http://2012.igem.org/wiki/index.php?title=Special:Contributions&feed=atom&limit=250&target=Fred&year=&month=2012.igem.org - User contributions [en]2024-03-30T09:05:24ZFrom 2012.igem.orgMediaWiki 1.16.0http://2012.igem.org/Team:FreiburgTeam:Freiburg2012-10-26T23:05:40Z<p>Fred: </p>
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<h1>Let us tell you a fabulous TALE...</h1><br />
Transactivator-Like Effectors (TALEs) are a brand-new technology that currently revolutionizes the way researchers manipulate DNA with exceptional site specificity. Originally derived from ''Xanthomonas spp.'', this type of protein comprizes an effector domain and a modular DNA binding domain that can be rationally designed to bind to virtually any target sequence of DNA. Over the past two years, universal endonucleases (TALENs) and transcription factors have been tested in various organisms ranging from bacteria to humans. According to existing protocols, TALE assembly requires several weeks of work and substantial lab skills. In order to bring this technology within reach for iGEM students, we invented an extremely fast and easy TALE assembly strategy and developed a TALE platform with expression plasmids and new classes of TALEs. With our so called GATE assembly kit, future iGEM students will be able to precisely manipulate genomic loci easier and faster than anyone else in the world.<br />
</div><br />
<br />
<div class="slide"><br />
<h1>European iGEM Jamboree 2012 Amsterdam:</h1><br />
Team freiGEM won a gold medal and a special prize for the 'Best New BioBrick Part or Device, Engineered'! Team freiGEM also advanced to World Championship in Boston!<br />
<p align="center"><A HREF="http://www.flickr.com/photos/igemeurope/8096765971/in/photostream/" target="_blank"><img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/won1.png' width="75%" height="75%"/></A></p><br />
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<h1><iframe style="margin-left:10px" align="right" width="300" height="250" src="http://player.vimeo.com/video/49902809" frameborder="0" webkitAllowFullScreen mozallowfullscreen allowFullScreen></iframe>Watch our freiGEM movie...<h1><br />
<br><br />
<h1>...or get some impressions in the freiGEM Photo Gallery:</h1><br />
<p><a style="font-weight:bold; font-size:1.3em;" href="/Team:Freiburg/gallery">FreiGEM 2012 Gallery</a></p><br />
</div><br />
<br />
<div class="slide"><br />
<h1><iframe style="margin-right:10px" align="left" width="300" height="250" src="http://player.vimeo.com/video/52254697?badge=0" frameborder="0" webkitAllowFullScreen mozallowfullscreen allowFullScreen></iframe>See how easy it is to get your own custom made TAL...</h1><br />
<br><br><br />
<h1>For further information visit our project page:</h1><br />
<p><a style="font-weight:bold; font-size:1.3em;" href="/Team:Freiburg/Project">Overview TAL Project</a></p><br />
</div><br />
<br />
<div class="slide"><br />
<h1>Check out our modeling</h1><br />
<p align="center"><A HREF="https://2012.igem.org/Team:Freiburg/Modeling" target="_blank"><img class="thumbnail" img src='https://static.igem.org/mediawiki/2012/9/99/FreigemCompanelDNAlogo.png' width="60%" /></A></p><br />
Companel|DNA is dedicated to bringing biology closer to quantitative predictitive science. <br />
<p><a style="font-weight:bold; font-size:1.1em;" href="https://2012.igem.org/Team:Freiburg/Modeling">Let our application help you to clear up complicated or codepending effects in signaling or protein interaction for instance...</a></p><br />
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With kind support of<br />
<br><br />
<br><br />
</span><br />
<A HREF="http://www.bioss.uni-freiburg.de/cms/index.php" target="_blank"><img class="thumbnail" img src="https://static.igem.org/mediawiki/2012/7/7b/Logo_bioss.gif" width= "200" /></A><br />
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<A HREF="http://www.genscript.com/" target="_blank"><img class="thumbnail" img src='https://static.igem.org/mediawiki/2012/0/0d/Genscript_logo.gif' width= "180"/></A><br />
<A HREF="http://eu.idtdna.com/site" target="_blank"><img class="thumbnail" img src='https://static.igem.org/mediawiki/2012/2/21/IDTLogo2010.png' width= "200"/></A><br />
<A HREF="http://www.lifetechnologies.com" target="_blank"><img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/life.png' width= "150"/></A><br />
<A HREF="http://www.eurofinsdna.com/home.html" target="_blank"><img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/eurofins.jpg' width= "150"/></A><br />
<img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/gatc.png' width= "150"/><br />
<A HREF="http://www.erasynbio.net/" target="_blank"><img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/erasynbio.png' width= "200"/></A><br />
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<!--- The Mission, Experiments ---></div>Fredhttp://2012.igem.org/Team:FreiburgTeam:Freiburg2012-10-26T23:04:16Z<p>Fred: </p>
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<h1>Let us tell you a fabulous TALE...</h1><br />
Transactivator-Like Effectors (TALEs) are a brand-new technology that currently revolutionizes the way researchers manipulate DNA with exceptional site specificity. Originally derived from ''Xanthomonas spp.'', this type of protein comprizes an effector domain and a modular DNA binding domain that can be rationally designed to bind to virtually any target sequence of DNA. Over the past two years, universal endonucleases (TALENs) and transcription factors have been tested in various organisms ranging from bacteria to humans. According to existing protocols, TALE assembly requires several weeks of work and substantial lab skills. In order to bring this technology within reach for iGEM students, we invented an extremely fast and easy TALE assembly strategy and developed a TALE platform with expression plasmids and new classes of TALEs. With our so called GATE assembly kit, future iGEM students will be able to precisely manipulate genomic loci easier and faster than anyone else in the world.<br />
</div><br />
<br />
<div class="slide"><br />
<h1>European iGEM Jamboree 2012 Amsterdam:</h1><br />
Team freiGEM won a gold medal and a special prize for the 'Best New BioBrick Part or Device, Engineered'! Team freiGEM also advanced to World Championship in Boston!<br />
<p align="center"><A HREF="http://www.flickr.com/photos/igemeurope/8096765971/in/photostream/" target="_blank"><img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/won1.png' width="75%" height="75%"/></A></p><br />
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<br />
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<h1><iframe style="margin-left:10px" align="right" width="300" height="250" src="http://player.vimeo.com/video/49902809" frameborder="0" webkitAllowFullScreen mozallowfullscreen allowFullScreen></iframe>Watch our freiGEM movie...<h1><br />
<br><br />
<h1>...or get some impressions in the freiGEM Photo Gallery:</h1><br />
<p><a style="font-weight:bold; font-size:1.3em;" href="/Team:Freiburg/gallery">FreiGEM 2012 Gallery</a></p><br />
</div><br />
<br />
<div class="slide"><br />
<h1><iframe style="margin-right:10px" align="left" width="300" height="250" src="http://player.vimeo.com/video/52254697?badge=0" frameborder="0" webkitAllowFullScreen mozallowfullscreen allowFullScreen></iframe>See how easy it is to get your own custom made TAL...</h1><br />
<br><br><br />
<h1>For further information visit our project page:</h1><br />
<p><a style="font-weight:bold; font-size:1.3em;" href="/Team:Freiburg/Project">Overview TAL Project</a></p><br />
</div><br />
<br />
<div class="slide"><br />
<h1>Check out our modeling</h1><br />
<p align="center"><A HREF="https://2012.igem.org/Team:Freiburg/Modeling" target="_blank"><img class="thumbnail" img src='https://static.igem.org/mediawiki/2012/9/99/FreigemCompanelDNAlogo.png' width="60%" /></A></p><br />
Companel|DNA is dedicated to bringing biology closer to quantitative predictitive science. <br />
<p><a style="font-weight:bold; font-size:1.1em;" href="/Team:Freiburg/Project">Let our application help you to clear up complicated or codepending effects in signaling or protein interaction for instance...</a></p><br />
</div><br />
<br />
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With kind support of<br />
<br><br />
<br><br />
</span><br />
<A HREF="http://www.bioss.uni-freiburg.de/cms/index.php" target="_blank"><img class="thumbnail" img src="https://static.igem.org/mediawiki/2012/7/7b/Logo_bioss.gif" width= "200" /></A><br />
<A HREF="http://www.med.uni-freiburg.de/" target="_blank"><img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/uniklinik.png' width= "250"/></A><br />
<img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/metabion.png' width= "180"/><br />
<A HREF="http://www.genscript.com/" target="_blank"><img class="thumbnail" img src='https://static.igem.org/mediawiki/2012/0/0d/Genscript_logo.gif' width= "180"/></A><br />
<A HREF="http://eu.idtdna.com/site" target="_blank"><img class="thumbnail" img src='https://static.igem.org/mediawiki/2012/2/21/IDTLogo2010.png' width= "200"/></A><br />
<A HREF="http://www.lifetechnologies.com" target="_blank"><img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/life.png' width= "150"/></A><br />
<A HREF="http://www.eurofinsdna.com/home.html" target="_blank"><img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/eurofins.jpg' width= "150"/></A><br />
<img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/gatc.png' width= "150"/><br />
<A HREF="http://www.erasynbio.net/" target="_blank"><img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/erasynbio.png' width= "200"/></A><br />
</p><br />
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<br />
<br />
<!--- The Mission, Experiments ---></div>Fredhttp://2012.igem.org/Team:FreiburgTeam:Freiburg2012-10-26T23:03:00Z<p>Fred: </p>
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<br />
<br />
<div class="slide"><br />
<h1>Let us tell you a fabulous TALE...</h1><br />
Transactivator-Like Effectors (TALEs) are a brand-new technology that currently revolutionizes the way researchers manipulate DNA with exceptional site specificity. Originally derived from ''Xanthomonas spp.'', this type of protein comprizes an effector domain and a modular DNA binding domain that can be rationally designed to bind to virtually any target sequence of DNA. Over the past two years, universal endonucleases (TALENs) and transcription factors have been tested in various organisms ranging from bacteria to humans. According to existing protocols, TALE assembly requires several weeks of work and substantial lab skills. In order to bring this technology within reach for iGEM students, we invented an extremely fast and easy TALE assembly strategy and developed a TALE platform with expression plasmids and new classes of TALEs. With our so called GATE assembly kit, future iGEM students will be able to precisely manipulate genomic loci easier and faster than anyone else in the world.<br />
</div><br />
<br />
<div class="slide"><br />
<h1>European iGEM Jamboree 2012 Amsterdam:</h1><br />
Team freiGEM won a gold medal and a special prize for the 'Best New BioBrick Part or Device, Engineered'! Team freiGEM also advanced to World Championship in Boston!<br />
<p align="center"><A HREF="http://www.flickr.com/photos/igemeurope/8096765971/in/photostream/" target="_blank"><img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/won1.png' width="75%" height="75%"/></A></p><br />
</div><br />
<br />
<div class="slide"><br />
<h1><iframe style="margin-left:10px" align="right" width="300" height="250" src="http://player.vimeo.com/video/49902809" frameborder="0" webkitAllowFullScreen mozallowfullscreen allowFullScreen></iframe>Watch our freiGEM movie...<h1><br />
<br><br />
<h1>...or get some impressions in the freiGEM Photo Gallery:</h1><br />
<p><a style="font-weight:bold; font-size:1.3em;" href="/Team:Freiburg/gallery">FreiGEM 2012 Gallery</a></p><br />
</div><br />
<br />
<div class="slide"><br />
<h1><iframe style="margin-right:10px" align="left" width="300" height="250" src="http://player.vimeo.com/video/52254697?badge=0" frameborder="0" webkitAllowFullScreen mozallowfullscreen allowFullScreen></iframe>See how easy it is to get your own custom made TAL...</h1><br />
<br><br><br />
<h1>For further information visit our project page:</h1><br />
<p><a style="font-weight:bold; font-size:1.3em;" href="/Team:Freiburg/Project">Overview TAL Project</a></p><br />
</div><br />
<br />
<div class="slide"><br />
<h1>Check out our modeling</h1><br />
<p align="center"><A HREF="https://2012.igem.org/Team:Freiburg/Modeling" target="_blank"><img class="thumbnail" img src='https://static.igem.org/mediawiki/2012/9/99/FreigemCompanelDNAlogo.png' width="70%" /></A></p><br />
<p><a style="font-weight:bold; font-size:1.0em;" href="/Team:Freiburg/Project">Companel|DNA is dedicated to bringing biology closer to quantitative predictitive science. Let our application help you to clear up complicated or codepending effects in signaling or protein interaction for instance...</a></p><br />
</div><br />
<br />
</div><br />
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With kind support of<br />
<br><br />
<br><br />
</span><br />
<A HREF="http://www.bioss.uni-freiburg.de/cms/index.php" target="_blank"><img class="thumbnail" img src="https://static.igem.org/mediawiki/2012/7/7b/Logo_bioss.gif" width= "200" /></A><br />
<A HREF="http://www.med.uni-freiburg.de/" target="_blank"><img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/uniklinik.png' width= "250"/></A><br />
<img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/metabion.png' width= "180"/><br />
<A HREF="http://www.genscript.com/" target="_blank"><img class="thumbnail" img src='https://static.igem.org/mediawiki/2012/0/0d/Genscript_logo.gif' width= "180"/></A><br />
<A HREF="http://eu.idtdna.com/site" target="_blank"><img class="thumbnail" img src='https://static.igem.org/mediawiki/2012/2/21/IDTLogo2010.png' width= "200"/></A><br />
<A HREF="http://www.lifetechnologies.com" target="_blank"><img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/life.png' width= "150"/></A><br />
<A HREF="http://www.eurofinsdna.com/home.html" target="_blank"><img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/eurofins.jpg' width= "150"/></A><br />
<img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/gatc.png' width= "150"/><br />
<A HREF="http://www.erasynbio.net/" target="_blank"><img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/erasynbio.png' width= "200"/></A><br />
</p><br />
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<br />
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<!--- The Mission, Experiments ---></div>Fredhttp://2012.igem.org/Team:FreiburgTeam:Freiburg2012-10-26T23:01:25Z<p>Fred: </p>
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<div class="slide"><br />
<h1>Let us tell you a fabulous TALE...</h1><br />
Transactivator-Like Effectors (TALEs) are a brand-new technology that currently revolutionizes the way researchers manipulate DNA with exceptional site specificity. Originally derived from ''Xanthomonas spp.'', this type of protein comprizes an effector domain and a modular DNA binding domain that can be rationally designed to bind to virtually any target sequence of DNA. Over the past two years, universal endonucleases (TALENs) and transcription factors have been tested in various organisms ranging from bacteria to humans. According to existing protocols, TALE assembly requires several weeks of work and substantial lab skills. In order to bring this technology within reach for iGEM students, we invented an extremely fast and easy TALE assembly strategy and developed a TALE platform with expression plasmids and new classes of TALEs. With our so called GATE assembly kit, future iGEM students will be able to precisely manipulate genomic loci easier and faster than anyone else in the world.<br />
</div><br />
<br />
<div class="slide"><br />
<h1>European iGEM Jamboree 2012 Amsterdam:</h1><br />
Team freiGEM won a gold medal and a special prize for the 'Best New BioBrick Part or Device, Engineered'! Team freiGEM also advanced to World Championship in Boston!<br />
<p align="center"><A HREF="http://www.flickr.com/photos/igemeurope/8096765971/in/photostream/" target="_blank"><img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/won1.png' width="75%" height="75%"/></A></p><br />
</div><br />
<br />
<div class="slide"><br />
<h1><iframe style="margin-left:10px" align="right" width="300" height="250" src="http://player.vimeo.com/video/49902809" frameborder="0" webkitAllowFullScreen mozallowfullscreen allowFullScreen></iframe>Watch our freiGEM movie...<h1><br />
<br><br />
<h1>...or get some impressions in the freiGEM Photo Gallery:</h1><br />
<p><a style="font-weight:bold; font-size:1.3em;" href="/Team:Freiburg/gallery">FreiGEM 2012 Gallery</a></p><br />
</div><br />
<br />
<div class="slide"><br />
<h1><iframe style="margin-right:10px" align="left" width="300" height="250" src="http://player.vimeo.com/video/52254697?badge=0" frameborder="0" webkitAllowFullScreen mozallowfullscreen allowFullScreen></iframe>See how easy it is to get your own custom made TAL...</h1><br />
<br><br><br />
<h1>For further information visit our project page:</h1><br />
<p><a style="font-weight:bold; font-size:1.3em;" href="/Team:Freiburg/Project">Overview TAL Project</a></p><br />
</div><br />
<br />
<div class="slide"><br />
<h1>Check out our modeling</h1><br />
<p align="center"><A HREF="https://2012.igem.org/Team:Freiburg/Modeling" target="_blank"><img class="thumbnail" img src='https://static.igem.org/mediawiki/2012/9/99/FreigemCompanelDNAlogo.png' width="70%" /></A></p><br />
Companel|DNA is dedicated to bringing biology closer to quantitative predictitive science. Let our application help you to clear up complicated or codepending effects in signaling or protein interaction for instance...<br />
</div><br />
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<br><br />
<br><br />
</span><br />
<A HREF="http://www.bioss.uni-freiburg.de/cms/index.php" target="_blank"><img class="thumbnail" img src="https://static.igem.org/mediawiki/2012/7/7b/Logo_bioss.gif" width= "200" /></A><br />
<A HREF="http://www.med.uni-freiburg.de/" target="_blank"><img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/uniklinik.png' width= "250"/></A><br />
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<A HREF="http://www.genscript.com/" target="_blank"><img class="thumbnail" img src='https://static.igem.org/mediawiki/2012/0/0d/Genscript_logo.gif' width= "180"/></A><br />
<A HREF="http://eu.idtdna.com/site" target="_blank"><img class="thumbnail" img src='https://static.igem.org/mediawiki/2012/2/21/IDTLogo2010.png' width= "200"/></A><br />
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<A HREF="http://www.eurofinsdna.com/home.html" target="_blank"><img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/eurofins.jpg' width= "150"/></A><br />
<img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/gatc.png' width= "150"/><br />
<A HREF="http://www.erasynbio.net/" target="_blank"><img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/erasynbio.png' width= "200"/></A><br />
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<!--- The Mission, Experiments ---></div>Fredhttp://2012.igem.org/Team:FreiburgTeam:Freiburg2012-10-26T22:59:12Z<p>Fred: </p>
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<h1>Let us tell you a fabulous TALE...</h1><br />
Transactivator-Like Effectors (TALEs) are a brand-new technology that currently revolutionizes the way researchers manipulate DNA with exceptional site specificity. Originally derived from ''Xanthomonas spp.'', this type of protein comprizes an effector domain and a modular DNA binding domain that can be rationally designed to bind to virtually any target sequence of DNA. Over the past two years, universal endonucleases (TALENs) and transcription factors have been tested in various organisms ranging from bacteria to humans. According to existing protocols, TALE assembly requires several weeks of work and substantial lab skills. In order to bring this technology within reach for iGEM students, we invented an extremely fast and easy TALE assembly strategy and developed a TALE platform with expression plasmids and new classes of TALEs. With our so called GATE assembly kit, future iGEM students will be able to precisely manipulate genomic loci easier and faster than anyone else in the world.<br />
</div><br />
<br />
<div class="slide"><br />
<h1>European iGEM Jamboree 2012 Amsterdam:</h1><br />
Team freiGEM won a gold medal and a special prize for the 'Best New BioBrick Part or Device, Engineered'! Team freiGEM also advanced to World Championship in Boston!<br />
<p align="center"><A HREF="http://www.flickr.com/photos/igemeurope/8096765971/in/photostream/" target="_blank"><img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/won1.png' width="75%" height="75%"/></A></p><br />
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<br />
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<h1><iframe style="margin-left:10px" align="right" width="300" height="250" src="http://player.vimeo.com/video/49902809" frameborder="0" webkitAllowFullScreen mozallowfullscreen allowFullScreen></iframe>Watch our freiGEM movie...<h1><br />
<br><br />
<h1>...or get some impressions in the freiGEM Photo Gallery:</h1><br />
<p><a style="font-weight:bold; font-size:1.3em;" href="/Team:Freiburg/gallery">FreiGEM 2012 Gallery</a></p><br />
</div><br />
<br />
<div class="slide"><br />
<h1><iframe style="margin-right:10px" align="left" width="300" height="250" src="http://player.vimeo.com/video/52254697?badge=0" frameborder="0" webkitAllowFullScreen mozallowfullscreen allowFullScreen></iframe>See how easy it is to get your own custom made TAL...</h1><br />
<br><br><br />
<h1>For further information visit our project page:</h1><br />
<p><a style="font-weight:bold; font-size:1.3em;" href="/Team:Freiburg/Project">Overview TAL Project</a></p><br />
</div><br />
<br />
<div class="slide"><br />
<h1>Check out our modeling</h1><br />
<p align="right"><A HREF="https://2012.igem.org/Team:Freiburg/Modeling" target="_blank"><img class="thumbnail" img src='https://static.igem.org/mediawiki/2012/9/99/FreigemCompanelDNAlogo.png' width="70%" /></A></p><br />
<h1>Companel|DNA is dedicated to bringing biology closer to quantitative predictitive science. Let our application help you to clear up complicated or codepending effects in signaling or protein interaction for instance...</h1><br />
<p><a style="font-weight:bold; font-size:1.0em;" href="/Team:Freiburg/gallery">FreiGEM 2012 Gallery</a></p><br />
</div><br />
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<span style="color:#4F8DDE; font-weight:bold;"><br />
With kind support of<br />
<br><br />
<br><br />
</span><br />
<A HREF="http://www.bioss.uni-freiburg.de/cms/index.php" target="_blank"><img class="thumbnail" img src="https://static.igem.org/mediawiki/2012/7/7b/Logo_bioss.gif" width= "200" /></A><br />
<A HREF="http://www.med.uni-freiburg.de/" target="_blank"><img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/uniklinik.png' width= "250"/></A><br />
<img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/metabion.png' width= "180"/><br />
<A HREF="http://www.genscript.com/" target="_blank"><img class="thumbnail" img src='https://static.igem.org/mediawiki/2012/0/0d/Genscript_logo.gif' width= "180"/></A><br />
<A HREF="http://eu.idtdna.com/site" target="_blank"><img class="thumbnail" img src='https://static.igem.org/mediawiki/2012/2/21/IDTLogo2010.png' width= "200"/></A><br />
<A HREF="http://www.lifetechnologies.com" target="_blank"><img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/life.png' width= "150"/></A><br />
<A HREF="http://www.eurofinsdna.com/home.html" target="_blank"><img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/eurofins.jpg' width= "150"/></A><br />
<img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/gatc.png' width= "150"/><br />
<A HREF="http://www.erasynbio.net/" target="_blank"><img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/erasynbio.png' width= "200"/></A><br />
</p><br />
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<!--- The Mission, Experiments ---></div>Fredhttp://2012.igem.org/Team:FreiburgTeam:Freiburg2012-10-26T22:57:08Z<p>Fred: </p>
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<br />
<br />
<div class="slide"><br />
<h1>Let us tell you a fabulous TALE...</h1><br />
Transactivator-Like Effectors (TALEs) are a brand-new technology that currently revolutionizes the way researchers manipulate DNA with exceptional site specificity. Originally derived from ''Xanthomonas spp.'', this type of protein comprizes an effector domain and a modular DNA binding domain that can be rationally designed to bind to virtually any target sequence of DNA. Over the past two years, universal endonucleases (TALENs) and transcription factors have been tested in various organisms ranging from bacteria to humans. According to existing protocols, TALE assembly requires several weeks of work and substantial lab skills. In order to bring this technology within reach for iGEM students, we invented an extremely fast and easy TALE assembly strategy and developed a TALE platform with expression plasmids and new classes of TALEs. With our so called GATE assembly kit, future iGEM students will be able to precisely manipulate genomic loci easier and faster than anyone else in the world.<br />
</div><br />
<br />
<div class="slide"><br />
