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<!DOCTYPE html>
<!--[if IE]><![endif]-->
<html lang="en">
<head>
<meta charset="utf-8">
<title>IBL · Integrative Bioinformatics Laboratory</title>
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<!-- Le styles -->
<link href="css/bootstrap.min.css" rel="stylesheet" media="screen">
<link href="css/ibl.css" rel="stylesheet">
<!-- Fav icons -->
<link rel="shortcut icon" href="./favicon.ico">
<!-- Google Analytics tracking code -->
<script>
var _gaq;
_gaq = _gaq || [];
_gaq.push(["_setAccount", "UA-40046399-1"]);
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var ga, s;
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s = document.getElementsByTagName("script")[0];
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}());
</script>
</head>
<body id="top">
<div class="container-narrow">
<nav class="navbar navbar-default" role="navigation">
<div class="navbar-header">
<button type="button" class="navbar-toggle" data-toggle="collapse" data-target=".navbar-collapse">
<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="#">IBL</a>
</div>
<div class="collapse navbar-collapse">
<ul class="nav navbar-nav">
<li><a href="#projects">Projects</a></li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">
People
<b class="caret"></b>
</a>
<ul class="dropdown-menu">
<li><a href="#people">Current</a></li>
<!--
<li><a href="#friend">Friends and visitors</a></li>
-->
<li><a href="#alumni">Alumni</a></li>
</ul>
</li>
<li><a href="#links">Links</a></li>
<li><a href="#calendar">Calendar</a></li>
<li><a href="#contact">Contact</a></li>
</ul>
</div>
</nav>
<hr>
<header>
<div class="teaser">
<h1>Integrative Bioinformatics Laboratory</h1>
<p class="lead">
Translational solutions at the data-driven crossroads of
Computational Statistics, Computer Science, and Systems Biomedicine.
</p>
</div>
<p>
IBL is a research group working on transdisciplinary problems that
span computational statistics, computer science, and systems
biomedicine. The projects IBL pursues seek translational validation
in applications to precision medicine for novel ideas traversing
these fields.
</p>
<p>
In addition to the graduate research level projects, IBL also hosts
Pathology Informatics rotations for residents and fellows.
</p>
<p>
This combination of fields and career tracks is integrated through
immersive problem solving venues including
<a href="http://uab.mathbiol.org/workshop">weekly hackathons</a> and
software development bootcamps.
</p>
<p>
IBL is a research group in the
<a href="http://www.uab.edu/pathology/informatics">Division of Informatics</a>
of the UAB Department of Pathology.
</p>
</header>
<hr>
<section id="projects">
<h2>Projects <small><a href="#top"
class="glyphicon glyphicon-chevron-up"></a></small></h2>
<div>
<h3>Published</h3>
<div class="row">
<div class="col-md-6">
<h4>ImageJS</h4>
<p>
ImageJS is a browser-based image analysis environment inspired
by ImageJ and reimagined using HTML5 and JavaScript.
</p>
<p>
<a href="http://imagejs.org/" class="btn btn-info btn-xs">
<span class="glyphicon glyphicon-new-window"></span>
Learn More
</a>
</p>
</div>
<div class="col-md-6">
<h4>QMachine</h4>
<p>
QMachine is a web service that can incorporate ordinary
browsers into a World Wide Computer — without installing
anything.
</p>
<p>
<a href="https://www.qmachine.org/" class="btn btn-info btn-xs">
<span class="glyphicon glyphicon-new-window"></span>
Learn More
</a>
</p>
</div>
</div>
<div class="row">
<div class="col-md-6">
<h4>S3DB</h4>
<p>
S3DB (Simple Sloppy Semantic Database) is a way to represent
information on the Semantic Web without the rigidness of
relational/XML schema while avoiding the "spaghetti" of
unconstrained RDF stores.
</p>
<p>
<a href="http://s3db.org/" class="btn btn-info btn-xs">
<span class="glyphicon glyphicon-new-window"></span>
Learn More
</a>
</p>
</div>
<div class="col-md-6">
<h4>TCGA Roadmap</h4>
<p>
The TCGA Roadmap is a linked data resource indexing the TCGA
Open Access HTTP Repository. Queried using SPARQL, the TCGA
Roadmap enables the discovery of subsets of data files within
the TCGA.
