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Tue Feb 5 20:38:08 2008 UTC (11 years, 10 months ago) by overbeek
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
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<title>FIG Tutorials</title>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
</head>

<body>
<h1>FIG Tutorials</h1>
<p>The following tutorials are available:</p>
<ul>
  <li><a href="why_use_the_SEED.html">Why Use the SEED (a VERY basic tutorial)?</a>, a guide 
       to locating relevant gene clusters.</li>
  <li><a href="GettingStarted.html">Getting Started</a>, a guide to basic SEED
    use.</li>
  <li><a href="SEED_administration_issues.html">SEED Administration</a>, a guide to maintaining your SEED installation.</li>
  <li><a href="tut_abs.html">A Simple Abstraction for Computer Scientists and Mathematicians</a>.  An attempt to bridge the cultues..</li>
  <li><a href="API.html">API Tutorial</a>, a primer on programmatic use of the
    SEED system.</li>
  <li><a href="DataMining.html">Data Mining</a>, a guide to data mining with
    SEED.</li>
  <li><a href="phylogeny.html">Phylogeny Tools</a>, notes relating to a nascent effort to support phylogenetic analysis.</li>
  <li><a href="subsystem_tutorial.html">Subsystem Tutorial</a>, a tutorial to annotating subsystems.</li>
  <li><a href="subsystem_tutorial2.html">Subsystem Tutorial: a Continuation</a>, comments on where this might lead.</li>
  <li><a href="conflict_resolution.html">Subsystem conflict resolution</a></li>
  <li><a href="tyra_example.html">Ambiguity and the Choice of Functional Roles</a></li>
  <li><a href="splitting_roles.html">Splitting Functional Roles</a></li>
</ul>
<p>You may also find autogenerated POD documentation for the following modules:</p>
<ul>
  <li><a href="pod_docs/FIG.html">FIG</a></li>
  <li><a href="pod_docs/P2Pupdate.html">P2Pupdate</a></li>
  <li><a href="pod_docs/Subsystem.html">Subsystem</a></li>
</ul>
<p>Random documentation and position papers:</p>
<ul>
<li><a href="1KG.html">Project to Annotate 1000 Genomes and Produce 1000 Stoichiometric Matrices</a>
<li><a href="1KG_update.html">The Project to Annotate 1000 Genomes: An Update (Sept. 2007)</a>
<li><a href="exchange_of_assignments_and_annotations_Sept17_2004.html">Exchange of Assignments and Annotations</a>
<li><a href="SEED_functions.html">Some Comments on Gene Functions</a>
<li><a href="bioinf_first_classes.html">Comments on a Nonstandard First Class in Bioinformatics</a>
<li><a href="GenomeLog.html">The Genome Log as Implemented in the SEED: May 7, 2006</a>
<li><a href="evidence_codes.html">Evidence Codes for Annotations: Initial Thoughts</a>
<li><a href="code_to_invoke_compare_regions.html">How to compare regions for a set of PEGs</a>
<li><a href="subsystems_notion.html">An Attempt to Make the Notion <i>Subsystem</i> More Precise</a>
<li><a href="RAST_Supplement/AnnoComp.html">Rast paper supplement: RAST to KAAS comparison</a>
<li><a href="How_to_annotate_a_genome.html">How to Annotate a Single Genome</a>
<li><a href="TheCycle.html">Reflections on Accurate Annotations</a>
<li><a href="annotation_clearinghouse.html">The Annotation Clearinghouse</a>
</ul>

<hr>
<h2>Interesting Chromosomal Clusters</h2>
<br>
A set of <a href="http://www.theseed.org/Clusters/index.html">ramblings by Ross</a> relating to conserved chromosomal clusters.  
<hr>
<h2>HOPS: public depository of Hypotheses and Open Problems identified by SubSystem analysis</h2>
<br>
To get to the web site where we maintain a collection of open problems, conjectures and results
relating to missing genes <a href=http://www.theseed.org/HOPSS/>here</a>.

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