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<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01//EN""https://www.w3.org/TR/html4/strict.dtd">
<html lang="en-US">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1">
<!-- The above 3 meta tags *must* come first in the head; any other head content must come *after* these tags -->
<meta keywords="NIH, big data discovery science, big data to knowledge, BD2K, BDDS, LONI, USC, ISB">
<title>The BDDS Project</title>
<!-- Bootstrap core CSS -->
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css">
<link href="https://fonts.googleapis.com/css?family=Unica+One|Roboto:400,400italic,100,100italic,300,300italic,500italic,500,700,900,700italic,900italic" rel="stylesheet" type="text/css">
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/font-awesome/4.3.0/css/font-awesome.min.css">
<!-- Custom styles -->
<link href="resources/css/starter-template.css" rel="stylesheet">
<script src="https://ajax.googleapis.com/ajax/libs/jquery/2.1.3/jquery.min.js"></script>
<!--<script src="https://ajax.googleapis.com/ajax/libs/jquery/2.12.3/jquery.min.js"></script>-->
<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/js/bootstrap.min.js"></script>
<!-- Favicon Stuff -->
<link rel="apple-touch-icon" sizes="57x57" href="resources/images/apple-touch-icon-57x57.png">
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<link rel="mask-icon" href="resources/images/safari-pinned-tab.svg" color="#5bbad5">
<link rel="shortcut icon" href="resources/images/favicon.ico">
<meta name="msapplication-TileColor" content="#da532c">
<meta name="msapplication-config" content="resources/images/browserconfig.xml">
<meta name="theme-color" content="#ffffff">
</head>
<body>
<nav class="navbar navbar-default navbar-fixed-top navbar-top">
<div class="container">
<div class="navbar-header">
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false" aria-controls="navbar">
<span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a class="navbar-brand" href="http://bd2k.ini.usc.edu"><img style="max-width:100px; margin-top: -16px;" src="resources/images/bdds_logo.png"></a>
</div><!-- /.navbar-header-->
<div id="navbar" class="collapse navbar-collapse">
<ul class="nav navbar-nav">
<li><a href="https://github.com/ini-bdds/">GitHub</a></li>
</ul>
</div><!--/.nav-collapse -->
</div> <!-- /.container-->
</nav>
<div class="container" id ="head">
<div class="col-xs-12" style="height:40px;"></div>
<div class="starter-template text-center">
<h1>The Big Data to Discovery Science Project Toolset</h1>
<p class="lead">Applying Big Data Tools to Accelerate Scientific Knowledge Turns</p>
</div>
</div> <!-- /head -->
<!-- todo: navbar? -->
<div class="container gray_background" style="padding-left:5px; padding-right:5px; padding-top:5px;">
<div class="col-xs-12 col-sm-4 col-sm-push-8" id="right column">
<div class="white_background">
<table class="table">
<tr>
<td class="text-center">
<p class="text-center bg-primary">What is BDDS?</p>
<p class="text-justify" style="padding-left:5px; padding-right:5px;"><a href="http://bd2k.ini.usc.edu/">BDDS</a> is a <a href="https://datascience.nih.gov/bd2k/funded-programs/centers#title4">NIH Center of Excellence</a> developing new approaches, methods, software tools, and related resources for advancing Big Data science in the context of biomedical research.</p>
</td>
</tr>
</table>
</div> <!-- /right column box 1 -->
<div class="white_background">
<table class="table">
<tr>
<td>
<p class="text-center bg-primary">Tutorials</p>
<ul style="padding-left:15px; padding-right:5px;">
<li style="margin: 1em 0;"><a href="https://sites.google.com/site/tpptutorial/">Running the Trans-Proteomics Pipeline on BDDS Globus Genomics</a></li>