<h1>European iGEM Jamboree 2012 Amsterdam:</h1><br />
Team freiGEM won a gold medal and a special prize for the 'Best New BioBrick Part or Device, Engineered'! Team freiGEM also advanced to World Championship in Boston!<br />
<p align="center"><A HREF="http://www.flickr.com/photos/igemeurope/8096765971/in/photostream/" target="_blank"><img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/won1.png' width="75%" height="75%"/></A></p><br />
</div><br />
<br />
<div class="slide"><br />
<h1><iframe style="margin-left:10px" align="right" width="300" height="250" src="http://player.vimeo.com/video/49902809" frameborder="0" webkitAllowFullScreen mozallowfullscreen allowFullScreen></iframe>Watch our freiGEM movie...<h1><br />
<br><br />
<h1>...or get some impressions in the freiGEM Photo Gallery:</h1><br />
<p><a style="font-weight:bold; font-size:1.3em;" href="/Team:Freiburg/gallery">FreiGEM 2012 Gallery</a></p><br />
</div><br />
<br />
<div class="slide"><br />
<h1><iframe style="margin-right:10px" align="left" width="300" height="250" src="http://player.vimeo.com/video/52254697?badge=0" frameborder="0" webkitAllowFullScreen mozallowfullscreen allowFullScreen></iframe>See how easy it is to get your own custom made TAL...</h1><br />
<br><br><br />
<h1>For further information visit our project page:</h1><br />
<p><a style="font-weight:bold; font-size:1.3em;" href="/Team:Freiburg/Project">Overview TAL Project</a></p><br />
</div><br />
<br />
<div class="slide"><br />
<h1>Check out our modeling</h1><br />
Companel|DNA is dedicated to bringing biology closer to quantitative predictitive science. Let our application help you to clear up complicated or codepending effects in signaling or protein interaction for instance...<br />
<p align="right"><A HREF="https://2012.igem.org/Team:Freiburg/Modeling" target="_blank"><img class="thumbnail" img src='https://static.igem.org/mediawiki/2012/9/99/FreigemCompanelDNAlogo.png' width="70%" /></A></p><br />
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<span style="color:#4F8DDE; font-weight:bold;"><br />
With kind support of<br />
<br><br />
<br><br />
</span><br />
<A HREF="http://www.bioss.uni-freiburg.de/cms/index.php" target="_blank"><img class="thumbnail" img src="https://static.igem.org/mediawiki/2012/7/7b/Logo_bioss.gif" width= "200" /></A><br />
<A HREF="http://www.med.uni-freiburg.de/" target="_blank"><img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/uniklinik.png' width= "250"/></A><br />
<img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/metabion.png' width= "180"/><br />
<A HREF="http://www.genscript.com/" target="_blank"><img class="thumbnail" img src='https://static.igem.org/mediawiki/2012/0/0d/Genscript_logo.gif' width= "180"/></A><br />
<A HREF="http://eu.idtdna.com/site" target="_blank"><img class="thumbnail" img src='https://static.igem.org/mediawiki/2012/2/21/IDTLogo2010.png' width= "200"/></A><br />
<A HREF="http://www.lifetechnologies.com" target="_blank"><img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/life.png' width= "150"/></A><br />
<A HREF="http://www.eurofinsdna.com/home.html" target="_blank"><img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/eurofins.jpg' width= "150"/></A><br />
<img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/gatc.png' width= "150"/><br />
<A HREF="http://www.erasynbio.net/" target="_blank"><img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/erasynbio.png' width= "200"/></A><br />
</p><br />
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<!--- The Mission, Experiments ---></div>Fredhttp://2012.igem.org/Team:FreiburgTeam:Freiburg2012-10-26T22:50:30Z<p>Fred: </p>
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<div class="slides_container"><br />
<br />
<br />
<div class="slide"><br />
<h1>Let us tell you a fabulous TALE...</h1><br />
Transactivator-Like Effectors (TALEs) are a brand-new technology that currently revolutionizes the way researchers manipulate DNA with exceptional site specificity. Originally derived from ''Xanthomonas spp.'', this type of protein comprizes an effector domain and a modular DNA binding domain that can be rationally designed to bind to virtually any target sequence of DNA. Over the past two years, universal endonucleases (TALENs) and transcription factors have been tested in various organisms ranging from bacteria to humans. According to existing protocols, TALE assembly requires several weeks of work and substantial lab skills. In order to bring this technology within reach for iGEM students, we invented an extremely fast and easy TALE assembly strategy and developed a TALE platform with expression plasmids and new classes of TALEs. With our so called GATE assembly kit, future iGEM students will be able to precisely manipulate genomic loci easier and faster than anyone else in the world.<br />
</div><br />
<br />
<div class="slide"><br />
<h1>European iGEM Jamboree 2012 Amsterdam:</h1><br />
Team freiGEM won a gold medal and a special prize for the 'Best New BioBrick Part or Device, Engineered'! Team freiGEM also advanced to World Championship in Boston!<br />
<p align="center"><A HREF="http://www.flickr.com/photos/igemeurope/8096765971/in/photostream/" target="_blank"><img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/won1.png' width="75%" height="75%"/></A></p><br />
</div><br />
<br />
<div class="slide"><br />
<h1><iframe style="margin-left:10px" align="right" width="300" height="250" src="http://player.vimeo.com/video/49902809" frameborder="0" webkitAllowFullScreen mozallowfullscreen allowFullScreen></iframe>Watch our freiGEM movie...<h1><br />
<br><br />
<h1>...or get some impressions in the freiGEM Photo Gallery:</h1><br />
<p><a style="font-weight:bold; font-size:1.3em;" href="/Team:Freiburg/gallery">FreiGEM 2012 Gallery</a></p><br />
</div><br />
<br />
<div class="slide"><br />
<h1><iframe style="margin-right:10px" align="left" width="300" height="250" src="http://player.vimeo.com/video/52254697?badge=0" frameborder="0" webkitAllowFullScreen mozallowfullscreen allowFullScreen></iframe>See how easy it is to get your own custom made TAL...</h1><br />
<br><br><br />
<h1>For further information visit our project page:</h1><br />
<p><a style="font-weight:bold; font-size:1.3em;" href="/Team:Freiburg/Project">Overview TAL Project</a></p><br />
</div><br />
<br />
<div class="slide"><br />
<h1>Check out our modeling</h1><br />
Companel|DNA is dedicated to bringing biology closer to quantitative predictitive science<br />
<p align="right"><A HREF="https://2012.igem.org/Team:Freiburg/Modeling" target="_blank"><img class="thumbnail" img src='https://static.igem.org/mediawiki/2012/9/99/FreigemCompanelDNAlogo.png' width="100%" /></A></p><br />
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<br><br />
<br><br />
</span><br />
<A HREF="http://www.bioss.uni-freiburg.de/cms/index.php" target="_blank"><img class="thumbnail" img src="https://static.igem.org/mediawiki/2012/7/7b/Logo_bioss.gif" width= "200" /></A><br />
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<img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/metabion.png' width= "180"/><br />
<A HREF="http://www.genscript.com/" target="_blank"><img class="thumbnail" img src='https://static.igem.org/mediawiki/2012/0/0d/Genscript_logo.gif' width= "180"/></A><br />
<A HREF="http://eu.idtdna.com/site" target="_blank"><img class="thumbnail" img src='https://static.igem.org/mediawiki/2012/2/21/IDTLogo2010.png' width= "200"/></A><br />
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<A HREF="http://www.eurofinsdna.com/home.html" target="_blank"><img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/eurofins.jpg' width= "150"/></A><br />
<img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/gatc.png' width= "150"/><br />
<A HREF="http://www.erasynbio.net/" target="_blank"><img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/erasynbio.png' width= "200"/></A><br />
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<!--- The Mission, Experiments ---></div>Fredhttp://2012.igem.org/Team:FreiburgTeam:Freiburg2012-10-26T22:50:06Z<p>Fred: </p>
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<h1>Let us tell you a fabulous TALE...</h1><br />
Transactivator-Like Effectors (TALEs) are a brand-new technology that currently revolutionizes the way researchers manipulate DNA with exceptional site specificity. Originally derived from ''Xanthomonas spp.'', this type of protein comprizes an effector domain and a modular DNA binding domain that can be rationally designed to bind to virtually any target sequence of DNA. Over the past two years, universal endonucleases (TALENs) and transcription factors have been tested in various organisms ranging from bacteria to humans. According to existing protocols, TALE assembly requires several weeks of work and substantial lab skills. In order to bring this technology within reach for iGEM students, we invented an extremely fast and easy TALE assembly strategy and developed a TALE platform with expression plasmids and new classes of TALEs. With our so called GATE assembly kit, future iGEM students will be able to precisely manipulate genomic loci easier and faster than anyone else in the world.<br />
</div><br />
<br />
<div class="slide"><br />
<h1>European iGEM Jamboree 2012 Amsterdam:</h1><br />
Team freiGEM won a gold medal and a special prize for the 'Best New BioBrick Part or Device, Engineered'! Team freiGEM also advanced to World Championship in Boston!<br />
<p align="center"><A HREF="http://www.flickr.com/photos/igemeurope/8096765971/in/photostream/" target="_blank"><img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/won1.png' width="75%" height="75%"/></A></p><br />
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<br />
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<h1><iframe style="margin-left:10px" align="right" width="300" height="250" src="http://player.vimeo.com/video/49902809" frameborder="0" webkitAllowFullScreen mozallowfullscreen allowFullScreen></iframe>Watch our freiGEM movie...<h1><br />
<br><br />
<h1>...or get some impressions in the freiGEM Photo Gallery:</h1><br />
<p><a style="font-weight:bold; font-size:1.3em;" href="/Team:Freiburg/gallery">FreiGEM 2012 Gallery</a></p><br />
</div><br />
<br />
<div class="slide"><br />
<h1><iframe style="margin-right:10px" align="left" width="300" height="250" src="http://player.vimeo.com/video/52254697?badge=0" frameborder="0" webkitAllowFullScreen mozallowfullscreen allowFullScreen></iframe>See how easy it is to get your own custom made TAL...</h1><br />
<br><br><br />
<h1>For further information visit our project page:</h1><br />
<p><a style="font-weight:bold; font-size:1.3em;" href="/Team:Freiburg/Project">Overview TAL Project</a></p><br />
</div><br />
<br />
<div class="slide"><br />
<h1>Check out our modeling</h1><br />
Companel|DNA is dedicated to bringing biology closer to quantitative predictitive science<br />
<p align="center"><A HREF="http://www.flickr.com/photos/igemeurope/8096765971/in/photostream/" target="_blank"><img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/won1.png' width="75%" height="75%"/></A></p><br />
<p align="center"><A HREF="https://2012.igem.org/Team:Freiburg/Modeling" target="_blank"><img class="thumbnail" img src='https://static.igem.org/mediawiki/2012/9/99/FreigemCompanelDNAlogo.png' width="100%" /></A></p><br />
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With kind support of<br />
<br><br />
<br><br />
</span><br />
<A HREF="http://www.bioss.uni-freiburg.de/cms/index.php" target="_blank"><img class="thumbnail" img src="https://static.igem.org/mediawiki/2012/7/7b/Logo_bioss.gif" width= "200" /></A><br />
<A HREF="http://www.med.uni-freiburg.de/" target="_blank"><img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/uniklinik.png' width= "250"/></A><br />
<img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/metabion.png' width= "180"/><br />
<A HREF="http://www.genscript.com/" target="_blank"><img class="thumbnail" img src='https://static.igem.org/mediawiki/2012/0/0d/Genscript_logo.gif' width= "180"/></A><br />
<A HREF="http://eu.idtdna.com/site" target="_blank"><img class="thumbnail" img src='https://static.igem.org/mediawiki/2012/2/21/IDTLogo2010.png' width= "200"/></A><br />
<A HREF="http://www.lifetechnologies.com" target="_blank"><img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/life.png' width= "150"/></A><br />
<A HREF="http://www.eurofinsdna.com/home.html" target="_blank"><img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/eurofins.jpg' width= "150"/></A><br />
<img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/gatc.png' width= "150"/><br />
<A HREF="http://www.erasynbio.net/" target="_blank"><img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/erasynbio.png' width= "200"/></A><br />
</p><br />
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<!--- The Mission, Experiments ---></div>Fredhttp://2012.igem.org/Team:FreiburgTeam:Freiburg2012-10-26T22:45:34Z<p>Fred: </p>
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<br />
<br />
<div class="slide"><br />
<h1>Let us tell you a fabulous TALE...</h1><br />
Transactivator-Like Effectors (TALEs) are a brand-new technology that currently revolutionizes the way researchers manipulate DNA with exceptional site specificity. Originally derived from ''Xanthomonas spp.'', this type of protein comprizes an effector domain and a modular DNA binding domain that can be rationally designed to bind to virtually any target sequence of DNA. Over the past two years, universal endonucleases (TALENs) and transcription factors have been tested in various organisms ranging from bacteria to humans. According to existing protocols, TALE assembly requires several weeks of work and substantial lab skills. In order to bring this technology within reach for iGEM students, we invented an extremely fast and easy TALE assembly strategy and developed a TALE platform with expression plasmids and new classes of TALEs. With our so called GATE assembly kit, future iGEM students will be able to precisely manipulate genomic loci easier and faster than anyone else in the world.<br />
</div><br />
<br />
<div class="slide"><br />
<h1>European iGEM Jamboree 2012 Amsterdam:</h1><br />
Team freiGEM won a gold medal and a special prize for the 'Best New BioBrick Part or Device, Engineered'! Team freiGEM also advanced to World Championship in Boston!<br />
<p align="center"><A HREF="http://www.flickr.com/photos/igemeurope/8096765971/in/photostream/" target="_blank"><img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/won1.png' width="75%" height="75%"/></A></p><br />
</div><br />
<br />
<div class="slide"><br />
<h1><iframe style="margin-left:10px" align="right" width="300" height="250" src="http://player.vimeo.com/video/49902809" frameborder="0" webkitAllowFullScreen mozallowfullscreen allowFullScreen></iframe>Watch our freiGEM movie...<h1><br />
<br><br />
<h1>...or get some impressions in the freiGEM Photo Gallery:</h1><br />
<p><a style="font-weight:bold; font-size:1.3em;" href="/Team:Freiburg/gallery">FreiGEM 2012 Gallery</a></p><br />
</div><br />
<br />
<div class="slide"><br />
<h1><iframe style="margin-right:10px" align="left" width="300" height="250" src="http://player.vimeo.com/video/52254697?badge=0" frameborder="0" webkitAllowFullScreen mozallowfullscreen allowFullScreen></iframe>See how easy it is to get your own custom made TAL...</h1><br />
<br><br><br />
<h1>For further information visit our project page:</h1><br />
<p><a style="font-weight:bold; font-size:1.3em;" href="/Team:Freiburg/Project">Overview TAL Project</a></p><br />
</div><br />
<br />
<div class="slide"><br />
<h1>Check out our modeling</h1><br />
Companel|DNA is dedicated to bringing biology closer to quantitative predictitive science<br />
<p align="center"><A HREF="https://2012.igem.org/Team:Freiburg/Modeling" target="_blank"><img class="thumbnail" img src='https://2012.igem.org/File:FreigemCompanelDNAlogo.png' width="100%" /></A></p><br />
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<span style="color:#4F8DDE; font-weight:bold;"><br />
With kind support of<br />
<br><br />
<br><br />
</span><br />
<A HREF="http://www.bioss.uni-freiburg.de/cms/index.php" target="_blank"><img class="thumbnail" img src="https://static.igem.org/mediawiki/2012/7/7b/Logo_bioss.gif" width= "200" /></A><br />
<A HREF="http://www.med.uni-freiburg.de/" target="_blank"><img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/uniklinik.png' width= "250"/></A><br />
<img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/metabion.png' width= "180"/><br />
<A HREF="http://www.genscript.com/" target="_blank"><img class="thumbnail" img src='https://static.igem.org/mediawiki/2012/0/0d/Genscript_logo.gif' width= "180"/></A><br />
<A HREF="http://eu.idtdna.com/site" target="_blank"><img class="thumbnail" img src='https://static.igem.org/mediawiki/2012/2/21/IDTLogo2010.png' width= "200"/></A><br />
<A HREF="http://www.lifetechnologies.com" target="_blank"><img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/life.png' width= "150"/></A><br />
<A HREF="http://www.eurofinsdna.com/home.html" target="_blank"><img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/eurofins.jpg' width= "150"/></A><br />
<img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/gatc.png' width= "150"/><br />
<A HREF="http://www.erasynbio.net/" target="_blank"><img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/erasynbio.png' width= "200"/></A><br />
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<br />
<!--- The Mission, Experiments ---></div>Fredhttp://2012.igem.org/Team:FreiburgTeam:Freiburg2012-10-26T22:42:23Z<p>Fred: </p>
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<div class="slides_container"><br />
<br />
<br />
<div class="slide"><br />
<h1>Let us tell you a fabulous TALE...</h1><br />
Transactivator-Like Effectors (TALEs) are a brand-new technology that currently revolutionizes the way researchers manipulate DNA with exceptional site specificity. Originally derived from ''Xanthomonas spp.'', this type of protein comprizes an effector domain and a modular DNA binding domain that can be rationally designed to bind to virtually any target sequence of DNA. Over the past two years, universal endonucleases (TALENs) and transcription factors have been tested in various organisms ranging from bacteria to humans. According to existing protocols, TALE assembly requires several weeks of work and substantial lab skills. In order to bring this technology within reach for iGEM students, we invented an extremely fast and easy TALE assembly strategy and developed a TALE platform with expression plasmids and new classes of TALEs. With our so called GATE assembly kit, future iGEM students will be able to precisely manipulate genomic loci easier and faster than anyone else in the world.<br />
</div><br />
<br />
<div class="slide"><br />
<h1>European iGEM Jamboree 2012 Amsterdam:</h1><br />
Team freiGEM won a gold medal and a special prize for the 'Best New BioBrick Part or Device, Engineered'! Team freiGEM also advanced to World Championship in Boston!<br />
<p align="center"><A HREF="http://www.flickr.com/photos/igemeurope/8096765971/in/photostream/" target="_blank"><img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/won1.png' width="75%" height="75%"/></A></p><br />
</div><br />
<br />
<div class="slide"><br />
<h1><iframe style="margin-left:10px" align="right" width="300" height="250" src="http://player.vimeo.com/video/49902809" frameborder="0" webkitAllowFullScreen mozallowfullscreen allowFullScreen></iframe>Watch our freiGEM movie...<h1><br />
<br><br />
<h1>...or get some impressions in the freiGEM Photo Gallery:</h1><br />
<p><a style="font-weight:bold; font-size:1.3em;" href="/Team:Freiburg/gallery">FreiGEM 2012 Gallery</a></p><br />
</div><br />
<br />
<div class="slide"><br />
<h1><iframe style="margin-right:10px" align="left" width="300" height="250" src="http://player.vimeo.com/video/52254697?badge=0" frameborder="0" webkitAllowFullScreen mozallowfullscreen allowFullScreen></iframe>See how easy it is to get your own custom made TAL...</h1><br />
<br><br><br />
<h1>For further information visit our project page:</h1><br />
<p><a style="font-weight:bold; font-size:1.3em;" href="/Team:Freiburg/Project">Overview TAL Project</a></p><br />
</div><br />
<br />
<div class="slide"><br />
<h1>Check out our modeling</h1><br />
Companel|DNA is dedicated to bringing biology closer to quantitative predictitive science<br />
<p align="center"><A HREF="https://2012.igem.org/Team:Freiburg/Modeling" target="_blank"><img class="thumbnail" img src='https://2012.igem.org/File:FreigemCompanelDNAlogo.png' width="75%" height="75%"/></A></p><br />
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<html><br />
<div style="position:absolute; top:550px;"><br />
<p style="text-align:center"><br />
<span style="color:#4F8DDE; font-weight:bold;"><br />
With kind support of<br />
<br><br />
<br><br />
</span><br />
<A HREF="http://www.bioss.uni-freiburg.de/cms/index.php" target="_blank"><img class="thumbnail" img src="https://static.igem.org/mediawiki/2012/7/7b/Logo_bioss.gif" width= "200" /></A><br />
<A HREF="http://www.med.uni-freiburg.de/" target="_blank"><img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/uniklinik.png' width= "250"/></A><br />
<img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/metabion.png' width= "180"/><br />
<A HREF="http://www.genscript.com/" target="_blank"><img class="thumbnail" img src='https://static.igem.org/mediawiki/2012/0/0d/Genscript_logo.gif' width= "180"/></A><br />
<A HREF="http://eu.idtdna.com/site" target="_blank"><img class="thumbnail" img src='https://static.igem.org/mediawiki/2012/2/21/IDTLogo2010.png' width= "200"/></A><br />
<A HREF="http://www.lifetechnologies.com" target="_blank"><img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/life.png' width= "150"/></A><br />
<A HREF="http://www.eurofinsdna.com/home.html" target="_blank"><img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/eurofins.jpg' width= "150"/></A><br />
<img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/gatc.png' width= "150"/><br />
<A HREF="http://www.erasynbio.net/" target="_blank"><img class="thumbnail" img src='http://omnibus.uni-freiburg.de/~lb125/erasynbio.png' width= "200"/></A><br />
</p><br />
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<!--- The Mission, Experiments ---></div>Fredhttp://2012.igem.org/Team:Freiburg/ModelingTeam:Freiburg/Modeling2012-10-26T22:09:22Z<p>Fred: </p>
<hr />
<div>{{Template:Team:Freiburg}}<br />
__NOTOC__<br />
= Companel|DNA ''calculating competitive reactions'' =<br />
---- <br />
<br />
<br><br />
[[File:partssymbolT.png|center|180px|link=]]<br />
<br><br />
<br><br />
<div align="justify"><br />
[[Image:FreigemCompanelDNAlogo.png|right|300px|link=]] During the course of our project we encountered a question that we had never before thought about. We were thinking about different ways to synthesize a TAL protein. One of the ideas was to take advantage of the thermodynamic behavior of different DNA strands and synthesize a TAL proteins by means of different primers that anneal at different temperatures to the template strand. We thought it to be possible to elongate a sequence by using this mechanism - simply changing the annealing temperature slightly whilst running a usual PCR. We assumed that the difference in optimal annealing temperatures of different primer sequences would favor one replication product over the others. [[Image:Freigemquote.png|left|280px|link=]] The only thing we did not know was if this was significant enough to be used for the assembly of at least ten TAL domains. After unproductive research on this issue we decided to try modeling this scenario ourselves. <br />
<br />
<br />
The result of these efforts is '''CompanelDNA''', an excel application that allows for predicting the equilibrium concentrations of competitive annealing. It can of course be used for every kind of chemical equilibrium where two substances compete for reacting with the same third reactant. <br />
<br />
<br />
<br />
<br />
[[Image:schema4.png|center|720px|link=]]<br />
<br />
<br />
== Theoretical background ==<br />
----<br />
<br><br />
Although it seems to be a simple scenario, we did not find any preexisting solution to this problem - which came to us as quite a surprise. So we started by looking at the law of mass action behind the annealing reaction. Hereafter we will use the following abbreviations and symbols:<br />
<br />
[[Image:freigem1T.png|center|400px|link=]]<br />
<br />
The laws of mass action for the two independent reactions are:<br />
<br />
[[Image:freigem2T.png|center|150px|link=]]<br />
<br />
If we want to know what is going to happen to the concentrations we originally put in our reaction/PCR tube, we can express the term in relation to the overall concentrations:<br />
<br />
[[Image:freigem3T.png|center|300px|link=]]<br />
<br />
Bearing in mind that the only unknown variables are (AB) and (CB) (K can be calculated, see below), one would try to solve these two equations with two variables. A number of other equations can furthermore be generated. However, these equations had no exact solutions when we used Mathematica to have them solved. All the proposed solutions are not applicable to a<br />
wider combination of parameters. Even when we asked for mathematical advice (thanks to Paul Staab, Munich) we got no further. So we decided to solve graphically instead (thanks to Konrad Schieban, Zurich). <br />
In order to do so the equations need to be solved for one variabel:<br />
