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<!DOCTYPE html>
<!--[if lt IE 7 ]><html class="ie ie6" lang="en"> <![endif]-->
<!--[if IE 7 ]><html class="ie ie7" lang="en"> <![endif]-->
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<head>
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<meta name="viewport" content="width=device-width, initial-scale=1, maximum-scale=1">
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<title>iBioSim | Documentation</title>
<link rel="shortcut icon" href="https://www.async.ece.utah.edu/wp-content/themes/umctheme/images/favicon.ico"
type="image/x-icon">
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<div id="wrapper">
<div class="container">
<section id="top" class="section docs-heading">
<div class="row">
<div class="col-md-12">
<div class="big-title text-center">
<h1>iBioSim Documentation</h1>
</div>
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</div>
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<hr>
</section>
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<div class="col-md-3">
<nav class="docs-sidebar" data-spy="affix" data-offset-top="300" data-offset-bottom="200"
role="navigation">
<ul class="nav">Contents
<li><a href="#introduction">Introduction</a></li>
<li><a href="#installation">Installing iBioSim</a></li>
<li><a href="#getting-started">Getting Started</a></li>
<li><a href="#creating-a-project">Creating a Project</a></li>
<li><a href="#importing-from-repo">Importing from Repositories</a></li>
<li><a href="#uploading-to-repo">Uploading to an Online Repository</a></li>
<li><a href="#exporting-to-file">Exporting to Other File Formats</a></li>
<li><a href="#importing-from-file">Importing from Other File Formats</a></li>
<li><a href="#design-example">Design example</a></li>
<!--
<li><a href="#line7">How to Use Option Panel</a>
<ul class="nav">
<li><a href="#line7_1">General Options</a></li>
<li><a href="#line7_2">Style Options</a></li>
<li><a href="#line7_3">Header Options</a></li>
<li><a href="#line7_4">Font Options</a></li>
<li><a href="#line7_5">Slider Options</a></li>
<li><a href="#line7_6">Page Options</a></li>
<li><a href="#line7_7">Import & Export</a></li>
</ul>
</li>
<li><a href="#line8">Support Desk</a></li>
-->
<li><a href="#credits">Credits</a></li>
<li><a href="#copyright">Copyright and license</a></li>
</ul>
</nav>
</div>
<div class="col-md-9">
<section class="welcome" id="introduction">
<div class="row">
<div class="col-md-12 left-align">
<h2 class="dark-text">Introduction
<hr>
</h2>
<div class="row">
<p>iBioSim has been developed for the modeling, analysis, and design of genetic
circuits. While iBioSim primarily targets models of genetic circuits, models
representing metabolic networks, cell-signaling pathways, and other biological
and chemical systems can also be analyzed. iBioSim also includes modeling and
visualization support for multi-cellular and spatial models as well. It is
capable of importing and exporting models specified using the Systems Biology
Markup Language (SBML).Finally, it is one of the first tools to also support the
Synthetic Biology Open Language (SBOL), an emerging standard for information
exchange in synthetic biology.</p>
<p>IMPORTANT: this documentation is still under development. Older documentation and
tutorials are found here:</p>
<ul>
<li><a href="docs/iBioSim.html">iBioSim 2.8 Manual</a></li>
<li><a href="docs/iBioSim_SysBio_Tutorial.html">iBioSim 2.8 Systems Biology
Tutorial</a></li>
<li><a href="docs/iBioSim_SynBio_Tutorial.html">iBioSim 2.8 Synthetic Biology
Tutorial</a></li>
</ul>
<div class="intro1">
<ul>
<li><strong>Version : </strong> v 3.0</li>
<li><strong>Created by the </strong> <a
href="http://www.async.ece.utah.edu/SBOLDesigner"
target="_blank">Myers Research Group</a></li>
<li><strong>GitHub Repository : </strong> <a
href="https://github.com/MyersResearchGroup/iBioSim"
target="_blank">https://github.com/SynBioDex/SBOLDesigner</a>
</li>
<li><strong>Issue Tracker : </strong><a
href="https://github.com/MyersResearchGroup/iBioSim/issues"
target="_blank">https://github.com/SynBioDex/SBOLDesigner/issues</a>
</li>
<li><strong>Download : </strong> <a
href="https://github.com/SynBioDex/SBOLDesigner/releases/download/v3.0/SBOLDesigner-3.0.jar"
target="_blank">JAR File</a></li>
<li><strong>Readme : </strong><a
href="https://github.com/MyersResearchGroup/iBioSim/blob/master/README.md"
target="_blank">README.md</a></li>
</ul>
<div>
<p><strong>To cite iBioSim, please use the latest paper:</strong></p>
<p>Watanabe, Leandro, Tramy Nguyen, Michael Zhang, Zach Zundel, Zhen Zhang,
Curtis Madsen, Nicholas Roehner, and Chris Myers. 2018.
