:  The data and code stored within the SEED are organized as follows:
47  <pre>  <pre>
48          ~fig                                 on a Mac: /Users/fig; on Linux: /home/fig          ~fig                                 on a Mac: /Users/fig; on Linux: /home/fig
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97  would be a reasonable way to make a backup.  The copy preserves  would be a reasonable way to make a backup.  The copy preserves
98  permissions, copies recursively, and does not follow symbolic links.  permissions, copies recursively, and does not follow symbolic links.
99  <br>  <br>
100  <h2>Copying a Version of the SEED</h2>  <h2 id="copying">Copying a Version of the SEED</h2>
101    
102  To make a second copy of the SEED (either for a friend or for yourself), you should use tar  To make a second copy of the SEED (either for a friend or for yourself), you should use tar
103  to preserve a few symbolic links (which are relative, not absolute; this means that they can  to preserve a few symbolic links (which are relative, not absolute; this means that they can
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197  <blockquote>  <blockquote>
198    <p><a href="http://www-unix.mcs.anl.gov/SEEDWiki/moin.cgi/SeedInstallationInstructions">      http://www-unix.mcs.anl.gov/SEEDWiki/moin.cgi/SeedInstallationInstructions</a></p>    <p><a href="http://www-unix.mcs.anl.gov/SEEDWiki/moin.cgi/SeedInstallationInstructions">      http://www-unix.mcs.anl.gov/SEEDWiki/moin.cgi/SeedInstallationInstructions</a></p>
199  </blockquote>  </blockquote>
200  <h2>Running Multiple Copies of the SEED</h2>  <h2 id="multiple_copies">Running Multiple Copies of the SEED</h2>
201    
202  For individual users that use the SEED to support comparative analysis, a single copy is completely  For individual users that use the SEED to support comparative analysis, a single copy is completely
203  adequate.  Adding genomes can usually be done without disrupting normal use, and a very occasional major  adequate.  Adding genomes can usually be done without disrupting normal use, and a very occasional major
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354  desirable to spend a little more and get at least 1 gigabyte of main  desirable to spend a little more and get at least 1 gigabyte of main
355  memory and 200 gigabytes of external disk.  memory and 200 gigabytes of external disk.
356  <br>  <br>
357  <h2>Adding a New Genome to an Existing SEED</h2>  <h2 id="adding_genomes">Adding a New Genome to an Existing SEED</h2>
358  To add a new genome to a running SEED is fairly easy, but there are a  To add a new genome to a running SEED is fairly easy, but there are a
359  number of details that do have to be handled with care.  number of details that do have to be handled with care.
360  <p>  <p>
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606  The <i>add_genome</i> request will add your new genome and queue a computational request that similarities  The <i>add_genome</i> request will add your new genome and queue a computational request that similarities
607  be computed for the protein-encoding genes.  be computed for the protein-encoding genes.
608    
609  <h2>Computing Similarities</h2>  <h2 id="sims">Computing Similarities</h2>
610    
611  Adding a genome does not automatically get similarities computed for the new genome; it queues the request.  Adding a genome does not automatically get similarities computed for the new genome; it queues the request.
612  To get the similarities actually computed, you need to establish a computational environment on which  To get the similarities actually computed, you need to establish a computational environment on which
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657  interfaces for handling high-volume requests.  At FIG, we will maintain a set of instructions on how to set up  interfaces for handling high-volume requests.  At FIG, we will maintain a set of instructions on how to set up
658  your configuration to exploit these resources.  your configuration to exploit these resources.
659    
660  <h2>Deleting Genomes from a Version of the SEED </h2>  <h2 id="deleting_genomes">Deleting Genomes from a Version of the SEED</h2>
661    
662  There are two common instances in which one wishes to delete genomes from a running version of the SEED: one is  There are two common instances in which one wishes to delete genomes from a running version of the SEED: one is
663  when you wish to replace an existing version of a genome (in which case the replacement is viewed as first  when you wish to replace an existing version of a genome (in which case the replacement is viewed as first
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695          rm -rf /Volumes/Tmp/ExtractedData          rm -rf /Volumes/Tmp/ExtractedData
696  </pre>  </pre>
697    
698   <h2>Periodic Reintegration of Similarities</h2>   <h2 id="reintegrate_sims">Periodic Reintegration of Similarities</h2>
699    
700  When the initial SEED was constructed, similarities were computed.  For most similarities of the form  When the initial SEED was constructed, similarities were computed.  For most similarities of the form
701  "Id1 and Id2 are similar", entries were "recorded" for both Id1 and Id2.  This is not always true,  "Id1 and Id2 are similar", entries were "recorded" for both Id1 and Id2.  This is not always true,
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713  </pre>  </pre>
714  The job will probably run for quite a while (perhaps as much as a day or two).  The job will probably run for quite a while (perhaps as much as a day or two).
715    
716  <h2>Computing "Pins" and "Clusters"</h2>  <h2 id="pins_and_clusters">Computing "Pins" and "Clusters"</h2>
717    
718  The SEED displays potentially significant clusters on prokaryotic chromosomes.  In the  The SEED displays potentially significant clusters on prokaryotic chromosomes.  In the
719  process of finding preserved contiguity, it computes "pins", which are simply a set of genes  process of finding preserved contiguity, it computes "pins", which are simply a set of genes

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