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index.html
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index.html
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<!DOCTYPE html>
<html lang="en">
<head>
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<meta charset="utf-8">
<!-- Change the title of the webpage in the <title> tag -->
<title>Microbe-ID | Welcome</title>
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<meta name="description" content="">
<meta name="author" content="root">
<!-- Le styles, make sure that the Bootstrap_files folder is in the same directory than your homepage -->
<link href="Bootstrap_files/bootstrap.css" rel="stylesheet">
<link href="Bootstrap_files/phytophthora-lab.css" rel="stylesheet">
<style>
/* CUSTOMIZE THE CAROUSEL
-------------------------------------------------- */
/* Carousel base class */
/* GLOBAL STYLES
-------------------------------------------------- */
/* Padding below the footer and lighter body text */
body {
padding-bottom: 40px;
color: #5a5a5a;
}
/* CUSTOMIZE THE NAVBAR
-------------------------------------------------- */
/* Special class on .container surrounding .navbar, used for positioning it into place. */
.navbar-wrapper {
position: absolute;
top: 0;
right: 0;
left: 0;
z-index: 20;
}
/* Flip around the padding for proper display in narrow viewports */
.navbar-wrapper > .container {
padding-right: 0;
padding-left: 0;
}
.navbar-wrapper .navbar {
padding-right: 15px;
padding-left: 15px;
}
.navbar-wrapper .navbar .container {
width: auto;
}
/* CUSTOMIZE THE CAROUSEL
-------------------------------------------------- */
/* Carousel base class */
.carousel {
height: 500px;
margin-bottom: 60px;
}
/* Since positioning the image, we need to help out the caption */
.carousel-caption {
z-index: 10;
}
/* Declare heights because of positioning of img element */
.carousel .item {
height: 500px;
background-color: #777;
}
.carousel-inner > .item > img {
position: absolute;
top: 0;
left: 0;
min-width: 100%;
height: 500px;
}
/* MARKETING CONTENT
-------------------------------------------------- */
/* Center align the text within the three columns below the carousel */
.marketing .col-lg-4 {
margin-bottom: 20px;
text-align: center;
}
.marketing h2 {
font-weight: normal;
}
.marketing .col-lg-4 p {
margin-right: 10px;
margin-left: 10px;
}
/* Featurettes
------------------------- */
.featurette-divider {
margin: 80px 0; /* Space out the Bootstrap <hr> more */
}
/* Thin out the marketing headings */
.featurette-heading {
font-weight: 300;
line-height: 1;
letter-spacing: -1px;
}
/* RESPONSIVE CSS
-------------------------------------------------- */
@media (min-width: 768px) {
/* Navbar positioning foo */
.navbar-wrapper {
margin-top: 20px;
}
.navbar-wrapper .container {
padding-right: 15px;
padding-left: 15px;
}
.navbar-wrapper .navbar {
padding-right: 0;
padding-left: 0;
}
/* The navbar becomes detached from the top, so we round the corners */
.navbar-wrapper .navbar {
border-radius: 4px;
}
/* Bump up size of carousel content */
.carousel-caption p {
margin-bottom: 20px;
font-size: 21px;
line-height: 1.4;
}
.featurette-heading {
font-size: 50px;
}
}
@media (min-width: 992px) {
.featurette-heading {
margin-top: 120px;
}
}
</style>
<link href="Bootstrap_files/bootstrap-responsive.css" rel="stylesheet">
<!-- HTML5 shim, for IE6-8 support of HTML5 elements -->
<!--[if lt IE 9]>
<script src="../assets/js/html5shiv.js"></script>
<![endif]-->
<!-- Fav and touch icons -->
<link rel="apple-touch-icon-precomposed" sizes="144x144" href="http://twitter.github.com/bootstrap/assets/ico/apple-touch-icon-144-precomposed.png">
<link rel="apple-touch-icon-precomposed" sizes="114x114" href="http://twitter.github.com/bootstrap/assets/ico/apple-touch-icon-114-precomposed.png">
<link rel="apple-touch-icon-precomposed" sizes="72x72" href="http://twitter.github.com/bootstrap/assets/ico/apple-touch-icon-72-precomposed.png">
<link rel="apple-touch-icon-precomposed" href="http://twitter.github.com/bootstrap/assets/ico/apple-touch-icon-57-precomposed.png">
<link rel="shortcut icon" href="img/customIcon.png">
</head>
<body>
<div id="wrap">
<div class="navbar navbar-inverse navbar-fixed-top">
<div class="navbar-inner">
<div class="container">
<button type="button" class="btn btn-navbar" data-toggle="collapse" data-target=".nav-collapse">
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a class="brand" href="./index.html">Microbe-ID</a>
<div class="nav-collapse collapse">
<ul class="nav">
<!-- Names of the links are between the <a></a> tags. -->
<li class="./index.html"><a href="./index.html">Home</a></li>
<li><a href="./seq-id.html">Sequence-ID</a></li>
<li><a href="./geno-id.html">Genotype-ID</a></li>
<li><a href="./about.html">About</a></li>
</ul>
</div>
<!--/.nav-collapse -->
</div>
</div>
</div>
<!-- MICROBE-ID Specific. Carousel: The carousel is defined as the image contents on the javascript that rotates
the front page images. Here, the tags <img> are for the images you want to add, the content
inside of the <div class="carousel-caption"> are the captions of the figure. inside of <h1>
its the title of the figure and inside <p class="lead:> the subcontent.
