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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1">
<meta name="description" content="">
<meta name="author" content="">
<link rel="shortcut icon" href="img/eugene-favicon_small.jpg">
<title>Eugene</title>
<!-- Bootstrap core CSS -->
<link href="css/bootstrap.css" rel="stylesheet">
<link href="css/custom.css" rel="stylesheet">
<!-- Custom styles for this template -->
<link href="css/jumbotron-narrow.css" rel="stylesheet">
</head>
<body>
<div class="container">
<header class="navbar navbar-static-top bs-docs-nav" id="top" role="banner" style = "position: absolute;top: 0px;">
<div class="container">
<div class="navbar-header">
<button class="navbar-toggle" type="button" data-toggle="collapse" data-target=".bs-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 href="" class="navbar-brand">Eugene</a> -->
</div>
<nav class="navbar-collapse bs-navbar-collapse" role="navigation">
<ul class="nav navbar-nav">
<li>
<a href="index.html" class = "nav">Home</a>
</li>
<li class = "active" >
<a href="about.html" class = "nav">About</a>
</li>
<li>
<a href="downloads.html" class = "nav">Downloads</a>
</li>
<li>
<a href="contact.html" class = "nav" >Contact</a>
</li>
</ul>
</nav>
</div>
</header>
</div>
<img src = "img/Gradient.png" style = "width: 100%; height: 50px;position: absolute; top: 0px;">
<div class="container" style = "padding-top:40px;">
<div class="row">
<div class="col-xs-12" style = "border-bottom: 1px solid #cccccc;">
<h1 class = "head">What is Eugene?</h1>
</div>
</div>
<div style="margin-left:50px">
<br/>
Eugene is an ecosystem of human-readable and machine-executable languages developed to speed up and innovate the design process of
synthetic biology at various levels of abstraction, such as Sequences, Parts, Devices, and Systems. Eugene contributes towards standardized languages for communicating Synthetic Biology.
<br/><br/>
Eugene's facilities for synthetic biology include:
<ul>
<li>
Specification of <b>(synthetic) biological components</b>
</li>
<li>
Support of <b>Data Exchange</b> standards
</li>
<li>
<b>Library Management</b> of design and components
</li>
<li>
Specification of <b>design constraints ("Rules")</b> on composing components into novel systems
</li>
<li>
<b>Built-In functions</b> to enumerate rule-compliant designs automatically
</li>
<li>
<b>Control structures</b> and <b>functions</b> for the specification of design synthesis
</li>
</ul>
</div>
<div class="row">
<div class="col-xs-12">
<img src = "img/eugene.jpg" style = "display:block; margin-left: auto; margin-right:auto; padding-top:30px;">
</div>
</div>
<div class="row">
<div class="col-xs-12" style = "border-bottom: 1px solid #cccccc;">
<h1 class = "head">Publications</h1>
</div>
</div>
<div style="margin-left:50px">
<br/>
E. Oberortner, D. Densmore<br/>
miniEugene: Constraint-based Design of Synthetic Biological Systems<br/>
ACS Synthetic Biology - Technical Note<br/>
<a href="http://pubs.acs.org/doi/abs/10.1021/sb500352b" target="_blank">DOI:10.1021/sb500352b</a>
<br/><br/>
E. Oberortner, S. Bhatia, E. Lindgren, D. Densmore<br/>
A Rule-based Design Specification Language for Synthetic Biology<br/>
ACM Journal on Emerging Technologies in Computing Systems (JETC)<br/>
Special Issue on Synthetic Biology<br/>
<a href="http://dx.doi.org/10.1145/2641571" target="_blank">DOI:10.1145/2641571</a>
<br/><br/>
H. Huang, E. Oberortner, D. Densmore, and A. Kuchinsky<br/>
Eugene’s Enriched Set of Features to Design Synthetic Biological Devices<br/>
International Workshop on Bio-Design Automation (IWBDA),
<a href="http://www.iwbdaconf.org/2012/" target="_blank">2012</a>.
