Difference between revisions of "Team:Slovenia/Software"

 
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<head>
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<p>Regardless of the topic, iGEM projects often create or adapt computational tools to move the project forward. Because they are born out of a direct practical need, these software tools (or new computational methods) can be surprisingly useful for other teams. Without necessarily being big or complex, they can make the crucial difference to a project's success. This award tries to find and honor such "nuggets" of computational work.</p>
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    <title>Software</title>
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    <link rel="stylesheet"
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<h5> Inspiration </h5>
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          href="//2016.igem.org/Team:Slovenia/libraries/semantic-min-css?action=raw&ctype=text/css">
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<p>
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    <script type="text/javascript"
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Here are a few examples from previous teams:
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            src="//2016.igem.org/Team:Slovenia/libraries/semantic-min-js?action=raw&ctype=text/javascript"></script>
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</p>
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    <link rel="stylesheet" type="text/css" href="//2016.igem.org/Team:Slovenia/libraries/custom-css?action=raw&ctype=text/css">
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<ul>
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    <script type="text/javascript" src="//2016.igem.org/Team:Slovenia/libraries/custom-js?action=raw&ctype=text/javascript"></script>
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<li><a href="https://2013.igem.org/Team:TU-Munich/Results/Software">TU Munich 2013</a></li>
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    <script type="text/javascript"
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<li><a href="https://2014.igem.org/Team:Heidelberg/Software">Heidelberg 2014</a></li>
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            src="//2016.igem.org/Team:Slovenia/libraries/zitator-js?action=raw&ctype=text/javascript"></script>
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<li><a href="https://2014.igem.org/Team:Aachen/Project/Measurement_Device#Software">Aachen 2014</a></li>
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    <script type="text/javascript"
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</ul>
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            src="https://2016.igem.org/Team:Slovenia/libraries/bibtexparse-js?action=raw&ctype=text/javascript"></script>
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</head>
 +
<body>
 +
<div id="example">
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    <div class="pusher">
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        <div class="full height">
 +
            <div class="banana">
 +
<a href = "//2016.igem.org/Team:Slovenia">
 +
<img class="ui medium sticky image" src="//2016.igem.org/wiki/images/d/d1/T--Slovenia--logo.png">
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</a>
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                <div class="ui vertical sticky text menu">
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                    <a class="item" href="//2016.igem.org/Team:Slovenia/Model">
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                        <i class="chevron circle left icon"></i>
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                        <b>Modeling of ultrasound</b>
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                    </a>
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                    <a class="item" href="//2016.igem.org/Team:Slovenia/Software" style="color:#DB2828">
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                        <i class="selected radio icon"></i>
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                        <b>CaPTURE software</b>
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                    </a>
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                    <a class="item" href="#ach" style="margin-left: 10%">
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                        <i class="selected radio icon"></i>
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                        <b>Achievements</b>
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                    </a>
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                    <a class="item" href="#des" style="margin-left: 10%">
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                        <i class="selected radio icon"></i>
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                        <b>Description</b>
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                    </a>
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                    <a class="item" href="#req" style="margin-left: 10%">
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                        <i class="selected radio icon"></i>
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                        <b>System requirements</b>
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                    </a>
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                    <a class="item" href="#install" style="margin-left: 10%">
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                        <i class="selected radio icon"></i>
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                        <b>Installing and running</b>
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                    </a>
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                    <a class="item" href="#build" style="margin-left: 10%">
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                        <i class="selected radio icon"></i>
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                        <b>Building from source</b>
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                    </a>
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                    <a class="item" href="#faq" style="margin-left: 10%">