================================================== -->
<div class="container">
<div id="myCarousel" class="carousel slide">
<!-- Carousel items -->
<div class="carousel-inner">
<div class="item active">
<!-- Add image 1 here -->
<!--img alt="" src="img/first.png" /-->
<div class="container">
<div class="carousel-caption">
<h1>Title page 1</h1>
<p class="lead">Carousel page 1. Modify text in line 207 of index.html</p>
</div>
</div>
</div>
<div class="item">
<!-- Add image 2 here -->
<!--img alt="" src="img/second.png" /-->
<div class="container">
<div class="carousel-caption">
<h1>Title page 2</h1>
<p class="lead">Carousel page 2. Modify text in line 217 of index.html</p>
</div>
</div>
</div>
<div class="item">
<!-- Add image 3 here -->
<!--img alt="" src="img/third.png" /-->
<div class="container">
<div class="carousel-caption">
<h1>TItle page 3</h1>
<p class="lead">Carousel page 3. Modify text in line 227 of index.html</p>
</div>
</div>
</div>
<!-- Carousel nav -->
<a class="carousel-control left" href="#myCarousel" data-slide="prev">‹</a>
<a class="carousel-control right" href="#myCarousel" data-slide="prev">›</a>
</div>
</div>
<!-- MICROBE-ID customization: Change the body of the page here. -->
<h1>Welcome</h1>
<hr>
<p class="lead"> <b>Microbe-ID </b>is a toolbox that can readily be customized for any taxonomic group or species for sequence based identification of species or marker-based identification of strains.</p>
<p><b>Microbe-ID</b> aims to: </p>
<ul>
<li> Outline a method for development of a species and strain identification website using existing open source, online resources.</li>
<li> Integrate existing population genetic analyses and visualizations into the genotype identification tool in order to improve genotype diagnostic capabilities.</li>
</ul>
<p>This site provides all code and applications necessary for creating a website for species identification or strain genotyping.</p>
<h3>Components</h3>
<p><b>Microbe-ID</b> is comprised by two main applications: <b><a href="./seq-id.html">Sequence-ID</a></b> and <b><a href="./geno-id.html">Genotype-ID</a></b>.
<ul>
<li><b>Sequence-ID</b> allows identification of species by blasting a query sequence for any locus of interest against a custom reference sequence database using <code>BLAST</code></li>
<li><b>Genotype-ID</b> allows placement of an unknown genotype in either a minimum spanning network or dendrogram with bootstrap support comparing the queue against an user-created reference database using <code>R</code> and a suite of R packages designed for molecular markers</li>
</ul>
<p><b>Microbe-ID</b> groups these two applications in a HTML5 framework based on <a href="http://getbootstrap.com">Bootstrap</a> that links both applications into a simple, web-ready site to be deployed locally or in a server.</p>
<hr>
<p class=lead> Visit the project page in Github for details in requirements, installation and deployment of <b>Microbe-ID</b> at <a href="https://github.com/grunwaldlab/Microbe-ID">http://github.com/grunwaldlab/Microbe-ID</a></p>
</div>
<div id="push"></div>
</div>
<div id="footer">
<div class="container">
<br>
<p> add content here </p>
</div>
</div>
<!-- Le javascript
================================================== -->
<!-- Placed at the end of the document so the pages load faster -->
<script src="Bootstrap_files/jquery.js"></script>
<script src="Bootstrap_files/bootstrap-transition.js"></script>
<script src="Bootstrap_files/bootstrap-alert.js"></script>
<script src="Bootstrap_files/bootstrap-modal.js"></script>
<script src="Bootstrap_files/bootstrap-dropdown.js"></script>
<script src="Bootstrap_files/bootstrap-scrollspy.js"></script>
<script src="Bootstrap_files/bootstrap-tab.js"></script>
<script src="Bootstrap_files/bootstrap-tooltip.js"></script>
<script src="Bootstrap_files/bootstrap-popover.js"></script>
<script src="Bootstrap_files/bootstrap-button.js"></script>
<script src="Bootstrap_files/bootstrap-collapse.js"></script>
<script src="Bootstrap_files/bootstrap-carousel.js"></script>
<script src="Bootstrap_files/bootstrap-typeahead.js"></script>
<script src="Bootstrap_files/holder.js"></script>
</body>
</html>