<br />
[[Image:freigem4T.png|center|500px|link=]]<br />
<br />
These equations can now separately be calculated by varying the variable (AB). When a value of (AB) is found that yields the same value of (CB) in both equations, both conditions are fulfilled. Graphically this would be represented by the intersection of the graphs of both equations. Basically this is what our application does. As a first result it clearly showed that the temperature specificity is not strict enough to be used as a elongation determinant, as we had originally hoped.<br />
<br><br><br />
<br />
== How does Companel|DNA work? ==<br />
----<br />
<br><br />
When using Companel you need to "bring" your thermodynamical parameters dH° and dS° for each independent annealing reaction. Due to limited resources could no calculator for these numbers be included. However, there are several free calculators online. More information on how to obtain dH° and dS° can be found in the application.<br />
<br />
Once this sequence specific information has been entered into the application, the constants K for a series of temperatures are calculated by using the Gibbs function. Subsequently the melting plots for each individual reaction are displayed and give you a first impression of the annealing behavior of your primers. <br />
[[Image:freigemCompanel2.png|center|720px|link=]]<br />
<br />
<br />
Finally you enter concentrations, temperature range and expected product yield. The resulting concentrations of annealing product for each primer are shown graphically and in a list.<br />
[[Image:freigemCompanel1.png|center|720px|link=]]<br />
<br />
<br />
You just want to have one specific situation at a given temperature calculated? Just use the second part of the application '''Companel|chem''' and enter barely the concentrations as well as the two independent equilibrium constants there. <br />
[[Image:Constantsonly.png|center|720px|link=]]<br />
<br />
<br><br><br />
== What is Companel|DNA good for? ==<br />
----<br />
<br><br />
Besides the actual annealing of primers, which it has been intended for, Companel possesses an intrinsic universality when it comes to quantifying competitive processes. For instance a scientist could easily assess the binding priority of two or more (the system can of course be expanded) transcription factors or protein-protein interactions. He or she would just need to measure the two or more separate reactions, which could readily be achieved in an in vitro essay. One could then predict the interaction in vivo - at least thermodynamically. Numerous discoveries during the last years, such as the impact of the circadian clock on metabolism and drug efficacy, have shown that profound research and sometimes even successful treatment can no longer be based on the mere observation of qualitative effects alone. In the challenge to bring both biology and medicine closer to quantitative, predictable and hence more understandable science our application could play a helpful role.<br />
<br />
<br><br />
<br><br />
<html><br />
<a href="https://2012.igem.org/File:CompanelDNA1.1.zip" target="_blank"><img style="margin-left:220px; align:center;" src="https://static.igem.org/mediawiki/2012/a/a8/Freigemdownload.png" padding:0px; width="300px"; /></a></html><br />
<br><br />
<div style="margin-left:220px">''In case the file does not work properly,''<br><br />
''please send us an email to freigem2012(at)googlemail.com''</div><br />
<br><br />
<br><br />
<br><br />
<br><br />
[[#top|Back to top]]</div>Fredhttp://2012.igem.org/File:CompanelDNA1.1.zipFile:CompanelDNA1.1.zip2012-10-26T22:08:45Z<p>Fred: </p>
<hr />
<div></div>Fredhttp://2012.igem.org/Team:Freiburg/ModelingTeam:Freiburg/Modeling2012-10-26T15:40:49Z<p>Fred: </p>
<hr />
<div>{{Template:Team:Freiburg}}<br />
__NOTOC__<br />
= Companel|DNA ''calculating competitive reactions'' =<br />
---- <br />
<br />
<br><br />
[[File:partssymbolT.png|center|180px|link=]]<br />
<br><br />
<br><br />
<div align="justify"><br />
[[Image:FreigemCompanelDNAlogo.png|right|300px|link=]] During the course of our project we encountered a question that we had never before thought about. We were thinking about different ways to synthesize a TAL protein. One of the ideas was to take advantage of the thermodynamic behavior of different DNA strands and synthesize a TAL proteins by means of different primers that anneal at different temperatures to the template strand. We thought it to be possible to elongate a sequence by using this mechanism - simply changing the annealing temperature slightly whilst running a usual PCR. We assumed that the difference in optimal annealing temperatures of different primer sequences would favor one replication product over the others. [[Image:Freigemquote.png|left|280px|link=]] The only thing we did not know was if this was significant enough to be used for the assembly of at least ten TAL domains. After unproductive research on this issue we decided to try modeling this scenario ourselves. <br />
<br />
<br />
The result of these efforts is '''CompanelDNA''', an excel application that allows for predicting the equilibrium concentrations of competitive annealing. It can of course be used for every kind of chemical equilibrium where two substances compete for reacting with the same third reactant. <br />
<br />
<br />
<br />
<br />
[[Image:schema4.png|center|720px|link=]]<br />
<br />
<br />
== Theoretical background ==<br />
----<br />
<br><br />
Although it seems to be a simple scenario, we did not find any preexisting solution to this problem - which came to us as quite a surprise. So we started by looking at the law of mass action behind the annealing reaction. Hereafter we will use the following abbreviations and symbols:<br />
<br />
[[Image:freigem1T.png|center|400px|link=]]<br />
<br />
The laws of mass action for the two independent reactions are:<br />
<br />
[[Image:freigem2T.png|center|150px|link=]]<br />
<br />
If we want to know what is going to happen to the concentrations we originally put in our reaction/PCR tube, we can express the term in relation to the overall concentrations:<br />
<br />
[[Image:freigem3T.png|center|300px|link=]]<br />
<br />
Bearing in mind that the only unknown variables are (AB) and (CB) (K can be calculated, see below), one would try to solve these two equations with two variables. A number of other equations can furthermore be generated. However, these equations had no exact solutions when we used Mathematica to have them solved. All the proposed solutions are not applicable to a<br />
wider combination of parameters. Even when we asked for mathematical advice (thanks to Paul Staab, Munich) we got no further. So we decided to solve graphically instead (thanks to Konrad Schieban, Zurich). <br />
In order to do so the equations need to be solved for one variabel:<br />
<br />
[[Image:freigem4T.png|center|500px|link=]]<br />
<br />
These equations can now separately be calculated by varying the variable (AB). When a value of (AB) is found that yields the same value of (CB) in both equations, both conditions are fulfilled. Graphically this would be represented by the intersection of the graphs of both equations. Basically this is what our application does. As a first result it clearly showed that the temperature specificity is not strict enough to be used as a elongation determinant, as we had originally hoped.<br />
<br><br><br />
<br />
== How does Companel|DNA work? ==<br />
----<br />
<br><br />
When using Companel you need to "bring" your thermodynamical parameters dH° and dS° for each independent annealing reaction. Due to limited resources could no calculator for these numbers be included. However, there are several free calculators online. More information on how to obtain dH° and dS° can be found in the application.<br />
<br />
Once this sequence specific information has been entered into the application, the constants K for a series of temperatures are calculated by using the Gibbs function. Subsequently the melting plots for each individual reaction are displayed and give you a first impression of the annealing behavior of your primers. <br />
[[Image:freigemCompanel2.png|center|720px|link=]]<br />
<br />
<br />
Finally you enter concentrations, temperature range and expected product yield. The resulting concentrations of annealing product for each primer are shown graphically and in a list.<br />
[[Image:freigemCompanel1.png|center|720px|link=]]<br />
<br />
<br />
You just want to have one specific situation at a given temperature calculated? Just use the second part of the application '''Companel|chem''' and enter barely the concentrations as well as the two independent equilibrium constants there. <br />
[[Image:Constantsonly.png|center|720px|link=]]<br />
<br />
<br><br><br />
== What is Companel|DNA good for? ==<br />
----<br />
<br><br />
Besides the actual annealing of primers, which it has been intended for, Companel possesses an intrinsic universality when it comes to quantifying competitive processes. For instance a scientist could easily assess the binding priority of two or more (the system can of course be expanded) transcription factors or protein-protein interactions. He or she would just need to measure the two or more separate reactions, which could readily be achieved in an in vitro essay. One could then predict the interaction in vivo - at least thermodynamically. Numerous discoveries during the last years, such as the impact of the circadian clock on metabolism and drug efficacy, have shown that profound research and sometimes even successful treatment can no longer be based on the mere observation of qualitative effects alone. In the challenge to bring both biology and medicine closer to quantitative, predictable and hence more understandable science our application could play a helpful role.<br />
<br />
<br><br />
<br><br />
<html><br />
<a href="https://2012.igem.org/File:Freigem2012-CompanelDNA.zip" target="_blank"><img style="margin-left:220px; align:center;" src="https://static.igem.org/mediawiki/2012/a/a8/Freigemdownload.png" padding:0px; width="300px"; /></a></html><br />
<br><br />
<div style="margin-left:220px">''In case the file does not work properly,''<br><br />
''please send us an email to freigem2012(at)googlemail.com''</div><br />
<br><br />
<br><br />
<br><br />
<br><br />
[[#top|Back to top]]</div>Fredhttp://2012.igem.org/File:Schema4.pngFile:Schema4.png2012-10-26T15:40:24Z<p>Fred: </p>
<hr />
<div></div>Fredhttp://2012.igem.org/Team:Freiburg/ModelingTeam:Freiburg/Modeling2012-10-26T15:36:48Z<p>Fred: </p>
<hr />
<div>{{Template:Team:Freiburg}}<br />
__NOTOC__<br />
= Companel|DNA ''calculating competitive reactions'' =<br />
---- <br />
<br />
<br><br />
[[File:partssymbolT.png|center|180px|link=]]<br />
<br><br />
<br><br />
<div align="justify"><br />
[[Image:FreigemCompanelDNAlogo.png|right|300px|link=]] During the course of our project we encountered a question that we had never before thought about. We were thinking about different ways to synthesize a TAL protein. One of the ideas was to take advantage of the thermodynamic behavior of different DNA strands and synthesize a TAL proteins by means of different primers that anneal at different temperatures to the template strand. We thought it to be possible to elongate a sequence by using this mechanism - simply changing the annealing temperature slightly whilst running a usual PCR. We assumed that the difference in optimal annealing temperatures of different primer sequences would favor one replication product over the others. [[Image:Freigemquote.png|left|280px|link=]] The only thing we did not know was if this was significant enough to be used for the assembly of at least ten TAL domains. After unproductive research on this issue we decided to try modeling this scenario ourselves. <br />
<br />
<br />
The result of these efforts is '''CompanelDNA''', an excel application that allows for predicting the equilibrium concentrations of competitive annealing. It can of course be used for every kind of chemical equilibrium where two substances compete for reacting with the same third reactant. <br />
<br />
<br />
<br />
<br />
[[Image:schema3.png|center|720px|link=]]<br />
<br />
<br />
== Theoretical background ==<br />
----<br />
<br><br />
Although it seems to be a simple scenario, we did not find any preexisting solution to this problem - which came to us as quite a surprise. So we started by looking at the law of mass action behind the annealing reaction. Hereafter we will use the following abbreviations and symbols:<br />
<br />
[[Image:freigem1T.png|center|400px|link=]]<br />
<br />
The laws of mass action for the two independent reactions are:<br />
<br />
[[Image:freigem2T.png|center|150px|link=]]<br />
<br />
If we want to know what is going to happen to the concentrations we originally put in our reaction/PCR tube, we can express the term in relation to the overall concentrations:<br />
<br />
[[Image:freigem3T.png|center|300px|link=]]<br />
<br />
Bearing in mind that the only unknown variables are (AB) and (CB) (K can be calculated, see below), one would try to solve these two equations with two variables. A number of other equations can furthermore be generated. However, these equations had no exact solutions when we used Mathematica to have them solved. All the proposed solutions are not applicable to a<br />
wider combination of parameters. Even when we asked for mathematical advice (thanks to Paul Staab, Munich) we got no further. So we decided to solve graphically instead (thanks to Konrad Schieban, Zurich). <br />
In order to do so the equations need to be solved for one variabel:<br />
<br />
[[Image:freigem4T.png|center|500px|link=]]<br />
<br />
These equations can now separately be calculated by varying the variable (AB). When a value of (AB) is found that yields the same value of (CB) in both equations, both conditions are fulfilled. Graphically this would be represented by the intersection of the graphs of both equations. Basically this is what our application does. As a first result it clearly showed that the temperature specificity is not strict enough to be used as a elongation determinant, as we had originally hoped.<br />
<br><br><br />
<br />
== How does Companel|DNA work? ==<br />
----<br />
<br><br />
When using Companel you need to "bring" your thermodynamical parameters dH° and dS° for each independent annealing reaction. Due to limited resources could no calculator for these numbers be included. However, there are several free calculators online. More information on how to obtain dH° and dS° can be found in the application.<br />
<br />
Once this sequence specific information has been entered into the application, the constants K for a series of temperatures are calculated by using the Gibbs function. Subsequently the melting plots for each individual reaction are displayed and give you a first impression of the annealing behavior of your primers. <br />
[[Image:freigemCompanel2.png|center|720px|link=]]<br />
<br />
<br />
Finally you enter concentrations, temperature range and expected product yield. The resulting concentrations of annealing product for each primer are shown graphically and in a list.<br />
[[Image:freigemCompanel1.png|center|720px|link=]]<br />
<br />
<br />
You just want to have one specific situation at a given temperature calculated? Just use the second part of the application '''Companel|chem''' and enter barely the concentrations as well as the two independent equilibrium constants there. <br />
[[Image:Constantsonly.png|center|720px|link=]]<br />
<br />
<br><br><br />
== What is Companel|DNA good for? ==<br />
----<br />
<br><br />
Besides the actual annealing of primers, which it has been intended for, Companel possesses an intrinsic universality when it comes to quantifying competitive processes. For instance a scientist could easily assess the binding priority of two or more (the system can of course be expanded) transcription factors or protein-protein interactions. He or she would just need to measure the two or more separate reactions, which could readily be achieved in an in vitro essay. One could then predict the interaction in vivo - at least thermodynamically. Numerous discoveries during the last years, such as the impact of the circadian clock on metabolism and drug efficacy, have shown that profound research and sometimes even successful treatment can no longer be based on the mere observation of qualitative effects alone. In the challenge to bring both biology and medicine closer to quantitative, predictable and hence more understandable science our application could play a helpful role.<br />
<br />
<br><br />
<br><br />
<html><br />
<a href="https://2012.igem.org/File:Freigem2012-CompanelDNA.zip" target="_blank"><img style="margin-left:220px; align:center;" src="https://static.igem.org/mediawiki/2012/a/a8/Freigemdownload.png" padding:0px; width="300px"; /></a></html><br />
<br><br />
<div style="margin-left:220px">''In case the file does not work properly,''<br><br />
''please send us an email to freigem2012(at)googlemail.com''</div><br />
<br><br />
<br><br />
<br><br />
<br><br />
[[#top|Back to top]]</div>Fredhttp://2012.igem.org/File:Schema3.pngFile:Schema3.png2012-10-26T15:36:29Z<p>Fred: </p>
<hr />
<div></div>Fredhttp://2012.igem.org/Team:Freiburg/ModelingTeam:Freiburg/Modeling2012-10-26T15:35:25Z<p>Fred: </p>
<hr />
<div>{{Template:Team:Freiburg}}<br />
__NOTOC__<br />
= Companel|DNA ''calculating competitive reactions'' =<br />
---- <br />
<br />
<br><br />
[[File:partssymbolT.png|center|180px|link=]]<br />
<br><br />
<br><br />
<div align="justify"><br />
[[Image:FreigemCompanelDNAlogo.png|right|300px|link=]] During the course of our project we encountered a question that we had never before thought about. We were thinking about different ways to synthesize a TAL protein. One of the ideas was to take advantage of the thermodynamic behavior of different DNA strands and synthesize a TAL proteins by means of different primers that anneal at different temperatures to the template strand. We thought it to be possible to elongate a sequence by using this mechanism - simply changing the annealing temperature slightly whilst running a usual PCR. We assumed that the difference in optimal annealing temperatures of different primer sequences would favor one replication product over the others. [[Image:Freigemquote.png|left|280px|link=]] The only thing we did not know was if this was significant enough to be used for the assembly of at least ten TAL domains. After unproductive research on this issue we decided to try modeling this scenario ourselves. <br />
<br />
<br />
The result of these efforts is '''CompanelDNA''', an excel application that allows for predicting the equilibrium concentrations of competitive annealing. It can of course be used for every kind of chemical equilibrium where two substances compete for reacting with the same third reactant. <br />
<br />
<br />
<br />
<br />
[[Image:SCHEMA2.png|center|720px|link=]]<br />
<br />
<br />
== Theoretical background ==<br />
----<br />
<br><br />
Although it seems to be a simple scenario, we did not find any preexisting solution to this problem - which came to us as quite a surprise. So we started by looking at the law of mass action behind the annealing reaction. Hereafter we will use the following abbreviations and symbols:<br />
<br />
[[Image:freigem1T.png|center|400px|link=]]<br />
<br />
The laws of mass action for the two independent reactions are:<br />
<br />
[[Image:freigem2T.png|center|150px|link=]]<br />
<br />
If we want to know what is going to happen to the concentrations we originally put in our reaction/PCR tube, we can express the term in relation to the overall concentrations:<br />
<br />
[[Image:freigem3T.png|center|300px|link=]]<br />
<br />
Bearing in mind that the only unknown variables are (AB) and (CB) (K can be calculated, see below), one would try to solve these two equations with two variables. A number of other equations can furthermore be generated. However, these equations had no exact solutions when we used Mathematica to have them solved. All the proposed solutions are not applicable to a<br />
wider combination of parameters. Even when we asked for mathematical advice (thanks to Paul Staab, Munich) we got no further. So we decided to solve graphically instead (thanks to Konrad Schieban, Zurich). <br />
In order to do so the equations need to be solved for one variabel:<br />
<br />
[[Image:freigem4T.png|center|500px|link=]]<br />
<br />
These equations can now separately be calculated by varying the variable (AB). When a value of (AB) is found that yields the same value of (CB) in both equations, both conditions are fulfilled. Graphically this would be represented by the intersection of the graphs of both equations. Basically this is what our application does. As a first result it clearly showed that the temperature specificity is not strict enough to be used as a elongation determinant, as we had originally hoped.<br />
<br><br><br />
<br />
== How does Companel|DNA work? ==<br />
----<br />
<br><br />
When using Companel you need to "bring" your thermodynamical parameters dH° and dS° for each independent annealing reaction. Due to limited resources could no calculator for these numbers be included. However, there are several free calculators online. More information on how to obtain dH° and dS° can be found in the application.<br />
<br />
Once this sequence specific information has been entered into the application, the constants K for a series of temperatures are calculated by using the Gibbs function. Subsequently the melting plots for each individual reaction are displayed and give you a first impression of the annealing behavior of your primers. <br />
[[Image:freigemCompanel2.png|center|720px|link=]]<br />
<br />
<br />
Finally you enter concentrations, temperature range and expected product yield. The resulting concentrations of annealing product for each primer are shown graphically and in a list.<br />
[[Image:freigemCompanel1.png|center|720px|link=]]<br />
<br />
<br />
You just want to have one specific situation at a given temperature calculated? Just use the second part of the application '''Companel|chem''' and enter barely the concentrations as well as the two independent equilibrium constants there. <br />
[[Image:Constantsonly.png|center|720px|link=]]<br />
<br />
<br><br><br />
== What is Companel|DNA good for? ==<br />
----<br />
<br><br />
Besides the actual annealing of primers, which it has been intended for, Companel possesses an intrinsic universality when it comes to quantifying competitive processes. For instance a scientist could easily assess the binding priority of two or more (the system can of course be expanded) transcription factors or protein-protein interactions. He or she would just need to measure the two or more separate reactions, which could readily be achieved in an in vitro essay. One could then predict the interaction in vivo - at least thermodynamically. Numerous discoveries during the last years, such as the impact of the circadian clock on metabolism and drug efficacy, have shown that profound research and sometimes even successful treatment can no longer be based on the mere observation of qualitative effects alone. In the challenge to bring both biology and medicine closer to quantitative, predictable and hence more understandable science our application could play a helpful role.<br />
<br />
<br><br />
<br><br />
<html><br />
<a href="https://2012.igem.org/File:Freigem2012-CompanelDNA.zip" target="_blank"><img style="margin-left:220px; align:center;" src="https://static.igem.org/mediawiki/2012/a/a8/Freigemdownload.png" padding:0px; width="300px"; /></a></html><br />
<br><br />
<div style="margin-left:220px">''In case the file does not work properly,''<br><br />
''please send us an email to freigem2012(at)googlemail.com''</div><br />
<br><br />
<br><br />
<br><br />
<br><br />
[[#top|Back to top]]</div>Fredhttp://2012.igem.org/File:SCHEMA2.pngFile:SCHEMA2.png2012-10-26T15:33:28Z<p>Fred: </p>
<hr />
<div></div>Fredhttp://2012.igem.org/File:SCHEMA.pngFile:SCHEMA.png2012-10-26T15:32:23Z<p>Fred: </p>
<hr />
<div></div>Fredhttp://2012.igem.org/Team:Freiburg/ModelingTeam:Freiburg/Modeling2012-10-26T15:31:47Z<p>Fred: </p>
<hr />
<div>{{Template:Team:Freiburg}}<br />
__NOTOC__<br />
= Companel|DNA ''calculating competitive reactions'' =<br />
---- <br />
<br />
<br><br />
[[File:partssymbolT.png|center|180px|link=]]<br />
<br><br />
<br><br />
<div align="justify"><br />
[[Image:FreigemCompanelDNAlogo.png|right|300px|link=]] During the course of our project we encountered a question that we had never before thought about. We were thinking about different ways to synthesize a TAL protein. One of the ideas was to take advantage of the thermodynamic behavior of different DNA strands and synthesize a TAL proteins by means of different primers that anneal at different temperatures to the template strand. We thought it to be possible to elongate a sequence by using this mechanism - simply changing the annealing temperature slightly whilst running a usual PCR. We assumed that the difference in optimal annealing temperatures of different primer sequences would favor one replication product over the others. [[Image:Freigemquote.png|left|280px|link=]] The only thing we did not know was if this was significant enough to be used for the assembly of at least ten TAL domains. After unproductive research on this issue we decided to try modeling this scenario ourselves. <br />