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                        <i class="selected radio icon"></i>
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                        <b>FAQ</b>
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                    </a>
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                    <a class="item" href="//2016.igem.org/Team:Slovenia/ModelLogic">
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                        <i class="chevron circle right icon"></i>
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                        <b>Modeling logic gates</b>
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                    </a>
 +
                </div>
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            </div>
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            <div class="article" id="context">
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                <!-- menu goes here -->
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                <div class="main ui citing justified container">
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<h1 class = "ui left dividing header"><span class="section colorize">&nbsp;</span>CaPTURE software for Ca influx analysis </h1>
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<div class = "ui segment" style = "background-color: #ebc7c7; ">
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<p><span id = "ach" class = "section colorize"></span></p>
 +
<p><b><ul>
 +
<li>Digital image analysis software was designed to quantify the cellular response to ultrasound.
 +
<li>The software automatically scans for response regions using the sliding window technique
 +
<li>The source is available under GNU general public licence on <a href="//github.com/zigapusnik/CaPTURE">GitHub</a>.
 +
</b></ul></p>
 +
</div>
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<div class = "ui segment">
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<div>
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<h4><span id="des" class="section colorize"> &nbsp; </span></h4>
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<p>CaPTURE software was developed by the Slovenian 2016 iGEM team with an aim to analyze the calcium influx into mammalian cells upon ultrasound
 +
stimulation of mechanosensitive channels detected by the fluorescence microscopy. CaPTURE analyses the digital images from the confocal microscope
 +
to detect the cellular response to stimulation by change of the fluorescence. Software calculates the ratio of the fluorescence in two channels and
 +
it automatically scans for the response regions using the sliding window technique and provides the temporal response of cells. Track of each cell
 +
can be monitored or average calculated and different threshold and selection criteria can be set. The software was prepared for our Sonicell project,
 +
but it can be used for virtually any time dependent images the synthetic biology community.  
 +
</p>
 +
<div align="center">
 +
<video width="60%" controls>
 +
<source src="//2016.igem.org/wiki/images/e/e1/T--Slovenia--CAPTUREFINALTAKE.mp4"
 +
type="video/mp4">
 +
Your browser does not support HTML5 video.
 +
</video>
 +
</div>
 +
</div>
 +
<div>
 +
<h3><span id="req" class="section colorize"> &nbsp; </span> System requirements </h3>
 +
<p>CaPTURE runs on any system equipped with the Java Virtual Machine (1.7 or newer), which can be
 +
downloaded at no
 +
cost from <a href="//www.oracle.com/technetwork/java/javase/downloads/index.html">Oracle</a>.
 +
</p>
 +
</div>
 +
<div> 
 +
<h3><span id="install"  class="section colorize"> &nbsp; </span> Installing and running </h3>
 +
<p> Download the <a href="//2016.igem.org/wiki/images/8/8f/T--Slovenia--CaPTURE.zip">CaPTURE folder</a>
 +
and unzip it. CaPTURE is also available on <a href="//github.com/zigapusnik/CaPTURE">GitHub</a>. The simplest way to run the program is by double
 +
clicking on the CaPTURE.jar file, however, it might not work on some systems. Alternatively,
 +
execute the program
 +
from the command line using the following command:</p>
 +
<div class="ui message">
 +
java -jar CaPTURE.jar
 +
</div>
 +
<p>
 +
To run the application from the JAR file that is in another directory, you must specify the path
 +
of that
 +
directory:
 +
</p>
 +
<div class="ui message">
 +
java -jar path/CaPTURE.jar
 +
</div>
 +
<p>
 +
Note that on Windows the forward slash as the directory separator should be replaced with a
 +
backslash.
 +
To test the software you can download the example <a href="//2016.igem.org/wiki/images/9/97/T--Slovenia--MscS_optimization_CaPTURE_analysis.zip">.lif file</a>. Extract the file and open it with CaPTURE.
 +
</p>
 +
</div>
 +
<div>
 +
<h3><span id="build"  class="section colorize"> &nbsp; </span> Building from source </h3>
 +
<p>
 +
To build the application from source, follow the given steps: </p>
 +
<ul class="ui list">
 +
<li>Download <a href="//2016.igem.org/wiki/images/8/8f/T--Slovenia--CaPTURE.zip">CaPTURE</a> and unzip it.</li>
 +
<li>Change the working directory to unzipped CaPTURE folder.</li>
 +
<li>Then compile .java source files to executable .class files.</li>
 +
<li>Copy bioformats_package.jar and icon.png resource file from the src directory in the
 +
scanPackage directory that was created during the compilation.
 +
</li>
 +
<li>Create a single java archive file from multiple .class files.</li>
 +
<li>Then you can start the program.</li>
 +
</ul>
 +
<p> Linux & OS X:</p>
 +
<div class="ui message">
 +
cd CaPTURE <br>
 +
javac -d . -cp src/bioformats_package.jar src/*.java <br>
 +
cp src/icon.png scanPackage <br>
 +
jar cfm CaPTURE.jar MANIFEST.MF scanPackage <br>
 +
java -jar CaPTURE.jar
 +
</div>
 +
<p> Windows: </p>
 +
<div class="ui message">
 +
cd CaPTURE <br>
 +
javac -d . -cp src\bioformats_package.jar src\*.java <br>
 +
robocopy src scanPackage icon.png<br>
 +
jar cfm CaPTURE.jar MANIFEST.MF scanPackage <br>
 +
java -jar CaPTURE.jar
 +
</div>
 +
</div>
 +
<div>
 +
<h3><span id="faq"  class="section colorize">&nbsp; </span> FAQ</h3>
 +
<h5> I tried to open a file, but CaPTURE froze during the processing. What should I
 +
do? </h5>
 +
<p> Most likely your JVM ran out of memory. While it is not possible to address more than 4GB with 32
 +
bit Java, 64 bit version is preferred. It is also possible to increase the maximum heap size
 +
using the -Xmx switch. For maximum heap size of 1024 MB the following command should be executed
 +
from the command line:
 +
</p>
 +
<div class="ui message">
 +
java -Xmx1024m -jar CaPTURE.jar
 +
</div>
  
