Team:Heidelberg

From 2009.igem.org

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<div id="orangeBox"><h3>Design your own promoter</h3>
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<p>Here we present a new approach to synthesize synthetic promoters using a database that predicts the position of conserved promoter binding sequences. We coded an easy to use interface that is available for public use. </p>
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<a href="http://igem.bioquant.uni-heidelberg.de/embperl/GUI04/index.epl">HEARTBEAT: Start Design</a>
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=='''iGEM Heidelberg Mission 2009: Spybricks'''==
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Establishing new standards for iGEM, the Heidelberg 2009 team will be concerned with developing ways for measuring promoters in mammalian cells, a default chassis and a first evaluation of the recently postulated BioBrick beta proposal 2 (Tom Knight).
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<div id="greenBox"><h3>Mammalian biobricks</h3>
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Considering the importance of controlling gene expression, our team's work will focus on natural and synthetic mammalian promoters. Our vision is to provide the synthetic biology community with a methodical library of such promoters (with different output strength and sensitivity to different regulatory proteins) and a model which can provide guidance for the development of further synthetic promoters. Our efforts will therefore, from the very beginning, equally entail bioinformatics and wet lab work.
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<p>Mammalian synthetic biology has huge potential, but it is in need of new standards and of systematic construction of comprehensive part libraries. Learn more about our new mission on the project page. </p>
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<a href="https://2009.igem.org/Team:Heidelberg/Project">Go To Project Page</a>
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<div id="blueBox"><h3>Mission accomplished</h3>
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<p>We developed two novel, <i>in silico</i> guided methods for the rational construction of synthetic promoters and experimentally validated the predicted results. View our graphical abstract and get an overview of the achievements of our team.</p>
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<a href="https://static.igem.org/mediawiki/2009/a/a6/HD_GraphicalAbstract_high.jpg">Download Graphical Abstract</a>
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[[Image:HD09_IGEM_Team.png|center|150 px|border|Team]]
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'''Team''' <br>
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Thirteen students and eleven advisors are working on this four month project. We split up into several subgroups whos focus and results you can follow on the Notebook and Results page. If you want to know more about the subgroups and the people involved, meet us on our Team page and let's get to know each other better at the Jamboree in Boston.
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[https://2009.igem.org/Team:Heidelberg/Team Please read more]
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[[Image:HD09_iGEM_Project.png|center|150 px|border|Project]]
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'''Project'''<br>
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Mammalian synthetic biology has huge potential, but it is in need of new standards and of systematic construction of comprehensive part libraries. Promoters are the fundamental elements of every synthetic biological system. We have developed and successfully applied two novel, in silico guided methods for the rational construction of synthetic promoters which respond only to predefined transcription factors.                           
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[https://2009.igem.org/Team:Heidelberg/Project Please read more]
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<div id="mission_box">
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<h2> iGEM Team Heidelberg 2009: First Runner-Up, Winner of the PoPS Prize, Finalist, Best Wiki, Best New Standard </h2>
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[[Image:HD09_iGEM_Modeling.png|center|150 px|border|Modeling]]
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<h3> Mission: Spybricks </h3>
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'''The Heartbeat Database''' <br>
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<p> The Heidelberg 2009 team attempts to take Synthetic Biology a step further by introducing novel concepts for the work with mammalian cells, defining Synthetic Mammalian Biology (SMB). We are the first-ever team at iGEM trying to systematically develop a BioBrick library for use in mammalian cells. Being the first team of Heidelberg's "SMB initiative", we emphasize the central position of gene regulation. Our team's work therefore focused on synthetic mammalian promoters. We provide the foundations of a methodical library of such promoters, together with novel standards for their characterization.  We have developed an avant-garde method for the synthesis of mammalian promoters, and a bioinformatical model predicting such promoters which we test in vivo. <a href="https://2009.igem.org/Team:Heidelberg/Project">Go to Project Abstract</a></p></div>
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As one of the most important approaches to synthezise synthetic promotors we developed a database that predicts the position of conserved promotor binding sequences. We identified conserved sequences ourselves, analyzed the data and coded an easy to use interface that ise available for public use.  
