<commit_before><div id="static-content">
<div class="docbook-page">
  <div style="clear:" class="box">
<div class="heading2">What can I do with FlyMine?</div>
<div class="body">
<p style="">
      FlyMine is an integrated database of genomic, expression and
      protein data for <i>Drosophila</i>,
      <i>Anopheles</i> and
      <i>C. elegans</i>. Integrating data makes it
      possible to run sophisticated data mining queries that span
      domains of biological knowledge.
    </p>
<h3>Quick Search</h3>
<p style="">
      Enter any identifier or symbol in the search box on the FlyMine
      home page to access summary pages and integrated tools.  <!-- <a href="doc/tutorials/tutorial1-QuickSearch.shtml">Tutorial 1</a> <a href="doc/tutorials/tutorial2-ObjectDetailsPage.shtml">Tutorial 2</a>. --> </p>
<p style="">Some examples:
      <ul>
        <li>for the <i>Drosophila</i> gene zen, type
      FBgn0004053, CG1046, zen or any of its synonyms.<br />
</li>
        <li>for <i>A. gambiae</i> genes, use
      <a href="http://www.ensembl.org/Anopheles_gambiae/index.html">Ensembl</a> 
      identifiers (eg. ENSANGG00000001499).<br />
</li>
        <li>for <i>C. elegans</i> genes, use the 
      <a href="http://www.wormbase.org/">WormBase</a>
      identifiers or symbols (eg. M117.2, WBGene00003920, par-5).<br />
</li>
        <li>for proteins use <a href="http://www.uniprot.org">UniProt</a> identifiers or primary accessions (eg. 18C_DROME, P16909).<br />
</li>
      </ul>
    </p>
<h3>Browse Data Categories</h3>
<p style="">
      FlyMine presents data in categories, with each providing
      information on a particular type of data (for example Gene Expression
      or Protein Interactions). Use the icons in the Data box on the FlyMine
      home page to run a predefined template query or to build your
      own query (see below). Certain template queries, as well as the
      QueryBuilder itself, allow you to perform searches that span
      data from more than one category.
    </p>
<h3>Run Template Queries</h3>
<p style="">
      A number of specific queries have been predefined. These template queries range from 
      fairly simple queries to retrieve a particular type of data to more complex queries that 
      span the different types of data available in FlyMine. More template queries will be added 
      as FlyMine develops and we welcome <a href="http://pippin.flymine.org:8080/orth-test/feedback.do">suggestions</a>. Find lists of predefined template 
      queries in each data category or use the templates page to search through them.
      <!-- <a href="doc/tutorials/tutorial3-Templates.shtml">Tutorial 3</a> -->
    </p>
<h3>FlyMine QueryBuilder</h3>
<p style="">
      Advanced users can use a flexible query interface to construct
      their own data mining queries across the multiple integrated
      data sources, to modify existing template queries or to create
      your own template queries.
      <!-- <a href="doc/tutorials/tutorial6-QB.shtml">Tutorial 6</a> -->
    </p>
<h3>Operate on Lists</h3>
<p style="">
      All queries in FlyMine can be performed on lists of data. Lists can
      be created by typing or pasting in identifiers, or
      uploading a file. Data from previous queries
      can also be saved into a list using the boxes displayed
      underneath the query results. Saved lists of data can be used to
      constrain new queries, perform logical operations and can be
      analysed on a page that shows graphs, summary tables and statistics.  FlyMine now includes a number of public lists that we
      create and make available from published sources.
      <!-- <a href="doc/tutorials/tutorial4-BagsHistory.shtml">Tutorial 4</a> -->
    </p>
<h3>MyMine</h3>
<p style="">
      You can save your lists, queries and templates between sessions by
      <a href="http://pippin.flymine.org:8080/orth-test/login.do">creating an account</a> using the 'Log in' link
      in the header of every page.
      <!-- <a href="doc/tutorials/tutorial4-BagsHistory.shtml">Tutorial 4</a> -->
    </p>
    <h3>Help!</h3>
<p style="">
	To view context sensitive help for any page in FlyMine click on the 
	<a href="http://www.flymine.org/help/begin.html" 
	onclick="javascript:window.open('http://www.flymine.org/help/begin.html','_help','toolbar=0,scrollbars=1,location=1,statusbar=1,menubar=0,resizable=1,width=800,height=600');return false">
	<img src="/images/help.png" title="Click here for Help"/></a> in the the top right corner.  
	

    </p>
<br />
<br />
<!--
    <p style="">
      See the <a href="doc/tutorials/index.shtml">short tutorials</a> and 
      <a href="doc/manual/index.shtml">user manual</a> for more information.