<br/><br/>
D. Densmore, J. T. Kittleson, L. Bilitchenko, A. Liu, and J. C. Anderson<br/>
Rule based constraints for the construction of genetic devices<br/>
Proceedings of 2010 IEEE International Symposium on Circuits and Systems (ISCAS), 2010.<br/>
<a href="http://dx.doi.org/10.1109/ISCAS.2010.5537540" target="_blank">DOI:10.1109/ISCAS.2010.5537540</a>
<br/><br/>
L. Bilitchenko, A. Liu, S. Cheung, E. Weeding, B. Xia, M. Leguia, J. C. Anderson, and D. Densmore<br/>
Eugene – a domain specific language for specifying and constraining synthetic biological parts, devices, and systems<br/>
PLoS ONE, vol. 6, iss. 4, p. e18882, 2011.<br/>
<a href="http://dx.plos.org/10.1371/journal.pone.0018882" target="_blank">DOI:10.1371/journal.pone.0018882</a>
<br/><br/>
L. Bilitchenko, A. Liu, and D. Densmore<br/>
The Eugene language for synthetic biology<br/>
Methods of Enzymology, vol. 498, pp. 153-172, 2011.<br/>
<a href="http://linkinghub.elsevier.com/retrieve/pii/B978-0-12-385120-8.00007-3" target="_blank">DOI:10.1016/B978-0-12-385120-8.00007-3</a>
<br/><br/>
</div>
<div class="row">
<div class="col-xs-12" style = "border-bottom: 1px solid #cccccc;">
<h1 class="head">Contributors</h1>
</div>
</div>
<div style="margin-left:50px">
<br/>
The first version of Eugene was developed by the <a href="http://2009.igem.org/Team:Berkeley_Software" target="_blank">2009 iGEM UC Berkeley Software Team</a>, who also won the <b>Best Software Tool</b> award.
<br/><br/>
<b>Agilent Technologies</b> funded the development and evolution of Eugene in 2012 and 2013.<br/>
<div class="row">
<div class="col-xs-12">
<div class="text-center">
<a href="http://agilent.com" target="_blank"><img src="img/agilent_logo.jpg" width="50%"/></a>
</div>
</div>
</div>
<br/><br/>
The <b>Joint BioEnergy Institute (JBEI)</b> integrates Eugene into the <b>DeviceEditor</b> CAD Tool.<br/>
<a href="http://www.jbioleng.org/content/6/1/1" target="_blank">DOI:10.1186/1754-1611-6-1</a>
<br/><br/>
<b>Life Technologies</b> (a <b>Thermo Fisher Scientific</b> brand) integrates Eugene into the
<a href="http://www.lifetechnologies.com/us/en/home/life-science/cloning/vector-nti-software/vector-nti-express-designer-software.html" target="_blank">Vector NTI Express Designer Software</a>.
<br/><br/>
The <b>Boston University <a href="http://2012.igem.org/Team:BostonU" target="_blank">2012</a>, <a href="http://2013.igem.org/Team:BostonU" target="_blank">2013</a>, and <a href="http://2014.igem.org/Team:BostonU" target="_blank">2014</a> iGEM Teams</b> utilized Eugene in the
design of their iGEM projects.
<br/><br/>
All members of the <a href="http://cidarlab.org" target="_blank">CIDAR Group</a> contributed to Eugene. Specifically the following (current and affilated) supported Eugene's development:<br>
<ul>
<li>
<b>Evan Appleton</b>
</li>
<li>
<b>Swapnil Bhatia</b>
</li>
<li>
<b>Swati Carr</b>
</li>
<li>
<b>Bryan Der</b>
</li>
<li>
<b>Traci Haddock</b>
</li>
<li>
<b>Haiyao "Cassie" Huang</b>
</li>
<li>
<b>Nicholas Roehner</b>
</li>
<li>
<b>Jenhan Tao</b>
</li>
<li>
<b>Prashant Vaidyanathan</b>
</li>
</ul>
The following <b>Boston University</b> graduates contributed to Eugene:
<ul>
<li>
<b>Erik Lindgren</b>
</li>
<li>
<b>Carter Wheatley</b>
</li>
</ul>
Eugene is <a href="http://www.sbolstandard.org/sbolstandard" target="_blank">SBOL Standard</a> and <a href="http://www.sbolstandard.org/visual" target="_blank">SBOL Visual</a> compliant.
<br/><br/>
</div>
<div class="row">
<div class="col-xs-12" style = "border-bottom: 1px solid #cccccc;">
<h1 class="head">In Memory of</h1>
</div>
</div>
<div class="row">
<div class="col-xs-12">
<div class="text-center">
<br/>
<img src="img/allan.jpg"><br/>
<b>Allan Kuchinsky</b>
</div>
</div>
</div>
</div>
<!-- Footer (Nona + BU + License) -->
<div class="footer row text-center">
<!-- Trademark -->
Eugene is a trademark of Nona Research Foundation, Inc.
<br/>
CIDAR Group, Dept. of Electrical and Computer Engineering, Boston University, 2014
<br/>
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<a rel="license" href="http://creativecommons.org/licenses/by-sa/4.0/">
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<br />
This work is licensed under a <a rel="license" href="http://creativecommons.org/licenses/by-sa/4.0/">Creative Commons Attribution-ShareAlike 4.0 International License</a>.
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