<br />
<br />
The result of these efforts is '''CompanelDNA''', an excel application that allows for predicting the equilibrium concentrations of competitive annealing. It can of course be used for every kind of chemical equilibrium where two substances compete for reacting with the same third reactant. <br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
== Theoretical background ==<br />
----<br />
<br><br />
Although it seems to be a simple scenario, we did not find any preexisting solution to this problem - which came to us as quite a surprise. So we started by looking at the law of mass action behind the annealing reaction. Hereafter we will use the following abbreviations and symbols:<br />
<br />
[[Image:freigem1T.png|center|400px|link=]]<br />
<br />
The laws of mass action for the two independent reactions are:<br />
<br />
[[Image:freigem2T.png|center|150px|link=]]<br />
<br />
If we want to know what is going to happen to the concentrations we originally put in our reaction/PCR tube, we can express the term in relation to the overall concentrations:<br />
<br />
[[Image:freigem3T.png|center|300px|link=]]<br />
<br />
Bearing in mind that the only unknown variables are (AB) and (CB) (K can be calculated, see below), one would try to solve these two equations with two variables. A number of other equations can furthermore be generated. However, these equations had no exact solutions when we used Mathematica to have them solved. All the proposed solutions are not applicable to a<br />
wider combination of parameters. Even when we asked for mathematical advice (thanks to Paul Staab, Munich) we got no further. So we decided to solve graphically instead (thanks to Konrad Schieban, Zurich). <br />
In order to do so the equations need to be solved for one variabel:<br />
<br />
[[Image:freigem4T.png|center|500px|link=]]<br />
<br />
These equations can now separately be calculated by varying the variable (AB). When a value of (AB) is found that yields the same value of (CB) in both equations, both conditions are fulfilled. Graphically this would be represented by the intersection of the graphs of both equations. Basically this is what our application does. As a first result it clearly showed that the temperature specificity is not strict enough to be used as a elongation determinant, as we had originally hoped.<br />
<br><br><br />
<br />
== How does Companel|DNA work? ==<br />
----<br />
<br><br />
When using Companel you need to "bring" your thermodynamical parameters dH° and dS° for each independent annealing reaction. Due to limited resources could no calculator for these numbers be included. However, there are several free calculators online. More information on how to obtain dH° and dS° can be found in the application.<br />
<br />
Once this sequence specific information has been entered into the application, the constants K for a series of temperatures are calculated by using the Gibbs function. Subsequently the melting plots for each individual reaction are displayed and give you a first impression of the annealing behavior of your primers. <br />
[[Image:freigemCompanel2.png|center|720px|link=]]<br />
<br />
<br />
Finally you enter concentrations, temperature range and expected product yield. The resulting concentrations of annealing product for each primer are shown graphically and in a list.<br />
[[Image:freigemCompanel1.png|center|720px|link=]]<br />
<br />
<br />
You just want to have one specific situation at a given temperature calculated? Just use the second part of the application '''Companel|chem''' and enter barely the concentrations as well as the two independent equilibrium constants there. <br />
[[Image:Constantsonly.png|center|720px|link=]]<br />
<br />
<br><br><br />
== What is Companel|DNA good for? ==<br />
----<br />
<br><br />
Besides the actual annealing of primers, which it has been intended for, Companel possesses an intrinsic universality when it comes to quantifying competitive processes. For instance a scientist could easily assess the binding priority of two or more (the system can of course be expanded) transcription factors or protein-protein interactions. He or she would just need to measure the two or more separate reactions, which could readily be achieved in an in vitro essay. One could then predict the interaction in vivo - at least thermodynamically. Numerous discoveries during the last years, such as the impact of the circadian clock on metabolism and drug efficacy, have shown that profound research and sometimes even successful treatment can no longer be based on the mere observation of qualitative effects alone. In the challenge to bring both biology and medicine closer to quantitative, predictable and hence more understandable science our application could play a helpful role.<br />
<br />
<br><br />
<br><br />
<html><br />
<a href="https://2012.igem.org/File:Freigem2012-CompanelDNA.zip" target="_blank"><img style="margin-left:220px; align:center;" src="https://static.igem.org/mediawiki/2012/a/a8/Freigemdownload.png" padding:0px; width="300px"; /></a></html><br />
<br><br />
<div style="margin-left:220px">''In case the file does not work properly,''<br><br />
''please send us an email to freigem2012(at)googlemail.com''</div><br />
<br><br />
<br><br />
<br><br />
<br><br />
[[#top|Back to top]]</div>Fredhttp://2012.igem.org/File:Constantsonly.pngFile:Constantsonly.png2012-10-26T15:04:23Z<p>Fred: </p>
<hr />
<div></div>Fredhttp://2012.igem.org/Team:Freiburg/ModelingTeam:Freiburg/Modeling2012-09-27T02:53:18Z<p>Fred: </p>
<hr />
<div>{{Template:Team:Freiburg}}<br />
__NOTOC__<br />
= Companel|DNA ''calculating competitive reactions'' =<br />
<br />
[[Image:FreigemCompanelDNAlogo.png|right|300px]] During the course of our project we encountered a question that we had never before thought about. We were thinking about different ways to synthesize a TAL protein. One of the ideas was to take advantage of the thermodynamic behavior of different DNA strands and synthesize a TAL proteins by means of different primers that anneal at different temperatures to the template strand. We thought it to be possible to elongate a sequence by using this mechanism - simply changing the annealing temperature slightly whilst running a usual PCR. We assumed that the difference in optimal annealing temperatures of different primer sequences would favor one replication product over the others. [[Image:Freigemquote.png|left|280px]] The only thing we did not know was if this was significant enough to be used for the assembly of at least ten TAL domains. After unproductive research on this issue we decided to try modeling this scenario ourselves. <br />
<br />
<br />
The result of these efforts is CompanelDNA, an excel application that allows for predicting the equilibrium concentrations of competitive annealing. It can of course be used for every kind of chemical equilibrium where two substances compete for reacting with the same third reactant. <br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
== Theoretical background ==<br />
<br />
Although it seems to be a simple scenario, we did not find any preexisting solution to this problem - which came to us as quite a surprise. So we started by looking at the law of mass action behind the annealing reaction. Hereafter we will use the following abbreviations and symbols:<br />
<br />
[[Image:freigem1.png|center|400px]]<br />
<br />
The laws of mass action for the two independent reactions are:<br />
<br />
[[Image:freigem2.png|center|150px]]<br />
<br />
If we want to know what is going to happen to the concentrations we originally put in our reaction/PCR tube, we can express the term in relation to the overall concentrations:<br />
<br />
[[Image:freigem3.png|center|300px]]<br />
<br />
Bearing in mind that the only unknown variables are (AB) and (CB) (K can be calculated, see below), one would try to solve these two equations with two variables. A number of other equations can furthermore be generated. However, these equations had no exact solutions when we used Mathematica to have them solved. All the proposed solutions are not applicable to a<br />
wider combination of parameters. Even when we asked for mathematical advice (thanks to Paul Staab, Munich) we got no further. So we decided to solve graphically instead (thanks to Konrad Schieban, Zurich). <br />
In order to do so the equations need to be solved for one variabel:<br />
<br />
[[Image:freigem4.png|center|500px]]<br />
<br />
These equations can now separately be calculated by varying the variable (AB). When a value of (AB) is found that yields the same value of (CB) in both equations, both conditions are fulfilled. Graphically this would be represented by the intersection of the graphs of both equations. Basically this is what our application does. As a first result it clearly showed that the temperature specificity is not strict enough to be used as a elongation determinant, as we had originally hoped.<br />
<br />
<br />
<br />
<br />
== How does Companel|DNA work? ==<br />
<br />
When using Companel you need to "bring" your thermodynamical parameters dH° and dS° for each independent annealing reaction. Due to limited resources could no calculator for these numbers be included. However, there are several free calculators online. More information on how to obtain dH° and dS° can be found in the application.<br />
<br />
Once this sequence specific information has been entered into the application, the constants K for a series of temperatures are calculated by using the Gibbs function. Subsequently the melting plots for each individual reaction are displayed and give you a first impression of the annealing behavior of your primers. <br />
[[Image:freigemCompanel2.png|center|720px]]<br />
<br />
<br />
Finally you enter concentrations, temperature range and expected product yield. The resulting concentrations of annealing product for each primer are shown graphically and in a list.<br />
[[Image:freigemCompanel1.png|center|720px]]<br />
<br />
<br />
<br />
<br />
== What is Companel|DNA good for? ==<br />
<br />
Besides the actual annealing of primers, which it has been intended for, Companel possesses an intrinsic universality when it comes to quantifying competitive processes. For instance a scientist could easily assess the binding priority of two or more (the system can of course be expanded) transcription factors or protein-protein interactions. He or she would just need to measure the two or more separate reactions, which could readily be achieved in an in vitro essay. One could then predict the interaction in vivo - at least thermodynamically. Numerous discoveries during the last years, such as the impact of the circadian clock on metabolism and drug efficacy, have shown that profound research and sometimes even successful treatment can no longer be based on the mere observation of qualitative effects alone. In the challenge to bring both biology and medicine closer to quantitative, predictable and hence more understandable science our application could play a helpful role.<br />
<br />
<br><br />
<br><br />
<html><br />
<a href="https://2012.igem.org/File:Freigem2012-CompanelDNA.zip" target="_blank"><img style="margin-left:0px; align:center;" src="https://static.igem.org/mediawiki/2012/a/a8/Freigemdownload.png" padding:0px; width="300px"; /></a></html><br />
<br><br />
''In case the file does not work properly,''<br><br />
''please send us an email to freigem2012(at)googlemail.com''<br />
<br><br />
<br><br />
[[Image:FreigembarNEWBRIGHT.jpg|left|300px]]<br />
<br><br />
<br><br />
<br></div>Fredhttp://2012.igem.org/Template:Team:FreiburgTemplate:Team:Freiburg2012-09-27T02:45:55Z<p>Fred: </p>
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</head></div>Fredhttp://2012.igem.org/Team:Freiburg/ModelingTeam:Freiburg/Modeling2012-09-27T02:40:19Z<p>Fred: </p>
<hr />
<div>{{Template:Team:Freiburg}}<br />
__NOTOC__<br />
= Companel|DNA ''calculating competitive reactions'' =<br />
<br />
[[Image:FreigemCompanelDNAlogo.png|right|300px]] During the course of our project we encountered a question that we had never before thought about. We were thinking about different ways to synthesize a TAL protein. One of the ideas was to take advantage of the thermodynamic behavior of different DNA strands and synthesize a TAL proteins by means of different primers that anneal at different temperatures to the template strand. We thought it to be possible to elongate a sequence by using this mechanism - simply changing the annealing temperature slightly whilst running a usual PCR. We assumed that the difference in optimal annealing temperatures of different primer sequences would favor one replication product over the others. [[Image:Freigemquote.png|left|280px]] The only thing we did not know was if this was significant enough to be used for the assembly of at least ten TAL domains. After unproductive research on this issue we decided to try modeling this scenario ourselves. <br />
<br />
<br />
The result of these efforts is CompanelDNA, an excel application that allows for predicting the equilibrium concentrations of competitive annealing. It can of course be used for every kind of chemical equilibrium where two substances compete for reacting with the same third reactant. <br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
== Theoretical background ==<br />
<br />
Although it seems to be a simple scenario, we did not find any preexisting solution to this problem - which came to us as quite a surprise. So we started by looking at the law of mass action behind the annealing reaction. Hereafter we will use the following abbreviations and symbols:<br />
<br />
[[Image:freigem1.png|center|400px]]<br />
<br />
The laws of mass action for the two independent reactions are:<br />
<br />
[[Image:freigem2.png|center|150px]]<br />
<br />
If we want to know what is going to happen to the concentrations we originally put in our reaction/PCR tube, we can express the term in relation to the overall concentrations:<br />
<br />
[[Image:freigem3.png|center|300px]]<br />
<br />
Bearing in mind that the only unknown variables are (AB) and (CB) (K can be calculated, see below), one would try to solve these two equations with two variables. A number of other equations can furthermore be generated. However, these equations had no exact solutions when we used Mathematica to have them solved. All the proposed solutions are not applicable to a<br />
wider combination of parameters. Even when we asked for mathematical advice (thanks to Paul Staab, Munich) we got no further. So we decided to solve graphically instead (thanks to Konrad Schieban, Zurich). <br />
In order to do so the equations need to be solved for one variabel:<br />
<br />
[[Image:freigem4.png|center|500px]]<br />
<br />
These equations can now separately be calculated by varying the variable (AB). When a value of (AB) is found that yields the same value of (CB) in both equations, both conditions are fulfilled. Graphically this would be represented by the intersection of the graphs of both equations. Basically this is what our application does. As a first result it clearly showed that the temperature specificity is not strict enough to be used as a elongation determinant, as we had originally hoped.<br />
<br />
<br />
<br />
<br />
== How does Companel|DNA work? ==<br />
<br />
When using Companel you need to "bring" your thermodynamical parameters dH° and dS° for each independent annealing reaction. Due to limited resources could no calculator for these numbers be included. However, there are several free calculators online. More information on how to obtain dH° and dS° can be found in the application.<br />
<br />
Once this sequence specific information has been entered into the application, the constants K for a series of temperatures are calculated by using the Gibbs function. Subsequently the melting plots for each individual reaction are displayed and give you a first impression of the annealing behavior of your primers. <br />
[[Image:freigemCompanel2.png|center|720px]]<br />
<br />
<br />
Finally you enter concentrations, temperature range and expected product yield. The resulting concentrations of annealing product for each primer are shown graphically and in list.<br />
[[Image:freigemCompanel1.png|center|720px]]<br />
<br />
<br />
<br />
<br />
== What is Companel|DNA good for? ==<br />
<br />
Besides the actual annealing of primers, which it has been intended for, Companel possesses an intrinsic universality when it comes to quantifying competitive processes. For instance a scientist could easily assess the binding priority of two or more (the system can of course be expanded) transcription factors or protein-protein interactions. He or she would just need to measure the two or more separate reactions, which could readily be achieved in an in vitro essay. One could then predict the interaction in vivo - at least thermodynamically. Numerous discoveries during the last years, such as the impact of the circadian clock on metabolism and drug efficacy, have shown that profound research and sometimes even successful treatment can no longer be based on the mere observation of qualitative effects alone. In the challenge to bring both biology and medicine closer to quantitative, predictable and hence more understandable science our application could play a helpful role.<br />
<br />
<br><br />
<br><br />
<html><br />
<a href="https://2012.igem.org/File:Freigem2012-CompanelDNA.zip" target="_blank"><img style="margin-left:0px; align:center;" src="https://static.igem.org/mediawiki/2012/a/a8/Freigemdownload.png" padding:0px; width="300px"; /></a></html><br />
<br><br />
''In case the file does not work properly,''<br><br />
''please send us an email to freigem2012(at)googlemail.com''<br />
<br><br />
<br><br />
[[Image:FreigembarNEWBRIGHT.jpg|left|300px]]<br />
<br><br />
<br><br />
<br></div>Fredhttp://2012.igem.org/Team:Freiburg/ModelingTeam:Freiburg/Modeling2012-09-27T02:37:33Z<p>Fred: </p>
<hr />
<div>{{Template:Team:Freiburg}}<br />
__NOTOC__<br />
= Companel|DNA ''calculating competitive reactions'' =<br />
<br />
[[Image:FreigemCompanelDNAlogo.png|right|300px]] During the course of our project we encountered a question that we had never before thought about. We were thinking about different ways to synthesize a TAL protein. One of the ideas was to take advantage of the thermodynamic behavior of different DNA strands and synthesize a TAL proteins by means of different primers that anneal at different temperatures to the template strand. We thought it to be possible to elongate a sequence by using this mechanism - simply changing the annealing temperature slightly whilst running a usual PCR. We assumed that the difference in optimal annealing temperatures of different primer sequences would favor one replication product over the others. [[Image:Freigemquote.png|left|280px]] The only thing we did not know was if this was significant enough to be used for the assembly of at least ten TAL domains. After unproductive research on this issue we decided to try modeling this scenario ourselves. <br />
<br />
<br />
The result of these efforts is CompanelDNA, an excel application that allows for predicting the equilibrium concentrations of competitive annealing. It can of course be used for every kind of chemical equilibrium where two substances compete for reacting with the same third reactant. <br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
== Theoretical background ==<br />
<br />
Although it seems to be a simple scenario, we did not find any preexisting solution to this problem - which came to us as quite a surprise. So we started by looking at the law of mass action behind the annealing reaction. Hereafter we will use the following abbreviations and symbols:<br />
<br />
[[Image:freigem1.png|center|400px]]<br />
<br />
The laws of mass action for the two independent reactions are:<br />
<br />
[[Image:freigem2.png|center|150px]]<br />
<br />
If we want to know what is going to happen to the concentrations we originally put in our reaction/PCR tube, we can express the term in relation to the overall concentrations:<br />
<br />
[[Image:freigem3.png|center|300px]]<br />
<br />
Bearing in mind that the only unknown variables are (AB) and (CB) (K can be calculated, see below), one would try to solve these two equations with two variables. A number of other equations can furthermore be generated. However, these equations had no exact solutions when we used Mathematica to have them solved. All the proposed solutions are not applicable to a<br />
wider combination of parameters. Even when we asked for mathematical advice (thanks to Paul Staab, Munich) we got no further. So we decided to solve graphically instead (thanks to Konrad Schieban, Zurich). <br />
In order to do so the equations need to be solved for one variabel:<br />
<br />
[[Image:freigem4.png|center|500px]]<br />
<br />
These equations can now separately be calculated by varying the variable (AB). When a value of (AB) is found that yields the same value of (CB) in both equations, both conditions are fulfilled. Graphically this would be represented by the intersection of the graphs of both equations. Basically this is what our application does. As a first result it clearly showed that the temperature specificity is not strict enough to be used as a elongation determinant, as we had originally hoped.<br />
<br />
<br />
<br />
<br />
== How does Companel|DNA work? ==<br />
<br />
When using Companel you need to "bring" your thermodynamical parameters dH° and dS° for each independent annealing reaction. Due to limited resources could no calculator for these numbers be included. However, there are several free calculators online. More information on how to obtain dH° and dS° can be found in the application.<br />
<br />
<br />
Once this sequence specific information has been entered into the application, the constants K for a series of temperatures are calculated by using the Gibbs function. Subsequently the melting plots for each individual reaction are displayed and give you a first impression of the annealing behavior of your primers. <br />
[[Image:freigemCompanel2.png|center|720px]]<br />
<br />
<br />
Finally you enter concentrations, temperature range and expected product yield. The resulting concentrations of annealing product for each primer are shown graphically and in list.<br />
[[Image:freigemCompanel1.png|center|720px]]<br />
<br />
<br />
<br />
<br />
== What is Companel|DNA good for? ==<br />
<br />
Besides the actual annealing of primers, which it has been intended for, Companel possesses an intrinsic universality when it comes to quantifying competitive processes. For instance a scientist could easily assess the binding priority of two or more (the system can of course be expanded) transcription factors or protein-protein interactions. He or she would just need to measure the two or more separate reactions, which could readily be achieved in an in vitro essay. One could then predict the interaction in vivo - at least thermodynamically. Numerous discoveries during the last years, such as the impact of the circadian clock on metabolism and drug efficacy, have shown that profound research and sometimes even successful treatment can no longer be based on the mere observation of qualitative effects alone. In the challenge to bring both biology and medicine closer to quantitative, predictable and hence more understandable science our application could play a helpful role.<br />
<br />
<br><br />
<br><br />
<html><br />
<a href="https://2012.igem.org/File:Freigem2012-CompanelDNA.zip" target="_blank"><img style="margin-left:0px; align:center;" src="https://static.igem.org/mediawiki/2012/a/a8/Freigemdownload.png" padding:0px; width="300px"; /></a></html><br />
<br><br />
''In case the file does not work properly,''<br><br />
''please send us an email to freigem2012(at)googlemail.com''<br />
<br><br />
<br><br />
[[Image:FreigembarNEWBRIGHT.jpg|left|300px]]<br />
<br><br />
<br><br />
<br></div>Fredhttp://2012.igem.org/Team:Freiburg/ModelingTeam:Freiburg/Modeling2012-09-27T02:33:24Z<p>Fred: </p>
<hr />
<div>{{Template:Team:Freiburg}}<br />
__NOTOC__<br />
= Companel|DNA ''calculating competitive reactions'' =<br />
<br />
[[Image:FreigemCompanelDNAlogo.png|right|300px]] During the course of our project we encountered a question that we had never before thought about. We were thinking about different ways to synthesize a TAL protein. One of the ideas was to take advantage of the thermodynamic behavior of different DNA strands and synthesize a TAL proteins by means of different primers that anneal at different temperatures to the template strand. We thought it to be possible to elongate a sequence by using this mechanism - simply changing the annealing temperature slightly whilst running a usual PCR. We assumed that the difference in optimal annealing temperatures of different primer sequences would favor one replication product over the others. [[Image:Freigemquote.png|left|280px]] The only thing we did not know was if this was significant enough to be used for the assembly of at least ten TAL domains. After unproductive research on this issue we decided to try modeling this scenario ourselves. <br />
<br />
<br />
The result of these efforts is CompanelDNA, an excel application that allows for predicting the equilibrium concentrations of competitive annealing. It can of course be used for every kind of chemical equilibrium where two substances compete for reacting with the same third reactant. <br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