    </p>
-->
</div>
</div><commit_msg>updated some broken links<commit_after><div id="static-content">
<div class="docbook-page">
  <div style="clear:" class="box">
<div class="heading2">What can I do with FlyMine?</div>
<div class="body">
<p style="">
      FlyMine is an integrated database of genomic, expression and
      protein data for <i>Drosophila</i>,
      <i>Anopheles</i> and
      <i>C. elegans</i>. Integrating data makes it
      possible to run sophisticated data mining queries that span
      domains of biological knowledge.
    </p>
<h3>Quick Search</h3>
<p style="">
      Enter any identifier or symbol in the search box on the FlyMine
      home page to access summary pages and integrated tools.  <!-- <a href="doc/tutorials/tutorial1-QuickSearch.shtml">Tutorial 1</a> <a href="doc/tutorials/tutorial2-ObjectDetailsPage.shtml">Tutorial 2</a>. --> </p>
<p style="">Some examples:
      <ul>
        <li>for the <i>Drosophila</i> gene zen, type
      FBgn0004053, CG1046, zen or any of its synonyms.<br />
</li>
        <li>for <i>A. gambiae</i> genes, use
      <a href="http://www.ensembl.org/Anopheles_gambiae/index.html" target="_new">Ensembl</a> 
      identifiers (eg. ENSANGG00000001499).<br />
</li>
        <li>for <i>C. elegans</i> genes, use the 
      <a href="http://www.wormbase.org/" target="_new">WormBase</a>
      identifiers or symbols (eg. M117.2, WBGene00003920, par-5).<br />
</li>
        <li>for proteins use <a href="http://www.uniprot.org" target="_new">UniProt</a> identifiers or primary accessions (eg. 18C_DROME, P16909).<br />
</li>
      </ul>
    </p>
<h3>Browse Data Categories</h3>
<p style="">
      FlyMine presents data in categories, with each providing
      information on a particular type of data (for example Gene Expression
      or Protein Interactions). Use the icons in the Data box on the FlyMine
      home page to run a predefined template query or to build your
      own query (see below). Certain template queries, as well as the
      QueryBuilder itself, allow you to perform searches that span
      data from more than one category.
    </p>
<h3>Run Template Queries</h3>
<p style="">
      A number of specific queries have been predefined. These template queries range from 
      fairly simple queries to retrieve a particular type of data to more complex queries that 
      span the different types of data available in FlyMine. More template queries will be added 
      as FlyMine develops and we welcome <a href="/query/feedback.do">suggestions</a>. Find lists of predefined template 
      queries in each data category or use the templates page to search through them.
      <!-- <a href="doc/tutorials/tutorial3-Templates.shtml">Tutorial 3</a> -->
    </p>
<h3>FlyMine QueryBuilder</h3>
<p style="">
      Advanced users can use a flexible query interface to construct
      their own data mining queries across the multiple integrated
      data sources, to modify existing template queries or to create
      your own template queries.
      <!-- <a href="doc/tutorials/tutorial6-QB.shtml">Tutorial 6</a> -->
    </p>
<h3>Operate on Lists</h3>
<p style="">
      All queries in FlyMine can be performed on lists of data. Lists can
      be created by typing or pasting in identifiers, or
      uploading a file. Data from previous queries
      can also be saved into a list using the boxes displayed
      underneath the query results. Saved lists of data can be used to
      constrain new queries, perform logical operations and can be
      analysed on a page that shows graphs, summary tables and statistics.  FlyMine now includes a number of public lists that we
      create and make available from published sources.
      <!-- <a href="doc/tutorials/tutorial4-BagsHistory.shtml">Tutorial 4</a> -->
    </p>
<h3>MyMine</h3>
<p style="">
      You can save your lists, queries and templates between sessions by
      <a href="/query/login.do">creating an account</a> using the 'Log in' link
      in the header of every page.
      <!-- <a href="doc/tutorials/tutorial4-BagsHistory.shtml">Tutorial 4</a> -->
    </p>
    <h3>Help!</h3>
<p style="">
	To view context sensitive help for any page in FlyMine click on the 
	<a href="http://www.flymine.org/help/begin.html" 
	onclick="javascript:window.open('http://www.flymine.org/help/begin.html','_help','toolbar=0,scrollbars=1,location=1,statusbar=1,menubar=0,resizable=1,width=800,height=600');return false">
	<img src="/images/help.png" title="Click here for Help"/></a> in the the top right corner.  
	

    </p>
<br />
<br />
<!--
    <p style="">
      See the <a href="doc/tutorials/index.shtml">short tutorials</a> and 
      <a href="doc/manual/index.shtml">user manual</a> for more information.
    </p>
-->
</div>
</div>
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