<li style="margin: 1em 0;"><a href="http://pipeline.loni.usc.edu/files/serverlib/view_workflow.php?file=/ISB_Suite/Groups/TPP_Tutorial.pipe">Running the TPP on the LONI pipeline</a></li>
</ul>
</td>
</tr>
</table>
</div> <!-- /right column box 2 -->
<div class="white_background">
<table class="table">
<tr>
<td>
<p class="text-center bg-primary">Motivating Examples</p>
<ul style="padding-left:15px; padding-right:5px;">
<li style="margin: 1em 0;"><a href="https://">Amyloid Burden</a></li>
<li style="margin: 1em 0;"><a href="https://">TReNA</a></li>
<li style="margin: 1em 0;"><a href="https://">PheWAS</a></li>
<li style="margin: 1em 0;"><a href="https://">MinIDs for Peptide Atlas</a></li>
<li style="margin: 1em 0;"><a href="https://">PANTHER Enrichment Analysis</a></li>
<li style="margin: 1em 0;"><a href="https://">Quality Control of Genomic Sequencing Data</a></li>
</ul>
</td>
</tr>
</table>
</div> <!-- /right column box 3 -->
</div> <!--/right column -->
<div class="col-xs-12 col-sm-8 col-sm-pull-4" id="left column">
<div class="white_background">
<table class="table">
<tr>
<td class="text-center"><a href="http://minid.bd2k.org/"><img style="max-width:100px;" src="resources/images/minid-logo.png" class="img-responsive" alt="minid"></a></td>
<td><a href="http://minid.bd2k.org/" class="lead">Minid</a>
<br>Lightweight, globally unique identifiers for data products.
</td>
</tr>
<tr>
<td class="text-center"><a href="http://ithub.com/ini-bdds/bagit-python"><img style="max-width:100px;" src="resources/images/bag.png" class="img-responsive" alt="SciBag Tools"></a></td>
<td><a href="https://github.com/ini-bdds/bagit-python" class="lead">SciBag Tools</a>
<br>A set of tools for building and working with "SciBags", which are sets data files bundeled together using a hierarchical file packaging format based on the Library of Congress' "BagIt" format.
</td>
</tr>
<tr>
<td class="text-center"><a href="https://github.com/ini-bdds/iobox"><img style="max-width:100px;" src="resources/images/iobox-overview.jpg" class="img-responsive" alt="iobox"></a></td>
<td><a href="https://github.com/ini-bdds/iobox" class="lead">IObox</a>
<br>A collection of Extract, Transform, Load (ETL) utilities for ERMrest+Hatrac
</td>
</tr>
<tr>
<td class="text-center">graphic</td>
<td><a href="https://github.com/ini-bdds/ermrest" class="lead">ERMrest</a>
<br>A general relational data storage service for web-based, data-oriented collaboration
</td>
</tr>
<tr>
<td class="text-center"><a href="https://github.com/ini-bdds/bdqc"><img style="max-width:100px;" src="resources/images/bdqc_logo.png" class="img-responsive" alt="bdqc"></a></td>
<td><a href="https://github.com/ini-bdds/bdqc" class="lead">BDQC</a>
<br>An extensible Python3 framework for context-agnostic file-based data validation
</td>
</tr>
<tr>
<td class="text-center"><a href="https://bdds.globusgenomics.org/"><img style="max-width:75px;" src="resources/images/logo_globus_genomics.png" class="img-responsive" alt="Globus Genomics"></a></td>
<td><a href="https://bdds.globusgenomics.org/" class="lead">BDDS Globus Genomics</a>
<br>BDDS Globus Genomics provides a platform for Cloud-based Informatics Processing.
</td>
</tr>
<!-- <tr>
<td class="text-center">graphic</td>
<td class="lead">Network Visualization</td>
</tr>
-->
</table>
</div> <!-- /left column box 1-->
<div class="white_background">
<table class="table">
<tr>
<td class="text-center td-center"><a href="http://pantherdb.org/"><img style="max-width:100px;" src="resources/images/Panther_logo.jpg" class="img-responsive" alt="Panther"></a></td>
<td><a href="http://pantherdb.org/" class="lead">PANTHER</a>
<br>A Classification System designed to classify proteins and their genes to facilitate high-throughput analysis.