== Theoretical background ==<br />
<br />
Although it seems to be a simple scenario, we did not find any preexisting solution to this problem - which came to us as quite a surprise. So we started by looking at the law of mass action behind the annealing reaction. Hereafter we will use the following abbreviations and symbols:<br />
<br />
[[Image:freigem1.png|center|400px]]<br />
<br />
The laws of mass action for the two independent reactions are:<br />
<br />
[[Image:freigem2.png|center|150px]]<br />
<br />
If we want to know what is going to happen to the concentrations we originally put in our reaction/PCR tube, we can express the term in relation to the overall concentrations:<br />
<br />
[[Image:freigem3.png|center|300px]]<br />
<br />
Bearing in mind that the only unknown variables are (AB) and (CB) (K can be calculated, see below), one would try to solve these two equations with two variables. A number of other equations can furthermore be generated. However, these equations had no exact solutions when we used Mathematica to have them solved. All the proposed solutions are not applicable to a<br />
wider combination of parameters. Even when we asked for mathematical advice (thanks to Paul Staab, Munich) we got no further. So we decided to solve graphically instead (thanks to Konrad Schieban, Zurich). <br />
In order to do so the equations need to be solved for one variabel:<br />
<br />
[[Image:freigem4.png|center|500px]]<br />
<br />
These equations can now separately be calculated by varying the variable (AB). When a value of (AB) is found that yields the same value of (CB) in both equations, both conditions are fulfilled. Graphically this would be represented by the intersection of the graphs of both equations. Basically this is what our application does. As a first result it clearly showed that the temperature specificity is not strict enough to be used as a elongation determinant, as we had originally hoped.<br />
<br />
<br />
<br />
<br />
== How does Companel work? ==<br />
<br />
When using Companel you need to "bring" your thermodynamical parameters dH° and dS° for each independent annealing reaction. Due to limited resources could no calculator for these numbers be included. However, there are several free calculators online. More information on how to obtain dH° and dS° can be found in the application.<br />
<br />
[[Image:freigemCompanel2.png|right|500px]]<br />
<br />
Once this sequence specific information has been entered into the application, the constants K for a series of temperatures are calculated by using the Gibbs function. Subsequently the melting plots for each individual reaction are displayed and give you a first impression of the annealing behavior of your primers. <br />
<br />
[[Image:freigemCompanel1.png|right|500px]]<br />
<br />
Finally you enter concentrations, temperature range and expected product yield. The resulting concentrations of annealing product for each primer are shown graphically and in list.<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
== What is Companel good for? ==<br />
<br />
Besides the actual annealing of primers, which it has been intended for, Companel possesses an intrinsic universality when it comes to quantifying competitive processes. For instance a scientist could easily assess the binding priority of two or more (the system can of course be expanded) transcription factors or protein-protein interactions. He or she would just need to measure the two or more separate reactions, which could readily be achieved in an in vitro essay. One could then predict the interaction in vivo - at least thermodynamically. Numerous discoveries during the last years, such as the impact of the circadian clock on metabolism and drug efficacy, have shown that profound research and sometimes even successful treatment can no longer be based on the mere observation of qualitative effects alone. In the challenge to bring both biology and medicine closer to quantitative, predictable and hence more understandable science our application could play a helpful role.<br />
<br />
<br><br />
<br><br />
<html><br />
<a href="https://2012.igem.org/File:Freigem2012-CompanelDNA.zip" target="_blank"><img style="margin-left:0px; align:center;" src="https://static.igem.org/mediawiki/2012/a/a8/Freigemdownload.png" padding:0px; width="300px"; /></a></html><br />
<br><br />
''In case the file does not work properly,''<br><br />
''please send us an email to freigem2012(at)googlemail.com''<br />
<br><br />
<br><br />
[[Image:FreigembarNEWBRIGHT.jpg|left|300px]]<br />
<br><br />
<br><br />
<br></div>Fredhttp://2012.igem.org/Team:Freiburg/ModelingTeam:Freiburg/Modeling2012-09-27T02:28:36Z<p>Fred: </p>
<hr />
<div>{{Template:Team:Freiburg}}<br />
__NOTOC__<br />
= Companel|DNA ''calculating competitive reactions'' =<br />
<br />
[[Image:FreigemCompanelDNAlogo.png|right|300px]] During the course of our project we encountered a question that we had never before thought about. We were thinking about different ways to synthesize a TAL protein. One of the ideas was to take advantage of the thermodynamic behavior of different DNA strands and synthesize a TAL proteins by means of different primers that anneal at different temperatures to the template strand. We thought it to be possible to elongate a sequence by using this mechanism - simply changing the annealing temperature slightly whilst running a usual PCR. We assumed that the difference in optimal annealing temperatures of different primer sequences would favor one replication product over the others. [[Image:Freigemquote.png|left|280px]] The only thing we did not know was if this was significant enough to be used for the assembly of at least ten TAL domains. After unproductive research on this issue we decided to try modeling this scenario ourselves. <br />
<br />
<br />
The result of these efforts is CompanelDNA, an excel application that allows for predicting the equilibrium concentrations of competitive annealing. It can of course be used for every kind of chemical equilibrium where two substances compete for reacting with the same third reactant. <br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
== Theoretical background ==<br />
<br />
Although it seems to be a simple scenario, we did not find any preexisting solution to this problem - which came to us as quite a surprise. So we started by looking at the law of mass action behind the annealing reaction. Hereafter we will use the following abbreviations and symbols:<br />
<br />
[[Image:freigem1.png|center|400px]]<br />
<br />
The laws of mass action for the two independent reactions are:<br />
<br />
[[Image:freigem2.png|center|150px]]<br />
<br />
If we want to know what is going to happen to the concentrations we originally put in our reaction/PCR tube, we can express the term in relation to the overall concentrations:<br />
<br />
[[Image:freigem3.png|center|300px]]<br />
<br />
Bearing in mind that the only unknown variables are (AB) and (CB) (K can be calculated, see below), one would try to solve these two equations with two variables. A number of other equations can furthermore be generated. However, these equations had no exact solutions when we used Mathematica to have them solved. All the proposed solutions are not applicable to a<br />
wider combination of parameters. Even when we asked for mathematical advice (thanks to Paul Staab, Munich) we got no further. So we decided to solve graphically instead (thanks to Konrad Schieban, Zurich). <br />
In order to do so the equations need to be solved for one variabel:<br />
<br />
[[Image:freigem4.png|center|500px]]<br />
<br />
These equations can now separately be calculated by varying the variable (AB). When a value of (AB) is found that yields the same value of (CB) in both equations, both conditions are fulfilled. Graphically this would be represented by the intersection of the graphs of both equations. Basically this is what our application does. As a first result it clearly showed that the temperature specificity is not strict enough to be used as a elongation determinant, as we had originally hoped.<br />
<br />
<br />
<br />
<br />
== How does Companel work? ==<br />
<br />
When using Companel you need to "bring" your thermodynamical parameters dH° and dS° for each independent annealing reaction. Due to limited resources could no calculator for these numbers be included (which simply is a list of values for each combination of base pairs and neighboring bases). However, there are several free calculators online. More information on how to obtain dH° and dS° can be found in the application.<br />
<br />
[[Image:freigemCompanel2.png|right|500px]]<br />
<br />
Once these sequence specific information has been entered into the application, the constants K for a series of temperatures are calculated by using the Gibbs function. Subsequently the melting plots for each individual reaction are displayed and give you a first impression of the annealing behavior of your primers. <br />
<br />
[[Image:freigemCompanel1.png|right|500px]]<br />
<br />
Finally you enter concentrations, temperature range and expected product yield. The resulting concentrations of annealing product for each primer are shown graphically and in list.<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
== What is Companel good for? ==<br />
<br />
Besides the actual annealing of primers, which it has been intended for, Companel possesses an intrinsic universality when it comes to quantifying competitive processes. For instance a scientist could easily assess the binding priority of two or more (the system can of course be expanded) transcription factors or protein-protein interactions. He or she would just need to measure the two or more separate reactions, which could readily be achieved in an in vitro essay. One could then predict the interaction in vivo - at least thermodynamically. Numerous discoveries during the last years, such as the impact of the circadian clock on metabolism and drug efficacy, have shown that profound research and sometimes even successful treatment can no longer be based on the mere observation of qualitative effects alone. In the challenge to bring both biology and medicine closer to quantitative, predictable and hence more understandable science our application could play a helpful role.<br />
<br />
<br><br />
<br><br />
<html><br />
<a href="https://2012.igem.org/File:Freigem2012-CompanelDNA.zip" target="_blank"><img style="margin-left:0px; align:center;" src="https://static.igem.org/mediawiki/2012/a/a8/Freigemdownload.png" padding:0px; width="300px"; /></a></html><br />
<br><br />
''In case the file does not work properly,''<br><br />
''please send us an email to freigem2012(at)googlemail.com''<br />
<br><br />
<br><br />
[[Image:FreigembarNEWBRIGHT.jpg|left|300px]]<br />
<br><br />
<br><br />
<br></div>Fredhttp://2012.igem.org/Team:Freiburg/ModelingTeam:Freiburg/Modeling2012-09-27T02:27:39Z<p>Fred: </p>
<hr />
<div>{{Template:Team:Freiburg}}<br />
__NOTOC__<br />
= Companel|DNA ''calculating competitive reactions'' =<br />
<br />
[[Image:FreigemCompanelDNAlogo.png|right|300px]] During the course of our project we encountered a question that we had never before thought about. We were thinking about different ways to synthesize a TAL protein. One of the ideas was to take advantage of the thermodynamic behavior of different DNA strands and synthesize a TAL proteins by means of different primers that anneal at different temperatures to the template strand. We thought it to be possible to elongate a sequence by using this mechanism - simply changing the annealing temperature slightly whilst running a usual PCR. We assumed that the difference in optimal annealing temperatures of different primer sequences would favor one replication product over the others. [[Image:Freigemquote.png|left|280px]] The only thing we did not know was if this was significant enough to be used for the assembly of at least ten TAL domains. After unproductive research on this issue we decided to try modeling this scenario ourselves. <br />
<br />
<br />
The result of these efforts is CompanelDNA, an excel application that allows for predicting the equilibrium concentrations of competitive annealing. It can of course be used for every kind of chemical equilibrium where two substances compete for reacting with the same third reactant. <br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
== Theoretical background ==<br />
<br />
Although it seems to be a simple scenario, we did not find any preexisting solution to this problem - which came to us as quite a surprise. So we started by looking at the law of mass action behind the annealing reaction. Hereafter we will use the following abbreviations and symbols:<br />
<br />
[[Image:freigem1.png|center|400px]]<br />
<br />
The laws of mass action for the two independent reactions are:<br />
<br />
[[Image:freigem2.png|center|150px]]<br />
<br />
If we want to know what is going to happen to the concentrations we originally put in our reaction/PCR tube, we can expressed the term in relation to the overall concentrations:<br />
<br />
[[Image:freigem3.png|center|300px]]<br />
<br />
Bearing in mind that the only unknown variables are (AB) and (CB) (K can be calculated, see below), one would try to solve these two equations with two variables. A number of other equations can furthermore be generated. However, these equations had no exact solutions when we used Mathematica to have them solved. All the proposed solutions are not applicable to a<br />
wider combination of parameters. Even when we asked for mathematical advice (thanks to Paul Staab, Munich) we got no further. So we decided to solve graphically instead (thanks to Konrad Schieban, Zurich). <br />
In order to do so the equations need to be solved for one variabel:<br />
<br />
[[Image:freigem4.png|center|500px]]<br />
<br />
These equations can now separately be calculated by varying the variable (AB). When a value of (AB) is found that yields the same value of (CB) in both equations, both conditions are fulfilled. Graphically this would be represented by the intersection of the graphs of both equations. Basically this is what our application does. As a first result it clearly showed that the temperature specificity is not strict enough to be used as a elongation determinant, as we had originally hoped.<br />
<br />
<br />
<br />
<br />
== How does Companel work? ==<br />
<br />
When using Companel you need to "bring" your thermodynamical parameters dH° and dS° for each independent annealing reaction. Due to limited resources could no calculator for these numbers be included (which simply is a list of values for each combination of base pairs and neighboring bases). However, there are several free calculators online. More information on how to obtain dH° and dS° can be found in the application.<br />
<br />
[[Image:freigemCompanel2.png|right|500px]]<br />
<br />
Once these sequence specific information has been entered into the application, the constants K for a series of temperatures are calculated by using the Gibbs function. Subsequently the melting plots for each individual reaction are displayed and give you a first impression of the annealing behavior of your primers. <br />
<br />
[[Image:freigemCompanel1.png|right|500px]]<br />
<br />
Finally you enter concentrations, temperature range and expected product yield. The resulting concentrations of annealing product for each primer are shown graphically and in list.<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
== What is Companel good for? ==<br />
<br />
Besides the actual annealing of primers, which it has been intended for, Companel possesses an intrinsic universality when it comes to quantifying competitive processes. For instance a scientist could easily assess the binding priority of two or more (the system can of course be expanded) transcription factors or protein-protein interactions. He or she would just need to measure the two or more separate reactions, which could readily be achieved in an in vitro essay. One could then predict the interaction in vivo - at least thermodynamically. Numerous discoveries during the last years, such as the impact of the circadian clock on metabolism and drug efficacy, have shown that profound research and sometimes even successful treatment can no longer be based on the mere observation of qualitative effects alone. In the challenge to bring both biology and medicine closer to quantitative, predictable and hence more understandable science our application could play a helpful role.<br />
<br />
<br><br />
<br><br />
<html><br />
<a href="https://2012.igem.org/File:Freigem2012-CompanelDNA.zip" target="_blank"><img style="margin-left:0px; align:center;" src="https://static.igem.org/mediawiki/2012/a/a8/Freigemdownload.png" padding:0px; width="300px"; /></a></html><br />
<br><br />
''In case the file does not work properly,''<br><br />
''please send us an email to freigem2012(at)googlemail.com''<br />
<br><br />
<br><br />
[[Image:FreigembarNEWBRIGHT.jpg|left|300px]]<br />
<br><br />
<br><br />
<br></div>Fredhttp://2012.igem.org/Team:Freiburg/Team2Team:Freiburg/Team22012-09-27T02:25:55Z<p>Fred: </p>
<hr />
<div>{{Template:Team:Freiburg}}<br />
<br />
= Team = <br />
----<br />
<br><br />
[[File:teamsymbol.png|180px|center]]<br />
<br><br><br />
{|align="center"<br />
|[[Image:team_freiburg.jpg|400px|center]]<br />
|-<br />
|}<br />
<br />
<div style="text-align: center;"><span style="text-align:center; color:##C1E2FE; background:##00C000"> '''The FreiGEM 2012 Team'''<br />
</span><br />
</div><br />
<br />
<br />
<div align="justify">Our highly interdisciplinary team consists of 20 students from biology, medicine, molecular medicine, pharmacy, philosophy and microsystems engineering (see below). We receive advice from our postdoc Dr. Susanne Proksch. Moreover, we are under the patronage of Prof. Dr. Michael Reth and Prof. Dr. Heike Pahl.</div><br />
<br />
<br />
<br />
<br />
<br />
== Who we are ==<br />
----<br />
==Student Leader==<br />
<br><br />
<html><br />
<table border="0" cellspacing="30" style="background-color:transparent"><br />
<tr><br />
<th>Nicolas Wyvekens</th><br />
<tr><br />
<td><img src="https://static.igem.org/mediawiki/2012/f/fb/NicoW.jpg" width="200px"/></td><br />
<td><div align="justify">I´m a third-year medical student and the student group leader of our iGEM team. What I like most about iGEM is the opportunity to work on a project that we, as a team, have come up with and planned ourselves. As a medical student, I hadn’t received much training in molecular biology techniques, so it was very challenging for me to plan the project. Besides learning new lab skills, it was an important lesson to deal with frustration when days (and nights) of intense work turned up no positive results. In the end, it is even more rewarding to see that our idea actually works very well and that it attracts great interest from ’real’ scientists.</div></td><br />
</tr></table><br />
</html><br />
----<br />
<br />
==Master students==<br />
<br />
<html><br />
<table border="0" cellspacing="30" style="background-color:transparent"><br />
<tr><br />
<th>David Siegel</th></tr><br />
<tr><br />
<td><img src="https://static.igem.org/mediawiki/2012/7/7a/DavidS.jpg" width="200px"/></td><br />
<td><div align="justify">I'm 25 years old and studying biology in the 8th semster at the Albert-Ludwigs University Freiburg. Currently, I'm in the master programm and preparing to start my master thesis in the field of syntehtic biology and biotechnology.<br><br />
The whole theory of synthetic biology, the idea of organising the seemingly chaotic structure of nature thrilled me since the first time I heard of it. When I got news of a new iGEM team I instantly took the chance and joined. Through the iGEM contest I was able to follow a project from the idea on a piece of paper, all the way to proof of concept experiments and final evaluation. I experienced the ups and downs of being in a team with people of so many disciplines and I got the chance to take part in every step that was necessary to make something happen.</div></td><br />
</tr></table><br />
</html><br />
<br />
<html><br />
<table border="0" cellspacing="30" style="background-color:transparent"><br />
<tr><br />
<th>Lisa Jerabek</th></tr><br />
<tr><br />
<td><img src="https://static.igem.org/mediawiki/2012/a/a8/Lisa.jpg" width="200px"/></td><br />
<td><div align="justify">I´m studying biology in the 8th semester and will start my Master´s thesis in the research area of synthetic biology in October. <br />
By joining in on freiGEM2012 I accepted the challenge of planning and realizing a self-made project in my research area of interest. I considered my participation in the iGEM team as an opportunity to broaden my expertise in many respects. For me, a really important experience was to face the difficulties of lab work in a large team of members with profoundly varying skills and to learn how to cope with these discrepancies. My primary role in the team was the management of cell cultural issues, which is what made me the “cell culture lady” of the team. <br />
I´m very grateful for the opportunity to learn new methods as well as to get to know new approaches to solving scientific problems and for such a great time with freiGEM2012.</div><br />
</td><br />
</tr></table><br />
</html><br />
<br />
<html><br />
<table border="0" cellspacing="30" style="background-color:transparent"><br />
<tr><br />
<th>Natalie Knoll</th></tr><br />
<tr><br />
<td><img src="https://static.igem.org/mediawiki/2012/6/6a/Natalie.png" width="200px"/></td><br />
<td><div align="justify">I'm studying biology in the 8th semester and starting to prepare for my master thesis. The iGEM 2012 contest was a great experience for me and im glad i took my last chance to join a iGEM team. It was a great time and i'm sure i will miss my team when the iGEM time ends. When im thinking about the countless hours we spend in the lap, all the days and at the end even the nights, i'm already sure i will miss this time and all the great people of my team. </div><br />
</td><br />
</tr></table><br />
</html><br />
<br />
----<br />
<br />
==Bachelor students==<br />
<br />
<html><br />
<table border="0" cellspacing="30" style="background-color:transparent"><br />
<tr><br />
<th>Lucas Schneider</th></tr><br />
<tr><br />
<td><img src="https://static.igem.org/mediawiki/2012/b/bb/LucasS.jpg" width="200px"/></td><br />
<td><div align="justify">During completion of my bachelor of science degree in molecular biology, I joined the IGEM Team of Freiburg. My research interests are molecular biology, bioinformatics and plant biotechnology.<br />
My role in freiGEM 2012 was to instruct an interdisciplinary team of students in molecular cloning and experimental design. Finally, I am proud that we got the toolkit and the TAL-Vectors up and running. It was a valuable experience working with such a team.</div><br />
</td><br />
</tr></table><br />
</html><br />
<br />
<html><br />
<table border="0" cellspacing="30" style="background-color:transparent"><br />
<tr><br />
<th>Lukas Boeckelmann</th></tr><br />
<tr><br />
<td><img src="https://static.igem.org/mediawiki/2012/f/f9/Lukas.jpg" width="200px"/></td><br />
<td><div align="justify">I am a student of Medicine in my fourth year and have always been fascinated by the opportunities that modern Molecular Biology has to offer. I have just started my MD thesis and many of the experiences I've already made with iGEM help me greatly. I have benefited tremendously from the iGEM project: It has been very rewarding to research a topic in such depth, to discuss it with the wonderful and bright (and funny) people I have met in our team and to then develop methodical solutions that actually function well! <br />
I am incredibly excited about the work we have done so far and about the work we will continue to do!</div></td><br />
</tr></table><br />
</html><br />
<br />
<html><br />
<table border="0" cellspacing="30" style="background-color:transparent"><br />
<tr><br />
<th>Franz Dressler</th></tr><br />
<tr><br />
<td><img src="https://static.igem.org/mediawiki/2012/7/79/FranzD.jpg" width="200px"/></td><br />
<td><div align="justify">I´m a medical student in the 4th year and I joined iGEM due to the unlimited possibilities the project offers. It is a unique opportunity to explore a scientific question or to tackle an everyday biological problem - but the best thing about it: you are completely free to choose what field you want to engage in. From the medical point of view it is also intriguing to get more familiar with molecular methods. In all these regards my expectations have completely been fulfilled. We had an amazing time in the lab, but also exciting discussions and presentations, a vivid and enriching exchange of ideas and knowledge amongst the team members and thanks to the iGEM community. <br />
My special contributions to our project were modeling as well as layout and design of our website and posters.</div><br />
</td><br />
</tr></table><br />
</html><br />
<br />
<html><br />
<table border="0" cellspacing="30" style="background-color:transparent"><br />
<tr><br />
<th>Kimon Runge</th></tr><br />
<tr><br />
<td><img src="https://static.igem.org/mediawiki/2012/e/e2/Kimon.jpg" width="200px"/></td><br />
<td><div align="justify">I´m studying medicine in the 4th year and I participate in iGEM because I want to get a better insight in the workings of a laboratory. And what better source of insight can you get than operating your own lab as a team? Of course it’s much more than that and an experience I can recommend to anyone. My special mission is to plan the travels of the group.</div></td><br />