</p>
<p>
<a href="http://tcga.github.io/Roadmap/" class="btn btn-info btn-xs">
<span class="glyphicon glyphicon-new-window"></span>
Learn More
</a>
</p>
</div>
</div>
<div class="row">
<div class="col-md-6">
<h4>USM</h4>
<p>
Universal Sequence Maps (USM) is an iterated procedure that
maps symbolic sequences into numeric spaces where
<b>alignment-free sequence analysis</b> can be performed. For a
review see <i>Almeida JS (2013) Sequence analysis by iterated
maps, a review." Briefings in bioinformatics. bbt072 Epub Oct
25 <a href="http://www.ncbi.nlm.nih.gov/pubmed/24162172"
target=_blank>PMID:24162172</a>.</i>
</p>
<p>
<a href="http://usm.github.io/" class="btn btn-info btn-xs">
<span class="glyphicon glyphicon-new-window"></span>
Learn More
</a>
</p>
</div>
</div>
<h3>In-Progress</h3>
<div class="row">
<div class="col-md-6">
<h4>EvalSpace</h4>
<p>
A WebRTC experiment to find out the feasibility of assembly
"evaluation spaces" aggregating multiple browsers.
</p>
<p>
<a href="https://github.com/jonasalmeida/evalSpace"
class="btn btn-info btn-xs">
<span class="glyphicon glyphicon-new-window"></span>
Learn More
</a>
</p>
</div>
<div class="col-md-6">
<h4>Formalin</h4>
<p>
Formalin (formerly
<a href="//wilkinson.github.io/hpath/">HPath</a>) is a
browser-based, user-extensible report generator for clinical
environments.
</p>
<p>
<a href="//wilkinson.github.io/formalin/"
class="btn btn-info btn-xs">
<span class="glyphicon glyphicon-new-window"></span>
Learn More
</a>
</p>
</div>
</div>
<div class="row">
<div class="col-md-6">
<h4>Kinomics Quality Control</h4>
<p>
Kinomics Quality Control is a toolbox for working with
Pamgene-generated kinomics data.
</p>
<p>
<a class="btn btn-info btn-xs"
href="http://adussaq.github.io/kinomicDataQC/">
<span class="glyphicon glyphicon-new-window"></span>
Learn More
</a>
</p>
</div>
<div class="col-md-6">
<h4>MinervaJS</h4>
<p>
MinervaJS is a tool for publishing and finding Javascript
libraries, and weaving them together.
</p>
<p>
<a href="http://minervajs.org/" class="btn btn-info btn-xs">
<span class="glyphicon glyphicon-new-window"></span>
Learn More
</a>
</p>
</div>
</div>
<div class="row">
<div class="col-md-6">
<h4>Ming</h4>
<p>
Ming is a quasi-RESTful and CORS-enabled web service that
allows reads, writes, and queries to one or more instances of
MongoDB over the HTTP protocol.
</p>
<p>
<a href="https://bitbucket.org/agrueneberg/ming" class="btn btn-info btn-xs">
<span class="glyphicon glyphicon-new-window"></span>
Learn More
</a>
</p>
</div>
<div class="col-md-6">
<h4>TCGA Toolbox</h4>
<p>
TCGA Toolbox provides a scripting environment to retrieve,
store, and analyze data from The Cancer Genome Atlas (TCGA) in
the browser. It can be extended by loading modules and/or used
interactively from the browser's JavaScript console.
</p>
<p>
<a href="http://tcga.github.io" class="btn btn-info btn-xs">
<span class="glyphicon glyphicon-new-window"></span>
Learn More
</a>
</p>
</div>
</div>
<div class="row">
<div class="col-md-6">
<h4>wApps</h4>
<p>
A wApp is a web application in a hurry to be part of a webApp
ecosystem.