</td>
</tr>
<tr>
<td class="text-center"><a href="http://socr-dev.nursing.umich.edu:8080/new"><img style="max-width:75px;" src="resources/images/socr.gif" class="img-responsive" alt="SOCR Analytics Dashboard"></a></td>
<td><a href="http://socr-dev.nursing.umich.edu:8080/new" class="lead">SOCR Analytics Dashboard</a>
<br>SOCR Analytics Dashboard combines and integrates multiple socioeconomic and medical datasets using big data analytics, in order to provide a lightweight, scalable platform for drawing inferences related to medical care, sociology, and economy in the United States.
</td>
</tr>
<tr>
<td class="text-center"><a href="http://pipeline.loni.usc.edu/"><img style="max-width:75px;" src="resources/images/Loni_logo.jpg" class="img-responsive" alt="LONI Pipeline"></a></td>
<td><a href="http://pipeline.loni.usc.edu/" class="lead">LONI Pipeline</a>
<br>A Workflow application primarily aimed at computational scientists.
</td>
</tr>
<tr>
<td class="text-center"><a href="https://bdds.globus.org/"><img style="max-width:75px;" src="resources/images/Globus_logo.jpg" class="img-responsive" alt="Globus"></a></td>
<td><a href="https://www.globus.org/researchers" class="lead">Globus</a>
<br>Globus gives researchers everywhere access to a fast, powerful data management service that's easy to use.
</td>
</tr>
</table>
</div> <!-- /left column box 2 -->
<div class="white_background">
<table class="table">
<tr>
<td class="text-center td-center"><a href="http://tools.proteomecenter.org/software.php"><img style="max-width:100px;" src="resources/images/TPP.jpg" class="img-responsive" alt="Trans-Proteomic Pipeline"></a></td>
<td><a href="http://tools.proteomecenter.org/software.php" class="lead">Trans-Proteomic Pipeline</a>
<br>The Trans-Proteomic Pipeline (TPP) includes all of the steps of the ISB MS/MS analysis pipeline.
</td>
</tr>
<tr>
<td class="text-center"><a href="http://www.peptideatlas.org/"><img style="max-width:75px;" src="resources/images/peptideAtlas.jpg" class="img-responsive" alt="Peptide Atlas"></a></td>
<td><a href="http://peptideatlas.org/" class="lead">Peptide Atlas</a>
<br>PeptideAtlas is a multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments.
</td>
</tr>
</table>
</div> <!-- /left column box 3 -->
<!-- next cell would go here with div class="white_background" -->
</div> <!-- /left column row 1 -->
</div><!--content container-->
<footer>
<div class="fcontainer">
<div class="footer-nav text-center col-xs-12">
<a href="http://bd2k.ini.usc.edu/">BD2K HOME</a>
<a href="http://bd2k.ini.usc.edu/about/">ABOUT</a>
<a href="http://bd2k.ini.usc.edu/news/">NEWS/EVENTS</a>
<a href="http://bd2k.ini.usc.edu/documents/">DOCUMENTS</a>
<a href="http://bd2k.ini.usc.edu/publications/">PUBLICATIONS</a>
<a href="/">TOOLS</a>
<a href="http://bd2k.ini.usc.edu/contact/">CONTACT</a>
</div>
<div class="flogos col-xs-12">
<a href="http://loni.usc.edu/"><img src="http://bd2k.ini.usc.edu/assets/logos/logos_collaborators-stevens.png" /></a>
<a href="http://www.nih.gov/"><img src="http://bd2k.ini.usc.edu/assets/logos/logos_collaborators-NIH.png" /></a>
<a href="http://www.isi.edu/home"><img src="http://bd2k.ini.usc.edu/assets/logos/logos_collaborators-VISI.png" /></a>
<a href="https://www.systemsbiology.org/"><img src="http://bd2k.ini.usc.edu/assets/logos/logos_collaborators-ISB.png" /></a>
<a href="https://www.ci.uchicago.edu/"><img src="http://bd2k.ini.usc.edu/assets/logos/logos_collaborators-CI.png" /></a>
<a href="http://www.socr.umich.edu/"><img src="http://bd2k.ini.usc.edu/assets/logos/logos_collaborators-SOCR.png" /></a>
</div>
<div style="clear: both;"> </div>
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</footer>
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