</tr></table><br />
</html><br />
<br />
<html><br />
<table border="0" cellspacing="30" style="background-color:transparent"><br />
<tr><br />
<th>Sebastian Kuechlin</th></tr><br />
<tr><br />
<td><img src="https://static.igem.org/mediawiki/2012/5/55/Sebastian.jpg" width="200px"/></td><br />
<td><div align="justify">I'm a medical student and currently in my fourth year of studies. What fascinates me about synthetic biology is the engineering aspect: I love reconsidering the knowledge I have learned thus far in my medical education and applying it in new ways: Participating in iGEM has altered my way of thinking about biology for good. When I'm not in the hospital, the lecture halls or labs, I love making music and have found a wonderful opportunity to do so as a piano player in our university's big band."</div></td><br />
</tr></table><br />
</html><br />
<br />
<html><br />
<table border="0" cellspacing="30" style="background-color:transparent"><br />
<tr><br />
<th>Fabian Stritt</th></tr><br />
<tr><br />
<td><img src="https://static.igem.org/mediawiki/2012/d/d8/Fabian.jpg" width="200px"/></td><br />
<td><div align="justify">I have completed two years of my bachelor of science curriculum in biology in Freiburg and will continue my studies in Strasburg in a bioengineering program. It was my interest in the synthetic aspects of biology, which motivated me to join the iGEM team. My particular contribution to our project was the organization of the film project, the result of which you can see on our website, as well as the representation of our team in Berlin at the 'Biotechnologie2020+' . For me, iGEM was a valuable experience which strengthened my wish to become a bioengineer. ></div></td><br />
</tr></table><br />
</html><br />
<br />
<html><br />
<table border="0" cellspacing="30" style="background-color:transparent"><br />
<tr><br />
<th>Philipp Warmer</th></tr><br />
<tr><br />
<td><img src="https://static.igem.org/mediawiki/2012/2/25/PhillipW.jpg" width="200px"/></td><br />
<td><div align="justify">This is a TALE about Philipp who grew up to become a bioengineer.<br />
Once upon a time this Philipp started studying biology at Freiburg University and got very attracted to the beauty that resides within the simplicity of SynBio.<br />
As he got older he joined the freiGEM Team to take part in the world wide challenge for SynBio.<br />
And so he and the freiGEM Team lived happily ever after...<br />
See you all at the Jamboree!<br />
</div></td><br />
</tr></table><br />
</html><br />
<br />
<html><br />
<table border="0" cellspacing="30" style="background-color:transparent"><br />
<tr><br />
<th>Jan Patrick Steitz</th></tr><br />
<tr><br />
<td><img src="https://static.igem.org/mediawiki/2012/a/a8/Jan-Phillip.jpg" width="200px"/></td><br />
<td><div align="justify">I´m a third year student of pharmaceutics, so most of the time I have to deal with chemistry.<br />
iGEM gave me a great opportunity to gain experience on the subject of synthetic biology and, of course, it was a lot of fun. <br />
</div></td><br />
</tr></table><br />
</html><br />
<br />
<html><br />
<table border="0" cellspacing="30" style="background-color:transparent"><br />
<tr><br />
<th>Leo Scheller</th></tr><br />
<tr><br />
<td><img src="https://static.igem.org/mediawiki/2012/8/8c/Leo.jpg" width="200px"/></td><br />
<td><div align="justify">I studied molecular medicine in Freiburg and I just moved to Edinburgh for Systems and Synthetic Biology. I hope to integrate Systems and Synthetic Biology into medical research and iGEM has been a great opportunity for gathering practical skills, for being creative, and for getting to know very cool people. Also I'm happy that we have a very promising project and I look forward to our presentation in Amsterdam.</div></td><br />
</tr></table><br />
</html><br />
<br />
<html><br />
<table border="0" cellspacing="30" style="background-color:transparent"><br />
<tr><br />
<th>Denis Grishin</th></tr><br />
<tr><br />
<td><img src="https://static.igem.org/mediawiki/2012/3/32/Denis.jpg" width="200px"/></td><br />
<td><div align="justify">I study molecular medicine and microelectromechanical systems. With this choice of fields of study my goal is to bring life sciences and engineering together. When I heard about iGEM I realized that for me it would be the perfect opportunity to pursue this objective. I am fascinated by synthetic biology and believe in the great potential of biological engineering approaches. freiGEM 2012 gave me the opportunity to take part in an exciting project and to further develop my lab skills. It was a lot of fun and I have very much enjoyed the work in our team.</div></td><br />
</tr></table><br />
</html><br />
<br />
<html><br />
<table border="0" cellspacing="30" style="background-color:transparent"><br />
<tr><br />
<th>Verena Waehle</th></tr><br />
<tr><br />
<td><img src="https://static.igem.org/mediawiki/2012/d/d0/Verena.jpg" width="200px"/></td><br />
<td><div align="justify">During the time of my bachelor studies in molecular medicine, I learned a lot about the function of cells as well as of whole organisms. Nevertheless, the field of synthetic biology remained something impalpable for me. When I first heard about iGEM, I was intrigued by the concept, that a group of students should plan and realize a whole project in the context of synthetic biology almost on their own. Considering this a challenge and a great opportunity to broaden my horizon by emerging into a research area that differs profoundly from everything I have done before, I joined in on the team. During the whole iGEM year, I was able to learn a lot about almost any aspect of research life, which is what makes the time with freiGEM such an invaluable experience. <br />
I really enjoy the opportunity to be part of such a fabulous project and of an even more fabulous team!<br />
</div></td><br />
</tr></table><br />
</html><br />
<br />
<html><br />
<table border="0" cellspacing="30" style="background-color:transparent"><br />
<tr><br />
<th>Josip Herman</th></tr><br />
<tr><br />
<td><img src="https://static.igem.org/mediawiki/2012/7/77/Josip.jpg" width="200px"/></td><br />
<td><div align="justify">I´m studying molecular medicine and I was curious about iGEM. iGEM gives me the opportunity to get first insights into the emerging field of synthetic biology, which will very likely influence our future lives. During the time as a freiGEM team member I earned a lot of lab experience and enjoyed the time in the team.<br />
May the TALs be with you.<br />
See you.<br />
</div></td><br />
</tr></table><br />
</html><br />
<br />
<html><br />
<table border="0" cellspacing="30" style="background-color:transparent"><br />
<tr><br />
<th>David Fuchs</th></tr><br />
<tr><br />
<td><img src="https://static.igem.org/mediawiki/2012/a/ab/DavidF.jpg" width="200px"/></td><br />
<td><div align="justify">Biology is going synthetic and it's going there fast. It poses many new and exciting frontiers, so joining in on such a high profile competition as iGEM came natural. Working with people from every corner of the life science landscape and beyond was an eye-opening experience. I learned quite a bit about every facet of lab life during my time with freiGEM, which is what makes this whole endeavor so invaluable.<br />
Cheers to all.<br />
</div></td><br />
</tr></table><br />
</html><br />
----<br />
===Human Practice===<br />
<br />
<html><br />
<table border="0" cellspacing="30" style="background-color:transparent"><br />
<tr><br />
<th>Pablo Grassi</th></tr><br />
<tr><br />
<td><img src="https://static.igem.org/mediawiki/2012/9/99/Pablo.jpg" width="200px"/></td><br />
<td><div align="justify"><br />
I will try to make a long story short: I obtained a bachelor´s degree in biology and I´m currently studying philosophy. I joined the freiGEM-team because of just two reasons. On the one hand, since 2010 I organize an interdisciplinary project at the University of Freiburg concerning the concept of life. In this project, I intend to combine theoretical biology and philosophy of biology to encounter the phenomena of the living. On the other hand, I specialized in the fields of synthetic biology and biochemistry during my bachelor studies. Through combination of these two aspects, the iGEM competition revealed itself as an unique chance for exploring arising philosophical questions concerning our understanding of life. I was lucky I had the possibility to be a member of this great team, which lively promoted philosophical reflection and precise thinking.<br />
</div></td><br />
</tr></table><br />
</html><br />
<br />
----<br />
<br />
===Advisors===<br />
<br />
<html><br />
<table border="0" cellspacing="30" style="background-color:transparent"><br />
<tr><br />
<th>Dr. Susanne Proksch</th></tr><br />
<tr><br />
<td><img src="https://static.igem.org/mediawiki/2012/0/0c/Susanne.jpg" width="200px"/></td><br />
<td><div align="justify">I have joined the iGEM team as an advisor to share my research experience with the younger team members. After studying dental medicine, and post doctoral work in Paris, I´m currently doing research on regenerative dentistry at the Clinic for Oral & Maxillofacial Surgery of the “Uniklinik Freiburg”. I decided to participate in the iGEM competition due to my enthusiasm, curiosity and passion for the world of science and my tremendous thirst for new knowledge. Furthermore, it is a great experience to get in touch with the initiative, creativity and cleverness of the undergraduate students which is quite impressive. I got to know synthetic biology as a fascinating field of research and I´m really grateful for this superb experience – Chapeau freiGEM 2012!</div></td><br />
</tr></table><br />
</html><br />
<br />
<br><br><br><br><br />
[[#top|Back to top]]</div>Fredhttp://2012.igem.org/Team:Freiburg/ModelingTeam:Freiburg/Modeling2012-09-27T02:23:33Z<p>Fred: </p>
<hr />
<div>{{Template:Team:Freiburg}}<br />
__NOTOC__<br />
= Companel|DNA ''calculating competitive reactions'' =<br />
<br />
[[Image:FreigemCompanelDNAlogo.png|right|300px]] During the course of our project we encountered a question that we had never before thought about. We were thinking about different ways to synthesize a TAL protein. One of the ideas was to take advantage of the thermodynamic behavior of different DNA strands and synthesize a TAL proteins by means of different primers that anneal at different temperatures to the template strand. We thought it to be possible to elongate a sequence by using this mechanism - simply changing the annealing temperature slightly whilst running a usual PCR. We assumed that the difference in optimal annealing temperatures of different primer sequences would favor one replication product over the others. [[Image:Freigemquote.png|left|280px]] The only thing we did not know was if this was significant enough to be used for the assembly of at least ten TAL domains. After unproductive research on this issue we decided to try modeling this scenario ourselves. <br />
<br />
<br />
The result of these efforts is CompanelDNA, an excel application that allows for predicting the equilibrium concentrations of competitive annealing. It can of course be used for every kind of chemical equilibrium where two substances compete for reacting with the same third reactant. <br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
== Theoretical background ==<br />
<br />
Although it seems to be a simple scenario, we did not find any preexisting solution to this problem - which came to us as quite a surprise. So we started by looking at the law of mass action behind the annealing reaction. Hereafter we shall use the following abbreviations and symbols:<br />
<br />
[[Image:freigem1.png|center|400px]]<br />
<br />
The laws of mass action for the two independent reactions are:<br />
<br />
[[Image:freigem2.png|center|150px]]<br />
<br />
If we want to know what is going to happen to the concentrations we originally put in our reaction/PCR tube, we can expressed the term in relation to the overall concentrations:<br />
<br />
[[Image:freigem3.png|center|300px]]<br />
<br />
Bearing in mind that the only unknown variables are (AB) and (CB) (K can be calculated, see below), one would try to solve these two equations with two variables. A number of other equations can furthermore be generated. However, these equations had no exact solutions when we used Mathematica to have them solved. All the proposed solutions are not applicable to a<br />
wider combination of parameters. Even when we asked for mathematical advice (thanks to Paul Staab, Munich) we got no further. So we decided to solve graphically instead (thanks to Konrad Schieban, Zurich). <br />
In order to do so the equations need to be solved for one variabel:<br />
<br />
[[Image:freigem4.png|center|500px]]<br />
<br />
These equations can now separately be calculated by varying the variable (AB). When a value of (AB) is found that yields the same value of (CB) in both equations, both conditions are fulfilled. Graphically this would be represented by the intersection of the graphs of both equations. Basically this is what our application does. As a first result it clearly showed that the temperature specificity is not strict enough to be used as a elongation determinant, as we had originally hoped.<br />
<br />
<br />
<br />
<br />
== How does Companel work? ==<br />
<br />
When using Companel you need to "bring" your thermodynamical parameters dH° and dS° for each independent annealing reaction. Due to limited resources could no calculator for these numbers be included (which simply is a list of values for each combination of base pairs and neighboring bases). However, there are several free calculators online. More information on how to obtain dH° and dS° can be found in the application.<br />
<br />
[[Image:freigemCompanel2.png|right|500px]]<br />
<br />
Once these sequence specific information has been entered into the application, the constants K for a series of temperatures are calculated by using the Gibbs function. Subsequently the melting plots for each individual reaction are displayed and give you a first impression of the annealing behavior of your primers. <br />
<br />
[[Image:freigemCompanel1.png|right|500px]]<br />
<br />
Finally you enter concentrations, temperature range and expected product yield. The resulting concentrations of annealing product for each primer are shown graphically and in list.<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
== What is Companel good for? ==<br />
<br />
Besides the actual annealing of primers, which it has been intended for, Companel possesses an intrinsic universality when it comes to quantifying competitive processes. For instance a scientist could easily assess the binding priority of two or more (the system can of course be expanded) transcription factors or protein-protein interactions. He or she would just need to measure the two or more separate reactions, which could readily be achieved in an in vitro essay. One could then predict the interaction in vivo - at least thermodynamically. Numerous discoveries during the last years, such as the impact of the circadian clock on metabolism and drug efficacy, have shown that profound research and sometimes even successful treatment can no longer be based on the mere observation of qualitative effects alone. In the challenge to bring both biology and medicine closer to quantitative, predictable and hence more understandable science our application could play a helpful role.<br />
<br />
<br><br />
<br><br />
<html><br />
<a href="https://2012.igem.org/File:Freigem2012-CompanelDNA.zip" target="_blank"><img style="margin-left:0px; align:center;" src="https://static.igem.org/mediawiki/2012/a/a8/Freigemdownload.png" padding:0px; width="300px"; /></a></html><br />
<br><br />
''In case the file does not work properly,''<br><br />
''please send us an email to freigem2012(at)googlemail.com''<br />
<br><br />
<br><br />
[[Image:FreigembarNEWBRIGHT.jpg|left|300px]]<br />
<br><br />
<br><br />
<br></div>Fredhttp://2012.igem.org/Team:Freiburg/ModelingTeam:Freiburg/Modeling2012-09-27T02:17:48Z<p>Fred: </p>
<hr />
<div>{{Template:Team:Freiburg}}<br />
__NOTOC__<br />
= Companel|DNA ''calculating competitive reactions'' =<br />
<br />
[[Image:FreigemCompanelDNAlogo.png|right|300px]] During the course of our project we encountered a question that we had never before thought about. We were thinking about different ways to synthesize a TAL protein. One of the ideas was to take advantage of the thermodynamic behavior of different DNA strands and synthesize a TAL proteins by means of different primers that anneal at different temperatures to the template strand. We thought it to be possible to elongate a sequence by using this mechanism - simply changing the annealing temperature slightly whilst running a usual PCR. We assumed that the difference in optimal annealing temperatures of different primer sequences would favor one replication product over the others. [[Image:Freigemquote.png|left|280px]] The only thing we did not know was if this was significant enough to be used for the assembly of at least ten TAL domains. After unproductive research on this issue we decided to try modeling this scenario ourselves. <br />
<br />
<br />
The result of these efforts is CompanelDNA, an excel application that allows for predicting the equilibrium concentrations of competitive annealing. It can of course be used for every kind of chemical equilibrium where two substances compete for reacting with the same third reactant. <br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
== Theoretical background ==<br />
<br />
Although it seems to be a simple scenario, we did not find any preexisting solution to this problem - which came to us as quite a surprise. So we started by looking at the law of mass action behind the annealing reaction. Hereafter we shall use the following abbreviations and symbols:<br />
<br />
[[Image:freigem1.png|center|400px]]<br />
<br />
The laws of mass action for the two independent reactions are:<br />
<br />
[[Image:freigem2.png|center|150px]]<br />
<br />
If we want to know what is going to happen to the concentrations we originally put in our reaction/PCR tube, we can expressed the term in relation to the overall concentrations:<br />
<br />
[[Image:freigem3.png|center|300px]]<br />
<br />
Bearing in mind that the only unknown variables are (AB) and (CB) (K can be calculated, see below), one would try to solve these two equations with two variables. A number of other equations can furthermore be generated. However, these equations had no exact solutions when we used Mathematica to have them solved. All the proposed solutions are not applicable to a<br />
wider combination of parameters. Even when we asked for mathematical advice (thanks to Paul Staab, Munich) we got no further. So we decided to solve graphically instead (thanks to Konrad Schieban, Zurich). <br />
In order to do so the equations need to be solved for one variabel:<br />
<br />
[[Image:freigem4.png|center|500px]]<br />
<br />
These equations can now separately be calculated by varying the variable (AB). When a value of (AB) is found that yields the same value of (CB) in both equations, both conditions are fulfilled. Graphically this would be represented by the intersection of the graphs of both equations. Basically this is what our application does. As a first result it clearly showed that the temperature specificity is not strict enough to be used as a elongation determinant, as we had originally hoped.<br />
<br />
<br />
<br />
<br />
== How does Companel work? ==<br />
<br />
When using Companel you need to "bring" your thermodynamical parameters dH° and dS° for each independent annealing reaction. Due to limited resources could no calculator for these numbers be included (which simply is a list of values for each combination of base pairs and neighboring bases). However, there are several free calculators online. More information on how to obtain dH° and dS° can be found in the application.<br />
<br />
[[Image:freigemCompanel2.png|right|500px]]<br />
<br />
Once these sequence specific information has been entered into the application, the constants K for a series of temperatures are calculated by using the Gibbs function. Subsequently the melting plots for each individual reaction are displayed and give you a first impression of the annealing behavior of your primers. <br />
<br />
[[Image:freigemCompanel1.png|right|500px]]<br />
<br />
Finally you enter concentrations, temperature range and expected product yield. The resulting concentrations of annealing product for each primer are shown graphically and in list.<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
== What is Companel good for? ==<br />
<br />
Besides the actual annealing of primers, which it has been intended for, Companel possesses an intrinsic universality when it comes to quantifying competitive processes. For instance a scientist could easily assess the binding priority of two or more (the system can of course be expanded) transcription factors or protein-protein interactions. He or she would just need to measure the two or more separate reactions, which could readily be achieved in an in vitro essay. One could then predict the interaction in vivo - at least thermodynamically. Numerous discoveries during the last years, such as the impact of the circadian clock on metabolism and drug efficacy, have shown that profound research and sometimes even successful treatment can no longer be based on the mere observation of qualitative effects alone. In the challenge to bring both biology and medicine closer to quantitative, predictable and hence more understandable science our application could play a helpful role.<br />
<br />
<br><br />
<br><br />
<html><br />
<a href="https://2012.igem.org/File:Freigem2012-CompanelDNA.zip" target="_blank"><img style="margin-left:0px; align:center;" src="https://static.igem.org/mediawiki/2012/a/a8/Freigemdownload.png" padding:0px; width="300px"; /></a></html><br />
<br><br />
''In case the file does not work properly, please send us an email to freigem2012(at)googlemail.com''<br />
<br><br />
<br><br />
[[Image:FreigembarNEWBRIGHT.jpg|left|300px]]<br />
<br><br />
<br><br />
<br></div>Fredhttp://2012.igem.org/Team:Freiburg/ModelingTeam:Freiburg/Modeling2012-09-27T02:15:42Z<p>Fred: </p>
<hr />
<div>{{Template:Team:Freiburg}}<br />
__NOTOC__<br />
= Companel|DNA ''calculating competitive reactions'' =<br />
<br />
[[Image:FreigemCompanelDNAlogo.png|right|300px]] During the course of our project we encountered a question that we had never before thought about. We were thinking about different ways to synthesize a TAL protein. One of the ideas was to take advantage of the thermodynamic behavior of different DNA strands and synthesize a TAL proteins by means of different primers that anneal at different temperatures to the template strand. We thought it to be possible to elongate a sequence by using this mechanism - simply changing the annealing temperature slightly whilst running a usual PCR. We assumed that the difference in optimal annealing temperatures of different primer sequences would favor one replication product over the others. [[Image:Freigemquote.png|left|280px]] The only thing we did not know was if this was significant enough to be used for the assembly of at least ten TAL domains. After unproductive research on this issue we decided to try modeling this scenario ourselves. <br />
<br />
<br />
The result of these efforts is CompanelDNA, an excel application that allows for predicting the equilibrium concentrations of competitive annealing. It can of course be used for every kind of chemical equilibrium where two substances compete for reacting with the same third reactant. <br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
== Theoretical background ==<br />
<br />
Although it seems to be a simple scenario, we did not find any preexisting solution to this problem - which came to us as quite a surprise. So we started by looking at the law of mass action behind the annealing reaction. Hereafter we shall use the following abbreviations and symbols:<br />
<br />
[[Image:freigem1.png|center|400px]]<br />
<br />
The laws of mass action for the two independent reactions are:<br />
<br />
[[Image:freigem2.png|center|150px]]<br />
<br />
If we want to know what is going to happen to the concentrations we originally put in our reaction/PCR tube, we can expressed the term in relation to the overall concentrations:<br />
<br />
[[Image:freigem3.png|center|300px]]<br />
<br />
Bearing in mind that the only unknown variables are (AB) and (CB) (K can be calculated, see below), one would try to solve these two equations with two variables. A number of other equations can furthermore be generated. However, these equations had no exact solutions when we used Mathematica to have them solved. All the proposed solutions are not applicable to a<br />
wider combination of parameters. Even when we asked for mathematical advice (thanks to Paul Staab, Munich) we got no further. So we decided to solve graphically instead (thanks to Konrad Schieban, Zurich). <br />
In order to do so the equations need to be solved for one variabel:<br />
<br />
[[Image:freigem4.png|center|500px]]<br />
<br />