</p>
<p>
<a href="http://wapps.github.io/" class="btn btn-info btn-xs">
<span class="glyphicon glyphicon-new-window"></span>
Learn More
</a>
</p>
</div>
</div>
</div>
</section>
<hr>
<section id="people">
<h2>People <small><a href="#top" class="glyphicon glyphicon-chevron-up"></a></small></h2>
<h3>Current</h3>
<div class="member">
<div>
<h4>Jonas Almeida, PhD</h4>
<a href="http://jonasalmeida.info" class="btn btn-info btn-xs">
<span class="glyphicon glyphicon-new-window"></span>
Homepage
</a>
<a href="http://pub.jonasalmeida.info" class="btn btn-info btn-xs">
<span class="glyphicon glyphicon-new-window"></span>
Publications
</a>
<a href="https://github.com/jonasalmeida" class="btn btn-info btn-xs">
<span class="glyphicon glyphicon-new-window"></span>
GitHub
</a>
</div>
<p>Professor, Group Leader</p>
</div>
<div class="member">
<div>
<h4>Alex Dussaq</h4>
<a href="http://alexdussaq.info" class="btn btn-info btn-xs">
<span class="glyphicon glyphicon-new-window"></span>
Homepage
</a>
<a href="https://github.com/adussaq" class="btn btn-info btn-xs">
<span class="glyphicon glyphicon-new-window"></span>
GitHub
</a>
</div>
<p>MD/PhD student, Medical Scientist Training Program</p>
<p>Research interests: Kinomics</p>
</div>
<div class="member" itemscope itemtype="http://schema.org/Person">
<div>
<h4 itemprop="name">Alexander Grüneberg</h4>
<a href="https://agrueneberg.info" class="btn btn-info btn-xs" itemprop="url">
<span class="glyphicon glyphicon-new-window"></span>
Homepage
</a>
<a href="http://scholar.google.com/citations?user=j14410QAAAAJ" class="btn btn-info btn-xs">
<span class="glyphicon glyphicon-new-window"></span>
Publications
</a>
<a href="https://github.com/agrueneberg" class="btn btn-info btn-xs" itemprop="sameAs">
<span class="glyphicon glyphicon-new-window"></span>
GitHub
</a>
</div>
<p itemprop="jobTitle">Visiting Scientist</p>
<p itemprop="description">Research interests: Web Application Architectures</p>
</div>
<div class="member">
<div>
<h4>David Robbins, PhD</h4>
<a href="https://github.com/drobbins" class="btn btn-info btn-xs">
<span class="glyphicon glyphicon-new-window"></span>
GitHub
</a>
<a href="http://scholar.google.com/citations?user=U32NHqMAAAAJ" class="btn btn-info btn-xs">
<span class="glyphicon glyphicon-new-window"></span>
Publications
</a>
</div>
<p>Research Associate, Pathology Informatics</p>
<p>
Research interests: Software Ecosystems, Software Engineering, Analysis Ecosystems,
The Cancer Genome Atlas
</p>
</div>
<div class="member">
<div>
<h4>Sean Wilkinson</h4>
<a href="http://seanwilkinson.info" class="btn btn-info btn-xs">
<span class="glyphicon glyphicon-new-window"></span>
Homepage
</a>
<a href="http://scholar.google.com/citations?user=dYwPHwcAAAAJ" class="btn btn-info btn-xs">
<span class="glyphicon glyphicon-new-window"></span>
Publications
</a>
<a href="https://github.com/wilkinson" class="btn btn-info btn-xs">
<span class="glyphicon glyphicon-new-window"></span>
GitHub
</a>
</div>
<p>PhD student, Biomedical Engineering</p>
<p>Research interests: Distributed Computing, Web Science</p>
</div>
<!--
<h3 id="friends">Friends and visitors</h3>
-->
<h3 id="alumni">Alumni</h3>
<!--
We have forgotten Stuart and Matilde and *all* past students ...