<a href="https://pubs.acs.org/doi/full/10.1021/acssynbio.8b00078">
"IBioSim 3: A Tool for Model-Based Genetic Circuit Design."
</a>
<i>ACS Synthetic Biology</i> 8
(7): 1560–1563. doi:10.1021/acssynbio.8b00078.</p>
</div>
</div>
</div>
<!-- end row -->
</div>
</div>
</section>
<hr>
<section id="installation" class="section installation">
<div class="row">
<div class="col-md-12 left-align">
<h2 class="dark-text">Installing iBioSim <a href="#top">#back to top</a>
<hr>
</h2>
</div>
<!-- end col -->
</div>
<!-- end row -->
<div class="row">
<div class="col-md-12">
<p class="pb0">Before installing iBioSim, please make sure that the following software
is installed on your
system.</p>
<ul class="ml4">
<li>
<a href="https://www.oracle.com/java/technologies/javase-downloads.html"
class="link">
Java Runtime Environment
</a> (Version 1.7 or higher)
</li>
<li>
<a href="https://www.graphviz.org/" class="link">Graphviz</a> (optional)
</li>
</ul>
<p class="pb0">
To install, download the zip file for your operating system and unzip it where you
want the application to reside.
</p>
<ul class="ml4">
<li>
<a href="https://github.com/MyersResearchGroup/iBioSim/releases/download/3.0.0/iBioSim-win64.zip"
class="link">
iBioSim-win64.zip
</a>
</li>
<li>
<a href="https://github.com/MyersResearchGroup/iBioSim/releases/download/3.0.0/iBioSim-linux64.zip"
class="link">
iBioSim-linux64.zip
</a>
</li>
<li>
<a href="https://github.com/MyersResearchGroup/iBioSim/releases/download/3.0.0/iBioSim-mac64.zip"
class="link">
iBioSim-mac64.zip
</a>
</li>
</ul>
<p class="pb0">
To run iBioSim, execute iBioSim in the top directory.
</p>
<div class="intro1">
<div class="row m0">
<p class="pb0 m0"><strong>For Windows users:</strong></p>
<p class="pb0 m0">If the application font appears very small, you need to follow
the next steps:</p>
<ol class="pl2">
<li>
Go to where Java is installed (usually C:\Program Files\Java\jre\bin)
and right click on the java.exe
file.
Select Properties, click the Compatibility tab, click on "Change high
DPI settings", and select
"Override
high DPI scaling behavior." and finally select Scaling
performed by: System.
</li>
<li>
If the previous step didn't solve the problem, try repeating the last
steps for all java*.exe files
(i.e:
java.exe,
javaw.exe javacl.exe, etc).
</li>
<li>
If the previous step didn't solve the problem, open a Command Prompt and
type "where ava". This will
list if
you have
any other folders containing java.exe files. Find these other files, and
follow the instructions in step
1)
of each of
them.
</li>
</ol>
</div>
<div class="row m0">
<p class="pb0 mb0"><strong>For Linux users:</strong></p>
<p class="pb0 m0">Dependencies are resolved at runtime when iBioSim is opened
for the first time. <br> In order
to compile the dependencies, you need the following:</p>
<ul class="pl2">
<li>bison</li>
<li>flex</li>
<li>swig</li>
<li>python2</li>
<li>libxml2-dev</li>
</ul>
</div>
</div>
</div>
</div>
</section>
<hr>
<section id="getting-started" class="section">
<div class="row">
<div class="col-md-12 left-align">
<h2 class="dark-text">Getting Started <a href="#top">#back to top</a>
<hr>
</h2>
</div>
<!-- end col -->
</div>
<!-- end row -->
<div class="row">
<div class="col-md-12">
<p>Before beginning to use iBioSim, go to your preferences and change your
<strong>name</strong>, <strong>email</strong>, and <strong>URI</strong> to something
unique.</p>
<h4>Preferences Screen</h4>
<div class="text-center">
<img src="images/preference.PNG" width="500" height="400">
</div>
</div>
<!-- end col -->
</div>
<!-- end row -->
</section>
<!-- end section -->
<section id="creating-a-project" class="section">
<div class="row">
<div class="col-md-12 left-align">
<h2 class="dark-text">Creating a Project <a href="#top">#back to top</a></h2>
</div>
<!-- end col -->
</div>
<!-- end row -->
<hr>
<div class="row">
<div class="col-md-12">
<p> To create a new project, select New → Project from the File menu as shown below. You
will then be prompted to browse to a desired location and to give a name to the
project
directory. After you do this, click the new button and a new project directory will
be
created. To open a project, select Open Project from the File menu. You will then be
prompted to browse to a project directory to open, and clicking open will open the
project. You may also open a project by selecting one of your ten most recently
opened
projects by selecting the project name shown in the Open Recent menu within the File
menu.</p>
<div class="text-center">
<img src="images/creatproject.PNG" width="400" height="450">
</div>
<hr>
<h4>Main Screen</h4>
<div class="text-center">
<img src="images/mainScreen.PNG" width="700" height="450">
</div>
<p>This is the main screen of iBioSim. The top bar comprises of functions such
as
saving and exporting, while the bottom bar holds parts available for use.
