about.php

<div><h1>Introduction</h1>
<p>WholeCellViz is a web-based software program for visually analyzing whole-cell simulations of the Gram-positive bacterium <i>Mycoplasma genitalium</i>. WholeCellViz enables users to analyze several aspects of cell physiology including
<ul>
<li>The cell mass, volume, and shape,</li>
<li>The copy number of every metabolite, RNA, and protein,</li>
<li>The flux of every metabolic reaction,</li>
<li>The status of every molecular machine &ndash; DNA polymerase, RNA polymerase, ribosome, FtsZ ring, and</li>
<li>The copy number, superhelicity, integrity, and DNA binding status of every chromosome.</li>
</ul>
</p>
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<div><h1>Getting started</h1>
<p>The best ways to get started are to browse or search WholeCellViz using the menu or the search box at the top of this page. See the tutorial for additional help getting started.</p>
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<div><h1>Installing WholeCellViz locally</h1>
<p>The WholeCellViz source code and simulated data are freely available at <a href="http://simtk.org/project/xml/downloads.xml?group_id=714">SimTK</a>.</p>
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<div><h1>Citing WholeCellViz</h1>
<p>Please use the following references to cite WholeCellViz:</p>
<ul>
<li>Lee R<sup>*</sup>, Karr JR<sup>*</sup>, Covert MW. WholeCellViz: Data Visualization for Whole-Cell Models. (In preparation).</li>
<li>Karr JR et al. A Whole-Cell Computational Model Predicts Phenotype from Genotype. <i>Cell</i> 150 <b>2</b>, 389-401 (2012). <a href="http://www.cell.com/abstract/S0092-8674(12)00776-3">Cell</a> | <a href="http://www.ncbi.nlm.nih.gov/pubmed/22817898">PubMed</a> | <a href="http://simtk.org/home/wholecell">SimTK</a></li>
</ul>
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<div><h1>Development Team</h1>
<p>WholeCellViz was developed by a team of three researchers at Stanford University:
<ul>
<li><a href="http://www.stanford.edu/~rubylee">Ruby Lee</a>, Undergraduate Student in Bioengineering</li>
<li><a href="http://www.stanford.edu/~jkarr">Jonathan Karr</a>, Graduate Student in Biophysics</li>
<li><a href="http://covertlab.stanford.edu/">Markus Covert</a>, Assistant Professor of Bioengineering</li>
</ul></p>
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<div><h1>Implementation</h1>
<p>WholeCellViz consists of a graphical user interface and storage server. The WholeCellViz user interface was implemented in javascript using <a href="http://jquery.com/">jQuery</a>, <a href="http://code.google.com/p/flot/">flot</a>, and <a href="http://threejs.org/">three.js</a>. The WholeCellViz server was implemented using <a href="http://php.net/">PHP</a> and <a href="http://www.mysql.com/">MySQL</a>. Simulations were stored on the server using <a href="http://www.json.org/">JSON</a>. The user interface and server communicated using <a href="http://www.json.org/">JSON</a>.</p>
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<div><h1>Questions &amp; comments</h1>
<p>Please contact us at <a href="mailto:wholecell@lists.stanford.edu">wholecell@lists.stanford.edu</a> with any questions and/or comments about WholeCellViz.</p>
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