These equations can now separately be calculated by varying the variable (AB). When a value of (AB) is found that yields the same value of (CB) in both equations, both conditions are fulfilled. Graphically this would be represented by the intersection of the graphs of both equations. Basically this is what our application does. As a first result it clearly showed that the temperature specificity is not strict enough to be used as a elongation determinant, as we had originally hoped.<br />
<br />
<br />
<br />
<br />
== How does Companel work? ==<br />
<br />
When using Companel you need to "bring" your thermodynamical parameters dH° and dS° for each independent annealing reaction. Due to limited resources could no calculator for these numbers be included (which simply is a list of values for each combination of base pairs and neighboring bases). However, there are several free calculators online. More information on how to obtain dH° and dS° can be found in the application.<br />
<br />
[[Image:freigemCompanel2.png|right|500px]]<br />
<br />
Once these sequence specific information has been entered into the application, the constants K for a series of temperatures are calculated by using the Gibbs function. Subsequently the melting plots for each individual reaction are displayed and give you a first impression of the annealing behavior of your primers. <br />
<br />
[[Image:freigemCompanel1.png|right|500px]]<br />
<br />
Finally you enter concentrations, temperature range and expected product yield. The resulting concentrations of annealing product for each primer are shown graphically and in list.<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
== What is Companel good for? ==<br />
<br />
Besides the actual annealing of primers, which it has been intended for, Companel possesses an intrinsic universality when it comes to quantifying competitive processes. For instance a scientist could easily assess the binding priority of two or more (the system can of course be expanded) transcription factors or protein-protein interactions. He or she would just need to measure the two or more separate reactions, which could readily be achieved in an in vitro essay. One could then predict the interaction in vivo - at least thermodynamically. Numerous discoveries during the last years, such as the impact of the circadian clock on metabolism and drug efficacy, have shown that profound research and sometimes even successful treatment can no longer be based on the mere observation of qualitative effects alone. In the challenge to bring both biology and medicine closer to quantitative, predictable and hence more understandable science our application could play a helpful role.<br />
<br />
<br><br />
<br><br />
<html><br />
<a href="https://2012.igem.org/File:Freigem2012-CompanelDNA.zip" target="_blank"><img style="margin-left:0px; align:center;" src="https://static.igem.org/mediawiki/2012/a/a8/Freigemdownload.png" padding:0px; width="300px"; /></a></html><br />
<br><br />
<br><br />
''In case the file does not work properly, please send us an email to freigem2012(at)googlemail.com''</div>Fredhttp://2012.igem.org/Team:Freiburg/ModelingTeam:Freiburg/Modeling2012-09-27T02:03:13Z<p>Fred: </p>
<hr />
<div>{{Template:Team:Freiburg}}<br />
__NOTOC__<br />
= Companel|DNA ''calculating competitive reactions'' =<br />
<br />
[[Image:FreigemCompanelDNAlogo.png|right|300px]] During the course of our project we encountered a question that we had never before thought about. We were thinking about different ways to synthesize a TAL protein. One of the ideas was to take advantage of the thermodynamic behavior of different DNA strands and synthesize a TAL proteins by means of different primers that anneal at different temperatures to the template strand. We thought it to be possible to elongate a sequence by using this mechanism - simply changing the annealing temperature slightly whilst running a usual PCR. We assumed that the difference in optimal annealing temperatures of different primer sequences would favor one replication product over the others. [[Image:Freigemquote.png|left|280px]] The only thing we did not know was if this was significant enough to be used for the assembly of at least ten TAL domains. After unproductive research on this issue we decided to try modeling this scenario ourselves. <br />
<br />
<br />
The result of these efforts is CompanelDNA, an excel application that allows for predicting the equilibrium concentrations of competitive annealing. It can of course be used for every kind of chemical equilibrium where two substances compete for reacting with the same third reactant. <br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
== Theoretical background ==<br />
<br />
Although it seems to be a simple scenario, we did not find any preexisting solution to this problem - which came to us as quite a surprise. So we started by looking at the law of mass action behind the annealing reaction. Hereafter we shall use the following abbreviations and symbols:<br />
<br />
[[Image:freigem1.png|center|400px]]<br />
<br />
The laws of mass action for the two independent reactions are:<br />
<br />
[[Image:freigem2.png|center|150px]]<br />
<br />
If we want to know what is going to happen to the concentrations we originally put in our reaction/PCR tube, we can expressed the term in relation to the overall concentrations:<br />
<br />
[[Image:freigem3.png|center|300px]]<br />
<br />
Bearing in mind that the only unknown variables are (AB) and (CB) (K can be calculated, see below), one would try to solve these two equations with two variables. A number of other equations can furthermore be generated. However, these equations had no exact solutions when we used Mathematica to have them solved. All the proposed solutions are not applicable to a<br />
wider combination of parameters. Even when we asked for mathematical advice (thanks to Paul Staab, Munich) we got no further. So we decided to solve graphically instead (thanks to Konrad Schieban, Zurich). <br />
In order to do so the equations need to be solved for one variabel:<br />
<br />
[[Image:freigem4.png|center|500px]]<br />
<br />
These equations can now separately be calculated by varying the variable (AB). When a value of (AB) is found that yields the same value of (CB) in both equations, both conditions are fulfilled. Graphically this would be represented by the intersection of the graphs of both equations. Basically this is what our application does. As a first result it clearly showed that the temperature specificity is not strict enough to be used as a elongation determinant, as we had originally hoped.<br />
<br />
<br />
<br />
<br />
== How does Companel work? ==<br />
<br />
When using Companel you need to "bring" your thermodynamical parameters dH° and dS° for each independent annealing reaction. Due to limited resources could no calculator for these numbers be included (which simply is a list of values for each combination of base pairs and neighboring bases). However, there are several free calculators online. More information on how to obtain dH° and dS° can be found in the application.<br />
<br />
[[Image:freigemCompanel2.png|right|500px]]<br />
<br />
Once these sequence specific information has been entered into the application, the constants K for a series of temperatures are calculated by using the Gibbs function. Subsequently the melting plots for each individual reaction are displayed and give you a first impression of the annealing behavior of your primers. <br />
<br />
[[Image:freigemCompanel1.png|right|500px]]<br />
<br />
Finally you enter concentrations, temperature range and expected product yield. The resulting concentrations of annealing product for each primer are shown graphically and in list.<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
== What is Companel good for? ==<br />
<br />
Besides the actual annealing of primers, which it has been intended for, Companel possesses an intrinsic universality when it comes to quantifying competitive processes. For instance a scientist could easily assess the binding priority of two or more (the system can of course be expanded) transcription factors or protein-protein interactions. He or she would just need to measure the two or more separate reactions, which could readily be achieved in an in vitro essay. One could then predict the interaction in vivo - at least thermodynamically. Numerous discoveries during the last years, such as the impact of the circadian clock on metabolism and drug efficacy, have shown that profound research and sometimes even successful treatment can no longer be based on the mere observation of qualitative effects alone. In the challenge to bring both biology and medicine closer to quantitative, predictable and hence more understandable science our application could play a helpful role.<br />
<br />
<br><br />
<br><br />
<html><br />
<a href="https://2012.igem.org/File:Freigem2012-CompanelDNA.zip" target="_blank"><img style="margin-left:0px; align:center;" src="https://static.igem.org/mediawiki/2012/a/a8/Freigemdownload.png" padding:0px; width="300px"; /></a><br />
<br><br />
<br></div>Fredhttp://2012.igem.org/File:Freigem2012-CompanelDNA.zipFile:Freigem2012-CompanelDNA.zip2012-09-27T02:02:50Z<p>Fred: </p>
<hr />
<div></div>Fredhttp://2012.igem.org/Team:Freiburg/ModelingTeam:Freiburg/Modeling2012-09-27T01:52:18Z<p>Fred: </p>
<hr />
<div>{{Template:Team:Freiburg}}<br />
__NOTOC__<br />
= Companel|DNA ''calculating competitive reactions'' =<br />
<br />
[[Image:FreigemCompanelDNAlogo.png|right|300px]] During the course of our project we encountered a question that we had never before thought about. We were thinking about different ways to synthesize a TAL protein. One of the ideas was to take advantage of the thermodynamic behavior of different DNA strands and synthesize a TAL proteins by means of different primers that anneal at different temperatures to the template strand. We thought it to be possible to elongate a sequence by using this mechanism - simply changing the annealing temperature slightly whilst running a usual PCR. We assumed that the difference in optimal annealing temperatures of different primer sequences would favor one replication product over the others. [[Image:Freigemquote.png|left|280px]] The only thing we did not know was if this was significant enough to be used for the assembly of at least ten TAL domains. After unproductive research on this issue we decided to try modeling this scenario ourselves. <br />
<br />
<br />
The result of these efforts is CompanelDNA, an excel application that allows for predicting the equilibrium concentrations of competitive annealing. It can of course be used for every kind of chemical equilibrium where two substances compete for reacting with the same third reactant. <br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
== Theoretical background ==<br />
<br />
Although it seems to be a simple scenario, we did not find any preexisting solution to this problem - which came to us as quite a surprise. So we started by looking at the law of mass action behind the annealing reaction. Hereafter we shall use the following abbreviations and symbols:<br />
<br />
[[Image:freigem1.png|center|400px]]<br />
<br />
The laws of mass action for the two independent reactions are:<br />
<br />
[[Image:freigem2.png|center|150px]]<br />
<br />
If we want to know what is going to happen to the concentrations we originally put in our reaction/PCR tube, we can expressed the term in relation to the overall concentrations:<br />
<br />
[[Image:freigem3.png|center|300px]]<br />
<br />
Bearing in mind that the only unknown variables are (AB) and (CB) (K can be calculated, see below), one would try to solve these two equations with two variables. A number of other equations can furthermore be generated. However, these equations had no exact solutions when we used Mathematica to have them solved. All the proposed solutions are not applicable to a<br />
wider combination of parameters. Even when we asked for mathematical advice (thanks to Paul Staab, Munich) we got no further. So we decided to solve graphically instead (thanks to Konrad Schieban, Zurich). <br />
In order to do so the equations need to be solved for one variabel:<br />
<br />
[[Image:freigem4.png|center|500px]]<br />
<br />
These equations can now separately be calculated by varying the variable (AB). When a value of (AB) is found that yields the same value of (CB) in both equations, both conditions are fulfilled. Graphically this would be represented by the intersection of the graphs of both equations. Basically this is what our application does. As a first result it clearly showed that the temperature specificity is not strict enough to be used as a elongation determinant, as we had originally hoped.<br />
<br />
<br />
<br />
<br />
== How does Companel work? ==<br />
<br />
When using Companel you need to "bring" your thermodynamical parameters dH° and dS° for each independent annealing reaction. Due to limited resources could no calculator for these numbers be included (which simply is a list of values for each combination of base pairs and neighboring bases). However, there are several free calculators online. More information on how to obtain dH° and dS° can be found in the application.<br />
<br />
[[Image:freigemCompanel2.png|right|500px]]<br />
<br />
Once these sequence specific information has been entered into the application, the constants K for a series of temperatures are calculated by using the Gibbs function. Subsequently the melting plots for each individual reaction are displayed and give you a first impression of the annealing behavior of your primers. <br />
<br />
[[Image:freigemCompanel1.png|right|500px]]<br />
<br />
Finally you enter concentrations, temperature range and expected product yield. The resulting concentrations of annealing product for each primer are shown graphically and in list.<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
== What is Companel good for? ==<br />
<br />
Besides the actual annealing of primers, which it has been intended for, Companel possesses an intrinsic universality when it comes to quantifying competitive processes. For instance a scientist could easily assess the binding priority of two or more (the system can of course be expanded) transcription factors or protein-protein interactions. He or she would just need to measure the two or more separate reactions, which could readily be achieved in an in vitro essay. One could then predict the interaction in vivo - at least thermodynamically. Numerous discoveries during the last years, such as the impact of the circadian clock on metabolism and drug efficacy, have shown that profound research and sometimes even successful treatment can no longer be based on the mere observation of qualitative effects alone. In the challenge to bring both biology and medicine closer to quantitative, predictable and hence more understandable science our application could play a helpful role.<br />
<br />
<br><br />
<br><br />
<html><br />
<a href="https://2012.igem.org/File:Freigem2012_CompanelDNA-calculating_competitive_reactions.zip" target="_blank"><img style="margin-left:0px; align:center;" src="https://static.igem.org/mediawiki/2012/a/a8/Freigemdownload.png" padding:0px; width="300px"; /></a><br />
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<br></div>Fredhttp://2012.igem.org/File:Freigemdownload.pngFile:Freigemdownload.png2012-09-27T01:48:24Z<p>Fred: </p>
<hr />
<div></div>Fredhttp://2012.igem.org/File:Freigem2012_CompanelDNA-calculating_competitive_reactions.zipFile:Freigem2012 CompanelDNA-calculating competitive reactions.zip2012-09-27T01:43:38Z<p>Fred: </p>
<hr />
<div></div>Fredhttp://2012.igem.org/Template:Team:FreiburgTemplate:Team:Freiburg2012-09-27T01:41:06Z<p>Fred: </p>
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</head></div>Fredhttp://2012.igem.org/Team:Freiburg/ModelingTeam:Freiburg/Modeling2012-09-27T01:37:43Z<p>Fred: </p>
<hr />
<div>{{Template:Team:Freiburg}}<br />
__NOTOC__<br />
= Companel|DNA ''calculating competitive reactions'' =<br />
<br />
[[Image:FreigemCompanelDNAlogo.png|right|300px]] During the course of our project we encountered a question that we had never before thought about. We were thinking about different ways to synthesize a TAL protein. One of the ideas was to take advantage of the thermodynamic behavior of different DNA strands and synthesize a TAL proteins by means of different primers that anneal at different temperatures to the template strand. We thought it to be possible to elongate a sequence by using this mechanism - simply changing the annealing temperature slightly whilst running a usual PCR. We assumed that the difference in optimal annealing temperatures of different primer sequences would favor one replication product over the others. [[Image:Freigemquote.png|left|280px]] The only thing we did not know was if this was significant enough to be used for the assembly of at least ten TAL domains. After unproductive research on this issue we decided to try modeling this scenario ourselves. <br />
<br />
<br />
The result of these efforts is CompanelDNA, an excel application that allows for predicting the equilibrium concentrations of competitive annealing. It can of course be used for every kind of chemical equilibrium where two substances compete for reacting with the same third reactant. <br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
== Theoretical background ==<br />
<br />
Although it seems to be a simple scenario, we did not find any preexisting solution to this problem - which came to us as quite a surprise. So we started by looking at the law of mass action behind the annealing reaction. Hereafter we shall use the following abbreviations and symbols:<br />
<br />
[[Image:freigem1.png|center|400px]]<br />
<br />
The laws of mass action for the two independent reactions are:<br />
<br />
[[Image:freigem2.png|center|150px]]<br />
<br />
If we want to know what is going to happen to the concentrations we originally put in our reaction/PCR tube, we can expressed the term in relation to the overall concentrations:<br />
<br />
[[Image:freigem3.png|center|300px]]<br />
<br />
Bearing in mind that the only unknown variables are (AB) and (CB) (K can be calculated, see below), one would try to solve these two equations with two variables. A number of other equations can furthermore be generated. However, these equations had no exact solutions when we used Mathematica to have them solved. All the proposed solutions are not applicable to a<br />
wider combination of parameters. Even when we asked for mathematical advice (thanks to Paul Staab, Munich) we got no further. So we decided to solve graphically instead (thanks to Konrad Schieban, Zurich). <br />
In order to do so the equations need to be solved for one variabel:<br />
<br />
[[Image:freigem4.png|center|500px]]<br />
<br />
These equations can now separately be calculated by varying the variable (AB). When a value of (AB) is found that yields the same value of (CB) in both equations, both conditions are fulfilled. Graphically this would be represented by the intersection of the graphs of both equations. Basically this is what our application does. As a first result it clearly showed that the temperature specificity is not strict enough to be used as a elongation determinant, as we had originally hoped.<br />
<br />
<br />
<br />
<br />
== How does Companel work? ==<br />
<br />
When using Companel you need to "bring" your thermodynamical parameters dH° and dS° for each independent annealing reaction. Due to limited resources could no calculator for these numbers be included (which simply is a list of values for each combination of base pairs and neighboring bases). However, there are several free calculators online. More information on how to obtain dH° and dS° can be found in the application.<br />
<br />
[[Image:freigemCompanel2.png|right|500px]]<br />
<br />
Once these sequence specific information has been entered into the application, the constants K for a series of temperatures are calculated by using the Gibbs function. Subsequently the melting plots for each individual reaction are displayed and give you a first impression of the annealing behavior of your primers. <br />
<br />
[[Image:freigemCompanel1.png|right|500px]]<br />
<br />
Finally you enter concentrations, temperature range and expected product yield. The resulting concentrations of annealing product for each primer are shown graphically and in list.<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
== What is Companel good for? ==<br />
<br />
Besides the actual annealing of primers, which it has been intended for, Companel possesses an intrinsic universality when it comes to quantifying competitive processes. For instance a scientist could easily assess the binding priority of two or more (the system can of course be expanded) transcription factors or protein-protein interactions. He or she would just need to measure the two or more separate reactions, which could readily be achieved in an in vitro essay. One could then predict the interaction in vivo - at least thermodynamically. Numerous discoveries during the last years, such as the impact of the circadian clock on metabolism and drug efficacy, have shown that profound research and sometimes even successful treatment can no longer be based on the mere observation of qualitative effects alone. In the challenge to bring both biology and medicine closer to quantitative, predictable and hence more understandable science our application could play a helpful role.<br />
<br />
<br><br />
<br><br />
<br><br />
<br></div>Fredhttp://2012.igem.org/Team:Freiburg/ModelingTeam:Freiburg/Modeling2012-09-27T01:37:05Z<p>Fred: </p>
<hr />
<div>{{Template:Team:Freiburg}}<br />
__NOTOC__<br />
= Companel|DNA ''calculating competitive reactions'' =<br />
<br />
[[Image:FreigemCompanelDNAlogo.png|right|300px]] During the course of our project we encountered a question that we had never before thought about. We were thinking about different ways to synthesize a TAL protein. One of the ideas was to take advantage of the thermodynamic behavior of different DNA strands and synthesize a TAL proteins by means of different primers that anneal at different temperatures to the template strand. We thought it to be possible to elongate a sequence by using this mechanism - simply changing the annealing temperature slightly whilst running a usual PCR. We assumed that the difference in optimal annealing temperatures of different primer sequences would favor one replication product over the others. [[Image:Freigemquote.png|left|280px]] The only thing we did not know was if this was significant enough to be used for the assembly of at least ten TAL domains. After unproductive research on this issue we decided to try modeling this scenario ourselves. <br />
<br />
<br />
The result of these efforts is CompanelDNA, an excel application that allows for predicting the equilibrium concentrations of competitive annealing. It can of course be used for every kind of chemical equilibrium where two substances compete for reacting with the same third reactant. <br />
<br />
<br />
<br />
<br />
<br />
== Theoretical background ==<br />
<br />
Although it seems to be a simple scenario, we did not find any preexisting solution to this problem - which came to us as quite a surprise. So we started by looking at the law of mass action behind the annealing reaction. Hereafter we shall use the following abbreviations and symbols:<br />
<br />
[[Image:freigem1.png|center|400px]]<br />
<br />
The laws of mass action for the two independent reactions are:<br />
<br />
[[Image:freigem2.png|center|150px]]<br />
<br />
If we want to know what is going to happen to the concentrations we originally put in our reaction/PCR tube, we can expressed the term in relation to the overall concentrations:<br />
<br />
[[Image:freigem3.png|center|300px]]<br />
<br />
Bearing in mind that the only unknown variables are (AB) and (CB) (K can be calculated, see below), one would try to solve these two equations with two variables. A number of other equations can furthermore be generated. However, these equations had no exact solutions when we used Mathematica to have them solved. All the proposed solutions are not applicable to a<br />
wider combination of parameters. Even when we asked for mathematical advice (thanks to Paul Staab, Munich) we got no further. So we decided to solve graphically instead (thanks to Konrad Schieban, Zurich). <br />
In order to do so the equations need to be solved for one variabel:<br />
<br />
[[Image:freigem4.png|center|500px]]<br />
<br />
These equations can now separately be calculated by varying the variable (AB). When a value of (AB) is found that yields the same value of (CB) in both equations, both conditions are fulfilled. Graphically this would be represented by the intersection of the graphs of both equations. Basically this is what our application does. As a first result it clearly showed that the temperature specificity is not strict enough to be used as a elongation determinant, as we had originally hoped.<br />
<br />
<br />
== How does Companel work? ==<br />
<br />
When using Companel you need to "bring" your thermodynamical parameters dH° and dS° for each independent annealing reaction. Due to limited resources could no calculator for these numbers be included (which simply is a list of values for each combination of base pairs and neighboring bases). However, there are several free calculators online. More information on how to obtain dH° and dS° can be found in the application.<br />
<br />
[[Image:freigemCompanel2.png|right|500px]]<br />