</p>
</div>
</div>
</section>
<!-- end section -->
<section id="importing-from-repo" class="section">
<div class="row">
<div class="col-md-12 left-align">
<h2 class="dark-text">Importing from Repositories <a href="#top">#back to top</a>
<hr>
</h2>
<p>To import a registry part from an online repository, double click on a part to view
its
details, click on (import registry part) then choose and filter the desired
repository
such as synBioHub.</p>
<div class="text-center">
<img src="images/importRepo.png" width="350" height="350">
<img src="images/importReg.png" width="350" height="350">
</div>
<p> Here is a short video on how to do that.</p>
<div class="text-center">
<video width="500" height="300" controls>
<source src="videos/importingParts.mp4" type="video/mp4">
</video>
</div>
</div>
<!-- end col -->
</div>
<!-- end row -->
<hr>
</section>
<!-- end section -->
<section id="uploading-to-repo" class="section">
<div class="row">
<div class="col-md-12 left-align">
<h2 class="dark-text">Uploading to an Online Repository <a href="#top">#back to top</a>
<hr>
</h2>
<p>
You can share your design by uploading it to an online repository such as synBioHub.
</p>
<p>First, go to File → upload → Design, as showen below </p>
<div class='text-center'>
<img src="images/uploadTo.PNG" width="400" height="500">
</div>
<p> Second, choose the online repository, make sure you are logged in to synBioHub.
</p>
<div class="text-center">
<img src="images/uploadTo2.PNG">
</div>
</div>
<!-- end col -->
</div>
<!-- end row -->
<hr>
<div class="row">
<div class="col-md-12">
<p>If you need additional help, you can watch this tutorial video on how to upload to
SynBioHub.</p>
<div class="text-center">
<div class="media">
<iframe width="560" height="315" src="https://www.youtube.com/embed/Osbk5zNrJeA"
frameborder="0" allow="autoplay; encrypted-media" allowfullscreen>
</iframe>
</div>
</div>
</div>
</div>
</section>
<!-- end section -->
<section id="exporting-to-file" class="section">
<div class="row">
<div class="col-md-12 left-align">
<h2 class="dark-text">Exporting to Other File Formats <a href="#top">#back to top</a>
<hr>
</h2>
<p>iBioSim allows you to export to other file formats such as GenBank or FASTA. </p>
<p> To do that, simply go to Files → export → Design, and then you can choose the
desired formats.</p>
<div class="text-center">
<img src="images/export.PNG" width="400" height="500">
</div>
</div>
</div>
<!-- end row -->
</section>
<!-- end section -->
<section id="importing-from-file" class="section">
<div class="row">
<div class="col-md-12 left-align">
<h2 class="dark-text">Importing from Other File Formats <a href="#top">#back to top</a>
<hr>
</h2>
<p>iBioSim also allows you to import from other file formats saved on your computer.</p>
<p> Similar to exporting process, go to Files → import → Design/Model, then your desired
format.</p>
<div class="text-center">
<img src="images/import.PNG" width="400" height="500">
</div>
</div>
</div>
<!-- end row -->
</section>
<!-- end section -->
<section id="design-example" class="section">
<div class="row">
<div class="col-md-12 left-align">
<h2 class="dark-text">Design example <a href="#top">#back to top</a>
<hr>
</h2>
<p>Here is a tutorial video on how to create an example of a full design in iBioSim.</p>
<iframe width="560" height="315" src="https://www.youtube.com/embed/YfsUis2cV2A"
frameborder="0" allow="autoplay; encrypted-media" allowfullscreen></iframe>
</div>
</div>
</section>
<!-- end section -->
<!-- <section id="line7" class="section">
<div class="row">
<div class="col-md-12 left-align">
<h2 class="dark-text">How to Use Option Panel <a href="#top">#back to top</a><hr></h2>
</div>
</div>
<div class="row">
<div class="col-md-4">
<a href="upload/thumbnail.png" data-rel="prettyPhoto"><img src="images/upload/thumbnail.png" alt="" class="img-responsive img-thumbnail"></a>
</div>
<div class="col-md-8">
<h4 id="line7_1">General Options - <a href="#top">#back to top</a></h4>
<p>Lorem the It is a long established fact that a reader will be distracted by the readable content of a page when looking at its layout. The point of using Lorem Ipsum is that it has a more-or-less normal distribution of letters, as opposed to using 'Content here, content here', making it look like readable English. long established fact that a reader will English.</p>
</div>
</div>
<hr>