-->
<div class="member">
<div>
<h4>Matthew D. Cain, MD</h4>
<a href="https://github.com/cainmd" class="btn btn-info btn-xs">
<span class="glyphicon glyphicon-new-window"></span>
GitHub
</a>
</div>
<p>Pathology Resident Rotation, 2013</p>
</div>
<div class="member">
<div>
<h4>Robert Gish</h4>
<a href="https://github.com/robcgish" class="btn btn-info btn-xs">
<span class="glyphicon glyphicon-new-window"></span>
GitHub
</a>
</div>
<p>Summer student from UAB Medical School</p>
</div>
<div class="member">
<div>
<h4>Henrique Goncalves</h4>
<a href="https://github.com/rickygoncalves" class="btn btn-info btn-xs">
<span class="glyphicon glyphicon-new-window"></span>
GitHub
</a>
</div>
<p>
Summer student from Columbia University (Computer Science
undergraduate)
</p>
</div>
<div class="member">
<div>
<h4>James R. Hackney, MD</h4>
<a href="https://github.com/jrhackney" class="btn btn-info btn-xs">
<span class="glyphicon glyphicon-new-window"></span>
GitHub
</a>
</div>
<p>Neuropathology Fellowship research year, 2011-2012</p>
</div>
<div class="member">
<div>
<h4>Benjamin C. Hill, MD</h4>
<a href="https://github.com/benchill" class="btn btn-info btn-xs">
<span class="glyphicon glyphicon-new-window"></span>
GitHub
</a>
</div>
<p>Pathology Resident Rotation, 2012</p>
</div>
<div class="member">
<div>
<h4>Vincent Laufer</h4>
</div>
<p>MD/PhD student, Medical Scientist Training Program</p>
</div>
<div class="member">
<div>
<h4>Giuliana Pirovani</h4>
<a href="https://github.com/giulianapirovani" class="btn btn-info btn-xs">
<span class="glyphicon glyphicon-new-window"></span>
GitHub
</a>
</div>
<p>
Summer student from Universidade Presbiteriana Mackenzie (Computer
Science undergraduate)
</p>
</div>
<div class="member">
<div>
<h4>Young Soo Song, MD, PhD</h4>
<a href="https://github.com/cytrix1" class="btn btn-info btn-xs">
<span class="glyphicon glyphicon-new-window"></span>
GitHub
</a>
</div>
<p>Postdoctoral researcher, 2011-2012</p>
</div>
</section>
<hr>
<section id="links">
<h2 id="links">Other links <small><a href="#top" class="glyphicon glyphicon-chevron-up"></a></small></h2>
<div>
<h4>UAB</h4>
<p><a href="http://www.uab.edu/medicine/pathology/divisions-a-sections/informatics">Division Page</a></p>
<p><a href="http://uab.mathbiol.org/workshop">Weekly Workshop</a></p>
<p><a href="https://github.com/ibl/ibl.github.com/wiki">Wiki</a></p>
</div>
</section>
<hr>
<section id="calendar">
<h2>Calendar <small><a href="#top" class="glyphicon glyphicon-chevron-up"></a></small></h2>
<div>
<iframe src="https://www.google.com/calendar/embed?showTitle=0&showPrint=0&showCalendars=0&mode=AGENDA&height=300&wkst=1&bgcolor=%23FFFFFF&src=Informatics%40mathbiol.org&color=%23B1440E&ctz=America%2FChicago" style="border-width: 0" width="800" height="300" frameborder="0" scrolling="no"></iframe>
</div>
</section>
<hr>
<section id="contact">
<h2>Contact <small><a href="#top" class="glyphicon glyphicon-chevron-up"></a></small></h2>
<div>
<address>
<strong>Division of Informatics, Department of Pathology</strong><br>
P220 West Pavilion<br>
615 18th Street South<br>
Birmingham, AL 35294-7331<br>
<abbr title="Phone">P:</abbr> (205) 934-0533<br>
<a href="mailto:[email protected]">[email protected]</a>
</address>
</div>
</section>
<hr>
<footer>
<p>©
Division of Informatics,
Department of Pathology,
UAB 2013-2014
</p>
</footer>
</div> <!-- /container -->
<!-- Le javascript
================================================== -->
<script src="js/jquery.min.js"></script>
<script src="js/bootstrap.min.js"></script>
</body>
</html>