 +
<h5> I want to open several files at the same time. How to do it? </h5>
 +
<p> Currently only one file can be loaded. You can, however, open a new instance of CaPTURE and
 +
analyze the second file in it.
 +
</p>
 +
<h5> I cannot open other microscopic file formats. Are other formats not supported? </h5>
 +
<p> Currently only .lif format is supported, however in the future CaPTURE will support other
 +
microscopic image formats.
 +
</p>
 +
<h5 style="white-space:normal"> I tried to compile the source using my OpenJDK implementation, but
 +
got the following error "TimeLineJForm.java:37: error: package javafx.stage does not
 +
exist". </h5>
 +
<p><a href="//wiki.openjdk.java.net/display/OpenJFX/Main">OpenJFX</a> is needed to compile the
 +
source code. For many platforms you can simply install (or update) JDK 8.
 +
</p>
 +
</div>
 +
                    <!-- div article ends here -->
 +
                </div>
 +
</div>
 +
            </div>
 +
        </div>
 +
    </div>
 
</div>
 
</div>
−
 
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<div>
 +
<a href="//igem.org/Main_Page">
 +
<img border="0" alt="iGEM" src="//2016.igem.org/wiki/images/8/84/T--Slovenia--logo_250x250.png" width="5%" style = "position: fixed; bottom:0%; right:1%;">
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</a>
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</div>
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</body>
 
</html>
 
</html>

Latest revision as of 14:26, 19 October 2016

Software

Modeling of ultrasound CaPTURE software Achievements Description System requirements Installing and running Building from source FAQ Modeling logic gates

 CaPTURE software for Ca influx analysis

  • Digital image analysis software was designed to quantify the cellular response to ultrasound.
  • The software automatically scans for response regions using the sliding window technique
  • The source is available under GNU general public licence on GitHub.

 

CaPTURE software was developed by the Slovenian 2016 iGEM team with an aim to analyze the calcium influx into mammalian cells upon ultrasound stimulation of mechanosensitive channels detected by the fluorescence microscopy. CaPTURE analyses the digital images from the confocal microscope to detect the cellular response to stimulation by change of the fluorescence. Software calculates the ratio of the fluorescence in two channels and it automatically scans for the response regions using the sliding window technique and provides the temporal response of cells. Track of each cell can be monitored or average calculated and different threshold and selection criteria can be set. The software was prepared for our Sonicell project, but it can be used for virtually any time dependent images the synthetic biology community.

  System requirements

CaPTURE runs on any system equipped with the Java Virtual Machine (1.7 or newer), which can be downloaded at no cost from Oracle.

  Installing and running

Download the CaPTURE folder and unzip it. CaPTURE is also available on GitHub. The simplest way to run the program is by double clicking on the CaPTURE.jar file, however, it might not work on some systems. Alternatively, execute the program from the command line using the following command:

java -jar CaPTURE.jar

To run the application from the JAR file that is in another directory, you must specify the path of that directory:

java -jar path/CaPTURE.jar

Note that on Windows the forward slash as the directory separator should be replaced with a backslash. To test the software you can download the example .lif file. Extract the file and open it with CaPTURE.

  Building from source

To build the application from source, follow the given steps:

  • Download CaPTURE and unzip it.
  • Change the working directory to unzipped CaPTURE folder.
  • Then compile .java source files to executable .class files.
  • Copy bioformats_package.jar and icon.png resource file from the src directory in the scanPackage directory that was created during the compilation.
  • Create a single java archive file from multiple .class files.
  • Then you can start the program.

Linux & OS X:

cd CaPTURE
javac -d . -cp src/bioformats_package.jar src/*.java
cp src/icon.png scanPackage
jar cfm CaPTURE.jar MANIFEST.MF scanPackage
java -jar CaPTURE.jar

Windows:

cd CaPTURE
javac -d . -cp src\bioformats_package.jar src\*.java
robocopy src scanPackage icon.png
jar cfm CaPTURE.jar MANIFEST.MF scanPackage
java -jar CaPTURE.jar

  FAQ

I tried to open a file, but CaPTURE froze during the processing. What should I do?

Most likely your JVM ran out of memory. While it is not possible to address more than 4GB with 32 bit Java, 64 bit version is preferred. It is also possible to increase the maximum heap size using the -Xmx switch. For maximum heap size of 1024 MB the following command should be executed from the command line:

java -Xmx1024m -jar CaPTURE.jar
I want to open several files at the same time. How to do it?

Currently only one file can be loaded. You can, however, open a new instance of CaPTURE and analyze the second file in it.

I cannot open other microscopic file formats. Are other formats not supported?

Currently only .lif format is supported, however in the future CaPTURE will support other microscopic image formats.

I tried to compile the source using my OpenJDK implementation, but got the following error "TimeLineJForm.java:37: error: package javafx.stage does not exist".

OpenJFX is needed to compile the source code. For many platforms you can simply install (or update) JDK 8.