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index.php
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index.php
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<?php
$PageTitle = 'xGDBvm - Virtual Genome Environment';
$pgdbmenu = 'Home';
$submenu1= 'Home';
$submenu2= 'Home';
$leftmenu = 'Home';
$global_DB1= 'Genomes';
$global_DB2= 'Admin';
include '/xGDBvm/XGDB/phplib/sitedef.php';
include('/xGDBvm/XGDB/phplib/header.php');
include_once('/xGDBvm/XGDB/phplib/db.inc.php');
###### Connect to database ######
$dbpass=dbpass();
$db = mysql_connect("localhost", "gdbuser", $dbpass);
if(!$db)
{
echo "Error: Could not connect to database!";
exit;
}
mysql_select_db("$global_DB1");
global $count;
$Query="SELECT ID from xGDB_Log";
$get_records = $Query;
$check_get_records = mysql_query($get_records);
$result = $check_get_records;
if($count == mysql_fetch_array($result)){
$config_link = "/XGDB/conf/index.php";
$config_text =" Getting Started ";
}else{
$config_link = "/XGDB/conf/viewall.php";
$config_text =" View Configurations ";
}
?>
<div id="leftcolumncontainer">
<div class="minicolumnleft">
<?php include_once("/xGDBvm/XGDB/phplib/leftmenu.inc.php"); ?>
</div>
</div><!-- end leftcolumncontainer -->
<div id="maincontentscontainer" class="threecolumn">
<div id="maincontents">
<h1>Welcome to xGDB<i>vm</i>, <span class="heading indent"> a virtual environment for viewing and annotating genomes.</span></h1>
<hr class="featuredivider" />
<div class="feature">
<span class="heading largerfont"> Click below to learn more about xGDBvm:</span>
</div><!-- end feature -->
<!--Create Genomes-->
<div class="feature topmargin1">
<div class="showhide" id="create_genomes">
<p title="Click for more information" style="cursor:pointer">
<span class="bigfont bold reverse">Manage<span class="heading reverse"> - Create a Genome Browser using your own data</span></span></p>
<div class=" hidden">
<p>
Splice-align transcripts & proteins and build gene models automatically, then view/search output data in a full-featured genome browser that can be either public or private.
<a title='How xGDBvm works' class='image-button' id='xGDBvmFlow_large:550:560'>
<span class="highlight">(click to view schema)</span>
</a>
</p>
<div class="big_button">
<a title="Getting Started page" href="/XGDB/manage/index.php" class="xgdb_button colorConf1">Click to get started</a>
<span class="heading"> - If this is a new xGDBvm, start here for best results!</span>
<p class="topmargin2 indent2">
<br /><span class="warning"> NOTE: these pages are for administrators and may be password protected </span>
</p>
</div>
<p>See xGDBvm in action with <b>video tutorials:</b></p>
<div class="big_button">
<a title='Video is also available at https://youtu.be/Kcuy-3IZJ_E' class='xgdb_button smallerfont ytvideo-button video xgdb_button colorGR3 video-button-gr video' id='create_example_gdb' name='Kcuy-3IZJ_E'>
1: xGDBvm: An Overview</a>
<span class="topmargin1 heading"> (4:48) - xGDBvm: An Overview </span>
</div>
<div class="big_button">
<a title='Video is also available at http://www.youtube.com/watch?v=3KL9ceP11yo' class='xgdb_button smallerfont ytvideo-button video xgdb_button colorGR3 video-button-gr video' id='create_example_gdb' name='3KL9ceP11yo'>
2: Create/Configure a new VM</a>
<span class="topmargin1 heading"> (4:39) - Create/Configure a new xGDBvm instance on iPlant Atmosphere </span>
</div>
<div class="big_button">
<a title='Video is also available at https://www.youtube.com/watch?v=Pv58RNHDwIA' class='xgdb_button smallerfont ytvideo-button video xgdb_button colorGR3 video-button-gr video' id='create_example_gdb' name='Pv58RNHDwIA'>
3: Test your new VM</a>
<span class="topmargin1 heading"> (6:42) - Test a new xGDBvm instance with pre-configured sample data </span>
</div>
<p><a href="/XGDB/help/index.php#videos">more video tutorials</a></p>
</div><!-- end hidden div-->
</div><!-- end showhide -->
</div><!--end feature-->
<!--View Genomes-->
<div class="feature topmargin2 bottommargin2">
<div class="showhide" id="view_genomes">
<p title="Click for more information" style="cursor:pointer">
<span class="bigfont bold reverse">View <span class="heading reverse"> - Browse / Search Genomes on this VM</span> </span>
</p>
<div class="hidden">
<p>Once you have created a GDB using the above tools, the data are immediately displayed online. xGDBvm's <a class="help_style bold" title="Get help on genome browsers" href="/XGDB/help/genome_browser.php">genome browser</a> provides a wealth of tools for searching or querying your genome.</p>
<div class="big_button">
<a title="Existing genome" href="/XGDB/genomes.php" class="xgdb_button colorO1 largerfont">View Current Genomes</a> <span class="heading"> - See a list of current genomes and links to tools and views </span>
</div >
<div class="big_button">
<a title="Genome browsers at PlantGDB" class='flvideo-button bottommargin1 xgdb_button colorGR3 video-button-gr' id='genome_browser_demo' name='28518868'>Watch Video</a> <span class="heading"> - Take a visual tour of the basic features of xGDBvm's genome browser</span>
</div>
</div><!--end of hidden div-->
</div><!--end of showhide div-->
</div> <!-- end feature -->
<!--Community Annotation-->
<div class="feature bottommargin2">
<div class="showhide" id="community_annotation">
<p title="Click for more information" style="cursor:pointer">
<span class="bigfont bold reverse">Annotate <span class="heading reverse"> - Improve gene model annotations using the yrGATE tool</span> </span>
</p>
<div class="hidden">
<h3>Community Annotation Tool (yrGATE)</h3>
<p>xGDBvm's <a class="help_style bold" title="Get help on community annotation" href="/XGDB/help/yrgate.php">yrGATE Tool</a> allows users to improve the quality of gene structure predictions displayed on this VM. After curation, user-submitted annotations are immediately displayed for the entire community.</p>
<div class="big_button">
<a title="Existing genome" href="/src/yrGATE/index.php" class="xgdb_button colorGreen1 largerfont">View Community Annotations</a> <span class="heading"> - Links to Community Annotation pages</span>
</div >
<div class="big_button">
<a title="Annotating gene structure using yrGATE" class='flvideo-button bottommargin1 xgdb_button colorGR3 video-button-gr' id='yrgate_demo' name='7858561'>Watch Video</a>
</div>
<h3>Gene Quality Index (GAEVAL)</h3>
<p>Automated gene calls are not always accurate. xGDBvm's <a class="help_style bold" title="Get help on GAEVAL" href="/XGDB/help/gaeval.php">GAEVAL</a> script flags discrepancies between EST/cDNA evidence-based alignments and gene models, and makes it easy to spot gene models in need of re-annotation.</p>
</div><!--end of hidden div-->
</div><!--end of showhide div-->
</div><!--end feature-->
</div><!--end maincontents-->
<div style="clear:both; float:right">
<a href="http://validator.w3.org/check?uri=referer">
<img src="http://www.w3.org/Icons/valid-xhtml10" alt="Valid XHTML 1.0 Transitional" height="15" width="44" />
</a>
</div>
</div><!--end maincontentscontainer-->
<?php include('/xGDBvm/XGDB/phplib/footer.php'); ?>
</div><!--end pagewidth-->
</div><!--end innercontainer-->
</div><!--end outercontainer-->
</body>
</html>