<br />
Once these sequence specific information has been entered into the application, the constants K for a series of temperatures are calculated by using the Gibbs function. Subsequently the melting plots for each individual reaction are displayed and give you a first impression of the annealing behavior of your primers. <br />
<br />
[[Image:freigemCompanel1.png|right|500px]]<br />
<br />
Finally you enter concentrations, temperature range and expected product yield. The resulting concentrations of annealing product for each primer are shown graphically and in list.<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
== What is Companel good for? ==<br />
<br />
Besides the actual annealing of primers, which it has been intended for, Companel possesses an intrinsic universality when it comes to quantifying competitive processes. For instance a scientist could easily assess the binding priority of two or more (the system can of course be expanded) transcription factors or protein-protein interactions. He or she would just need to measure the two or more separate reactions, which could readily be achieved in an in vitro essay. One could then predict the interaction in vivo - at least thermodynamically. Numerous discoveries during the last years, such as the impact of the circadian clock on metabolism and drug efficacy, have shown that profound research and sometimes even successful treatment can no longer be based on the mere observation of qualitative effects alone. In the challenge to bring both biology and medicine closer to quantitative, predictable and hence more understandable science our application could play a helpful role.<br />
<br />
<br><br />
<br><br />
<br><br />
<br></div>Fredhttp://2012.igem.org/Team:Freiburg/ModelingTeam:Freiburg/Modeling2012-09-27T01:32:22Z<p>Fred: </p>
<hr />
<div>{{Template:Team:Freiburg}}<br />
__NOTOC__<br />
= Companel|DNA ''calculating competitive reactions'' =<br />
<br />
[[Image:FreigemCompanelDNAlogo.png|right|300px]] During the course of our project we encountered a question that we had never before thought about. We were thinking about different ways to synthesize a TAL protein. One of the ideas was to take advantage of the thermodynamic behavior of different DNA strands and synthesize a TAL proteins by means of different primers that anneal at different temperatures to the template strand. We thought it to be possible to elongate a sequence by using this mechanism - simply changing the annealing temperature slightly whilst running a usual PCR. We assumed that the difference in optimal annealing temperatures of different primer sequences would favor one replication product over the others. [[Image:Freigemquote.png|left|280px]] The only thing we did not know was if this was significant enough to be used for the assembly of at least ten TAL domains. After unproductive research on this issue we decided to try modeling this scenario ourselves. <br />
<br />
<br />
The result of these efforts is CompanelDNA, an excel application that allows for predicting the equilibrium concentrations of competitive annealing. It can of course be used for every kind of chemical equilibrium where two substances compete for reacting with the same third reactant. <br />
<br />
<br />
<br />
<br />
<br />
== Theoretical background ==<br />
<br />
Although it seems to be a simple scenario, we did not find any preexisting solution to this problem - which came to us as quite a surprise. So we started by looking at the law of mass action behind the annealing reaction. Hereafter we shall use the following abbreviations and symbols:<br />
<br />
[[Image:freigem1.png|center|400px]]<br />
<br />
The laws of mass action for the two independent reactions are:<br />
<br />
[[Image:freigem2.png|center|150px]]<br />
<br />
If we want to know what is going to happen to the concentrations we originally put in our reaction/PCR tube, we can expressed the term in relation to the overall concentrations:<br />
<br />
[[Image:freigem3.png|center|300px]]<br />
<br />
Bearing in mind that the only unknown variables are (AB) and (CB) (K can be calculated, see below), one would try to solve these two equations with two variables. A number of other equations can furthermore be generated. However, these equations had no exact solutions when we used Mathematica to have them solved. All the proposed solutions are not applicable to a<br />
wider combination of parameters. Even when we asked for mathematical advice (thanks to Paul Staab, Munich) we got no further. So we decided to solve graphically instead (thanks to Konrad Schieban, Zurich). <br />
In order to do so the equations need to be solved for one variabel:<br />
<br />
[[Image:freigem4.png|center|500px]]<br />
<br />
These equations can now separately be calculated by varying the variable (AB). When a value of (AB) is found that yields the same value of (CB) in both equations, both conditions are fulfilled. Graphically this would be represented by the intersection of the graphs of both equations. Basically this is what our application does. As a first result it clearly showed that the temperature specificity is not strict enough to be used as a elongation determinant, as we had originally hoped.<br />
<br />
<br />
== How does Companel work? ==<br />
<br />
When using Companel you need to "bring" your thermodynamical parameters dH° and dS° for each independent annealing reaction. Due to limited resources could no calculator for these numbers be included (which simply is a list of values for each combination of base pairs and neighboring bases). However, there are several free calculators online. More information on how to obtain dH° and dS° can be found in the application.<br />
<br />
[[Image:freigemCompanel2.png|right|500px]]<br />
<br />
Once these sequence specific information has been entered into the application, the constants K for a series of temperatures are calculated by using the Gibbs function. Subsequently the melting plots for each individual reaction are displayed and give you a first impression of the annealing behavior of your primers. <br />
<br />
[[Image:freigemCompanel1.png|right|500px]]<br />
<br />
Finally you enter concentrations, temperature range and expected product yield. The resulting concentrations of annealing product for each primer are shown graphically and in list.<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
== What is Companel good for? ==<br />
<br />
Besides the actual annealing of primers, which it has been intended for, Companel possesses an intrinsic universality when it comes to quantifying competitive processes. For instance a scientist could easily assess the binding priority of two or more (the system can of course be expanded) transcription factors or protein-protein interactions. He or she would just need to measure the two or more separate reactions, which could readily be achieved in an in vitro essay. One could then predict the interaction in vivo - at least thermodynamically. Numerous discoveries during the last years, such as the impact of the circadian clock on metabolism and drug efficacy, have shown that profound research and sometimes even successful treatment can no longer be based on the mere observation of qualitative effects alone. In the challenge to bring both biology and medicine closer to quantitative, predictable and hence more understandable science our application could play a helpful role.</div>Fredhttp://2012.igem.org/File:Freigemquote.pngFile:Freigemquote.png2012-09-27T01:26:47Z<p>Fred: </p>
<hr />
<div></div>Fredhttp://2012.igem.org/Team:Freiburg/ModelingTeam:Freiburg/Modeling2012-09-27T01:20:05Z<p>Fred: </p>
<hr />
<div>{{Template:Team:Freiburg}}<br />
__NOTOC__<br />
= Companel|DNA ''calculating competitive reactions'' =<br />
<br />
[[Image:FreigemCompanelDNAlogo.png|right|300px]] During the course of our project we encountered a question that we had never before thought about. We were thinking about different ways to synthesize a TAL protein. One of the ideas was to take advantage of the thermodynamic behavior of different DNA strands and synthesize a TAL proteins by means of different primers that anneal at different temperatures to the template strand. We thought it to be possible to elongate a sequence by using this mechanism - simply changing the annealing temperature slightly whilst running a usual PCR. We assumed that the difference in optimal annealing temperatures of different primer sequences would favor one replication product over the others. The only thing we did not know was if this was significant enough to be used for the assembly of at least ten TAL domains. After unproductive research on this issue we decided to try modeling this scenario ourselves. The result of these efforts is CompanelDNA, an excel application that allows for predicting the equilibrium concentrations of competitive annealing. It can of course be used for every kind of chemical equilibrium where two substances compete for reacting with the same third reactant.<br />
<br />
<br />
<br />
== Theoretical background ==<br />
<br />
Although it seems to be a simple scenario, we did not find any preexisting solution to this problem - which came to us as quite a surprise. So we started by looking at the law of mass action behind the annealing reaction. Hereafter we shall use the following abbreviations and symbols:<br />
<br />
[[Image:freigem1.png|center|400px]]<br />
<br />
The laws of mass action for the two independent reactions are:<br />
<br />
[[Image:freigem2.png|center|150px]]<br />
<br />
If we want to know what is going to happen to the concentrations we originally put in our reaction/PCR tube, we can expressed the term in relation to the overall concentrations:<br />
<br />
[[Image:freigem3.png|center|300px]]<br />
<br />
Bearing in mind that the only unknown variables are (AB) and (CB) (K can be calculated, see below), one would try to solve these two equations with two variables. A number of other equations can furthermore be generated. However, these equations had no exact solutions when we used Mathematica to have them solved. All the proposed solutions are not applicable to a<br />
wider combination of parameters. Even when we asked for mathematical advice (thanks to Paul Staab, Munich) we got no further. So we decided to solve graphically instead (thanks to Konrad Schieban, Zurich). <br />
In order to do so the equations need to be solved for one variabel:<br />
<br />
[[Image:freigem4.png|center|500px]]<br />
<br />
These equations can now separately be calculated by varying the variable (AB). When a value of (AB) is found that yields the same value of (CB) in both equations, both conditions are fulfilled. Graphically this would be represented by the intersection of the graphs of both equations. Basically this is what our application does. As a first result it clearly showed that the temperature specificity is not strict enough to be used as a elongation determinant, as we had originally hoped.<br />
<br />
<br />
== How does Companel work? ==<br />
<br />
When using Companel you need to "bring" your thermodynamical parameters dH° and dS° for each independent annealing reaction. Due to limited resources could no calculator for these numbers be included (which simply is a list of values for each combination of base pairs and neighboring bases). However, there are several free calculators online. More information on how to obtain dH° and dS° can be found in the application.<br />
<br />
[[Image:freigemCompanel2.png|right|500px]]<br />
<br />
Once these sequence specific information has been entered into the application, the constants K for a series of temperatures are calculated by using the Gibbs function. Subsequently the melting plots for each individual reaction are displayed and give you a first impression of the annealing behavior of your primers. <br />
<br />
[[Image:freigemCompanel1.png|right|500px]]<br />
<br />
Finally you enter concentrations, temperature range and expected product yield. The resulting concentrations of annealing product for each primer are shown graphically and in list.<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
== What is Companel good for? ==<br />
<br />
Besides the actual annealing of primers, which it has been intended for, Companel possesses an intrinsic universality when it comes to quantifying competitive processes. For instance a scientist could easily assess the binding priority of two or more (the system can of course be expanded) transcription factors or protein-protein interactions. He or she would just need to measure the two or more separate reactions, which could readily be achieved in an in vitro essay. One could then predict the interaction in vivo - at least thermodynamically. Numerous discoveries during the last years, such as the impact of the circadian clock on metabolism and drug efficacy, have shown that profound research and sometimes even successful treatment can no longer be based on the mere observation of qualitative effects alone. In the challenge to bring both biology and medicine closer to quantitative, predictable and hence more understandable science our application could play a helpful role.</div>Fredhttp://2012.igem.org/File:FreigemCompanelDNAlogo.pngFile:FreigemCompanelDNAlogo.png2012-09-27T00:44:43Z<p>Fred: </p>
<hr />
<div></div>Fredhttp://2012.igem.org/Team:Freiburg/ModelingTeam:Freiburg/Modeling2012-09-27T00:38:05Z<p>Fred: </p>
<hr />
<div>{{Template:Team:Freiburg}}<br />
__NOTOC__<br />
= Companel|DNA ''calculating competitive reactions'' =<br />
<br />
During the course of our project we encountered a question that we had never before thought about. We were thinking about different ways to synthesize a TAL protein. One of the ideas was to take advantage of the thermodynamic behavior of different DNA strands and synthesize a TAL proteins by means of different primers that anneal at different temperatures to the template strand. We thought it to be possible to elongate a sequence by using this mechanism - simply changing the annealing temperature slightly whilst running a usual PCR. We assumed that the difference in optimal annealing temperatures of different primer sequences would favor one replication product over the others. The only thing we did not know was if this was significant enough to be used for the assembly of at least ten TAL domains. After unproductive research on this issue we decided to try modeling this scenario ourselves. The result of these efforts is CompanelDNA, an excel application that allows for predicting the equilibrium concentrations of competitive annealing. It can of course be used for every kind of chemical equilibrium where two substances compete for reacting with the same third reactant.<br />
<br />
<br />
<br />
== Theoretical background ==<br />
<br />
Although it seems to be a simple scenario, we did not find any preexisting solution to this problem - which came to us as quite a surprise. So we started by looking at the law of mass action behind the annealing reaction. Hereafter we shall use the following abbreviations and symbols:<br />
<br />
[[Image:freigem1.png|center|400px]]<br />
<br />
The laws of mass action for the two independent reactions are:<br />
<br />
[[Image:freigem2.png|center|150px]]<br />
<br />
If we want to know what is going to happen to the concentrations we originally put in our reaction/PCR tube, we can expressed the term in relation to the overall concentrations:<br />
<br />
[[Image:freigem3.png|center|300px]]<br />
<br />
Bearing in mind that the only unknown variables are (AB) and (CB) (K can be calculated, see below), one would try to solve these two equations with two variables. A number of other equations can furthermore be generated. However, these equations had no exact solutions when we used Mathematica to have them solved. All the proposed solutions are not applicable to a<br />
wider combination of parameters. Even when we asked for mathematical advice (thanks to Paul Staab, Munich) we got no further. So we decided to solve graphically instead (thanks to Konrad Schieban, Zurich). <br />
In order to do so the equations need to be solved for one variabel:<br />
<br />
[[Image:freigem4.png|center|500px]]<br />
<br />
These equations can now separately be calculated by varying the variable (AB). When a value of (AB) is found that yields the same value of (CB) in both equations, both conditions are fulfilled. Graphically this would be represented by the intersection of the graphs of both equations. Basically this is what our application does.<br />
<br />
<br />
== How does Companel work? ==<br />
<br />
When using Companel you need to "bring" your thermodynamical parameters dH° and dS° for each independent annealing reaction. Due to limited resources could no calculator for these numbers be included (which simply is a list of values for each combination of base pairs and neighboring bases). However, there are several free calculators online. More information on how to obtain dH° and dS° can be found in the application.<br />
Once these sequence specific information has been entered into the application, the constants K for a series of temperatures are calculated by using the Gibbs function. Subsequently the melting plots for each individual reaction are displayed and give you a first impression of the annealing behavior of your primers. <br />
<br />
[[Image:freigemCompanel2.png|right|500px]]<br />
<br />
Finally you enter concentrations, temperature range and expected product yield. The resulting concentrations of annealing product for each primer are shown graphically and in list.<br />
<br />
[[Image:freigemCompanel1.png|right|500px]]</div>Fredhttp://2012.igem.org/Team:Freiburg/ModelingTeam:Freiburg/Modeling2012-09-27T00:37:28Z<p>Fred: </p>
<hr />
<div>{{Template:Team:Freiburg}}<br />
__NOTOC__<br />
= Companel|DNA ''calculating competitive reactions'' =<br />
<br />
During the course of our project we encountered a question that we had never before thought about. We were thinking about different ways to synthesize a TAL protein. One of the ideas was to take advantage of the thermodynamic behavior of different DNA strands and synthesize a TAL proteins by means of different primers that anneal at different temperatures to the template strand. We thought it to be possible to elongate a sequence by using this mechanism - simply changing the annealing temperature slightly whilst running a usual PCR. We assumed that the difference in optimal annealing temperatures of different primer sequences would favor one replication product over the others. The only thing we did not know was if this was significant enough to be used for the assembly of at least ten TAL domains. After unproductive research on this issue we decided to try modeling this scenario ourselves. The result of these efforts is CompanelDNA, an excel application that allows for predicting the equilibrium concentrations of competitive annealing. It can of course be used for every kind of chemical equilibrium where two substances compete for reacting with the same third reactant.<br />
<br />
<br />
<br />
== Theoretical background ==<br />
<br />
Although it seems to be a simple scenario, we did not find any preexisting solution to this problem - which came to us as quite a surprise. So we started by looking at the law of mass action behind the annealing reaction. Hereafter we shall use the following abbreviations and symbols:<br />
<br />
[[Image:freigem1.png|center|400px]]<br />
<br />
The laws of mass action for the two independent reactions are:<br />
<br />
[[Image:freigem2.png|center|150px]]<br />
<br />
If we want to know what is going to happen to the concentrations we originally put in our reaction/PCR tube, we can expressed the term in relation to the overall concentrations:<br />
<br />
[[Image:freigem3.png|center|300px]]<br />
<br />
Bearing in mind that the only unknown variables are (AB) and (CB) (K can be calculated, see below), one would try to solve these two equations with two variables. A number of other equations can furthermore be generated. However, these equations had no exact solutions when we used Mathematica to have them solved. All the proposed solutions are not applicable to a<br />
wider combination of parameters. Even when we asked for mathematical advice (thanks to Paul Staab, Munich) we got no further. So we decided to solve graphically instead (thanks to Konrad Schieban, Zurich). <br />
In order to do so the equations need to be solved for one variabel:<br />
<br />
[[Image:freigem4.png|center|500px]]<br />
<br />
These equations can now separately be calculated by varying the variable (AB). When a value of (AB) is found that yields the same value of (CB) in both equations, both conditions are fulfilled. Graphically this would be represented by the intersection of the graphs of both equations. Basically this is what our application does.<br />
<br />
<br />
== How does Companel work? ==<br />
<br />
When using Companel you need to "bring" your thermodynamical parameters dH° and dS° for each independent annealing reaction. Due to limited resources could no calculator for these numbers be included (which simply is a list of values for each combination of base pairs and neighboring bases). However, there are several free calculators online. More information on how to obtain dH° and dS° can be found in the application.<br />
Once these sequence specific information has been entered into the application, the constants K for a series of temperatures are calculated by using the Gibbs function. Subsequently the melting plots for each individual reaction are displayed and give you a first impression of the annealing behavior of your primers. <br />
<br />
[[Image:freigemCompanel2.png|center|500px]]<br />
<br />
Finally you enter concentrations, temperature range and expected product yield. The resulting concentrations of annealing product for each primer are shown graphically and in list.<br />
<br />
[[Image:freigemCompanel1.png|center|500px]]</div>Fredhttp://2012.igem.org/File:FreigemCompanel2.pngFile:FreigemCompanel2.png2012-09-27T00:31:22Z<p>Fred: </p>
<hr />
<div></div>Fredhttp://2012.igem.org/File:FreigemCompanel1.pngFile:FreigemCompanel1.png2012-09-27T00:27:23Z<p>Fred: </p>
<hr />
<div></div>Fredhttp://2012.igem.org/Team:Freiburg/ModelingTeam:Freiburg/Modeling2012-09-26T23:55:47Z<p>Fred: </p>
<hr />
<div>{{Template:Team:Freiburg}}<br />
__NOTOC__<br />
= Companel|DNA ''calculating competitive reactions'' =<br />
<br />
During the course of our project we encountered a question that we had never before thought about. We were thinking about different ways to synthesize a TAL protein. One of the ideas was to take advantage of the thermodynamic behavior of different DNA strands and synthesize a TAL proteins by means of different primers that anneal at different temperatures to the template strand. We thought it to be possible to elongate a sequence by using this mechanism - simply changing the annealing temperature slightly whilst running a usual PCR. We assumed that the difference in optimal annealing temperatures of different primer sequences would favor one replication product over the others. The only thing we did not know was if this was significant enough to be used for the assembly of at least ten TAL domains. After unproductive research on this issue we decided to try modeling this scenario ourselves. The result of these efforts is CompanelDNA, an excel application that allows for predicting the equilibrium concentrations of competitive annealing. It can of course be used for every kind of chemical equilibrium where two substances compete for reacting with the same third reactant.<br />
<br />
<br />
<br />
== Theoretical background ==<br />
<br />
Although it seems to be a simple scenario, we did not find any preexisting solution to this problem - which came to us as quite a surprise. So we started by looking at the law of mass action behind the annealing reaction. Hereafter we shall use the following abbreviations and symbols:<br />
<br />
[[Image:freigem1.png|center|400px]]<br />
<br />
The laws of mass action for the two independent reactions are:<br />
<br />
[[Image:freigem2.png|center|200px]]<br />
<br />
If we want to know what is going to happen to the concentrations we originally put in our reaction/PCR tube, we can expressed the term in relation to the overall concentrations:<br />
<br />
[[Image:freigem3.png|center|300px]]<br />
<br />
Bearing in mind that the only unknown variables are (AB) and (CB) (K can be calculated, see below), one would try to solve these two equations with two variables. A number of other equations can furthermore be generated. However, these equations had no exact solutions when we used Mathematica to have them solved. All the proposed solutions are not applicable to a<br />
wider combination of parameters. Even when we asked for mathematical advice (thanks to Paul Staab, Munich) we got no further. So we decided to solve graphically instead (thanks to Konrad Schieban, Zurich). <br />
In order to do so the equations need to be solved for one variabel:<br />
<br />
[[Image:freigem4.png|center|500px]]<br />
<br />
These equations can now separately be calculated by varying the variable (AB). When a value of (AB) is found that yields the same value of (CB) in both equations, both conditions are fulfilled. Graphically this would be represented by the intersection of the graphs of both equations. Basically this is what our application does.</div>Fredhttp://2012.igem.org/File:Freigem1.pngFile:Freigem1.png2012-09-26T23:29:51Z<p>Fred: </p>
<hr />
<div></div>Fred