<div class="row">
<div class="col-md-4">
<a href="upload/thumbnail.png" data-rel="prettyPhoto"><img src="images/upload/thumbnail.png" alt="" class="img-responsive img-thumbnail"></a>
</div>
<div class="col-md-8">
<h4 id="line7_2">Style Options - <a href="#top">#back to top</a></h4>
<p>Lorem the It is a long established fact that a reader will be distracted by the readable content of a page when looking at its layout. The point of using Lorem Ipsum is that it has a more-or-less normal distribution of letters, as opposed to using 'Content here, content here', making it look like readable English. long established fact that a reader will English.</p>
</div>
</div>
<hr>
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<p>Lorem the It is a long established fact that a reader will be distracted by the readable content of a page when looking at its layout. The point of using Lorem Ipsum is that it has a more-or-less normal distribution of letters, as opposed to using 'Content here, content here', making it look like readable English. long established fact that a reader will English.</p>
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<p>Lorem the It is a long established fact that a reader will be distracted by the readable content of a page when looking at its layout. The point of using Lorem Ipsum is that it has a more-or-less normal distribution of letters, as opposed to using 'Content here, content here', making it look like readable English. long established fact that a reader will English.</p>
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<p>Lorem the It is a long established fact that a reader will be distracted by the readable content of a page when looking at its layout. The point of using Lorem Ipsum is that it has a more-or-less normal distribution of letters, as opposed to using 'Content here, content here', making it look like readable English. long established fact that a reader will English.</p>
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<p>Lorem the It is a long established fact that a reader will be distracted by the readable content of a page when looking at its layout. The point of using Lorem Ipsum is that it has a more-or-less normal distribution of letters, as opposed to using 'Content here, content here', making it look like readable English. long established fact that a reader will English.</p>
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<p>Lorem the It is a long established fact that a reader will be distracted by the readable content of a page when looking at its layout. The point of using Lorem Ipsum is that it has a more-or-less normal distribution of letters, as opposed to using 'Content here, content here', making it look like readable English. long established fact that a reader will English.</p>
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<p>Please remember you have purchased a very affordable theme and you have not paid for a full-time web design agency. Occasionally we will help with small tweaks, but these requests will be put on a lower priority due to their nature. Support is also 100% optional and we provide it for your connivence, so please be patient, polite and respectful.</p>
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<p>The iBioSim tool is being developed by Chris Myers research group at the University
of
Utah. This project has involved many students including Nathan Barker, Scott Glass,
Kevin Jones, Hiroyuki Kuwahara, Curtis Madsen, Nam Nguyen, Tramy Nguyen, Tyler
Patterson, Nicholas Roehner, Jason Stevens, Leandro Watanabe, and Zhen Zhang.
</p>
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<p><strong>To cite iBioSim, please use the latest paper:</strong></p>
<p>Watanabe, Leandro, Tramy Nguyen, Michael Zhang, Zach Zundel, Zhen Zhang,
Curtis Madsen, Nicholas Roehner, and Chris Myers. 2018.
<a href="https://pubs.acs.org/doi/full/10.1021/acssynbio.8b00078">
"IBioSim 3: A Tool for Model-Based Genetic Circuit Design."
</a>
<i>ACS Synthetic Biology</i> 8
(7): 1560–1563. doi:10.1021/acssynbio.8b00078.</p>
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<p>IBIOSIM is released under the <a
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target="_blank">Apache 2.0</a> License.</p>
<p>For more information about the Apache license go to <a
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