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[https://2009.igem.org/Team:Heidelberg/Modeling Please read more]
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[[Image:HD_Notebook_klein3.png|center|150px|Notebook]]
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'''Notebook''' <br>
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What's about documenation? You will find the entire progress of the project and all the important steps on our Notebook page. The Notebook is divided into the individual subgroups.
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[https://2009.igem.org/Team:Heidelberg/Notebook/Overview Please read more]
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'''Results'''<br>
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Mission Status: accomlished. We generated and characterized sets of constitutive and inducible promotors of different strength using our heartbeat-database prediction software and a new method developed in our lab. We combined a subset of these promotors with our targeted fluorescent protein tag and could thus show... Furthermore we characterized the eukaryotic standart
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[https://2009.igem.org/Team:Heidelberg/Results Please read more]
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<div id="team_box"><center><a href="https://2009.igem.org/Team:Heidelberg/Team"><img src="https://static.igem.org/mediawiki/2009/0/06/HD09_Team_180px.png" alt=""/></a></center>
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<h3>Team</h3>  
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'''Parts'''<br>
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<p>Thirteen students and nine advisors are working on this four month project. We split up into several subgroups whose focus and results you can follow on the Notebook and Project pages. If you want to know more about the subgroups and the people involved, meet us on our <a href="https://2009.igem.org/Team:Heidelberg/Team">Team page </a> and let's get to know each other better at the Jamboree in Boston. </p></div>
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Our team submits a library of well characterized and standardized promotors and sensors for eukaryotic cells. We will also contribute the first eucaryotic standart chassis for iGEM featuring standardized genome integration sites.
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[https://2009.igem.org/Team:Heidelberg/Parts Please read more]
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<div id="heartbeat_box"> <center><a href="https://2009.igem.org/Team:Heidelberg/HEARTBEAT"><img src="https://static.igem.org/mediawiki/2009/3/37/Heartbeat_small.gif" alt=""/></a></center>
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<h3>HEARTBEAT </h3>
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'''Gallery'''<br>
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<p> Our team worked on a computational approach for the rational <a href="https://2009.igem.org/Team:Heidelberg/HEARTBEAT">design of promoter libraries</a>. Similar to existing methods which predict spatial preferences of transcription factor binding sites (TFBS) by detecting statistically overrepresented motives we used Promotersweep to analyze and process the information of over 4000 human promoter sequences.</p></div>
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Spy on our cells or join the Heidelberg Team in the lab with our gallery tour.
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[https://2009.igem.org/Team:Heidelberg/Gallery Please read more]
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'''Sponsors'''
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This year we have a lot of distinguished sponsors, which support us and this project.
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[https://2009.igem.org/Team:Heidelberg/Sponsors Please read more]
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'''Misc'''<br>
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Valencia Gold Medal...
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[ Please read more]
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<div id="notebook_box"> <center><a href="https://2009.igem.org/Team:Heidelberg/Eukaryopedia"><img src="https://static.igem.org/mediawiki/2009/d/dc/Brockhauscells.jpg" alt=""/></a></center>
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<h3>Eukaryopedia</h3>
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<p>You are working in bacteria and never heard of U2-OS, SREBP or CYP1A1? Don't worry! Browse our <a href="https://2009.igem.org/Team:Heidelberg/Eukaryopedia">Eukaryopedia</a> and enter the world of mammalian BioBricks.</p> </div>
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==Our Team==
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[[Image:Team_verySmall.jpg]]
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<div id="parts_box"> <center><a href="https://2009.igem.org/Team:Heidelberg/Parts"><img src="https://static.igem.org/mediawiki/2009/c/c0/Parts_HD.jpg" alt=""/></a></center>
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<h3>Parts </h3>
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<p>Our team <a href="https://2009.igem.org/Team:Heidelberg/Parts">submits a library </a> of thoroughly characterized and standardized parts. Therefore contributing towards the establishment of a new standard for eukaryotic cells in the iGEM context.</p> </div>
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This year 13 students are part of the [https://2009.igem.org/Team:Heidelberg/Team Heidelberg iGEM Team].
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<div id="gallery_box"><center><a href="https://2009.igem.org/Team:Heidelberg/Gallery"><img src="https://static.igem.org/mediawiki/2009/d/d9/Leopardeye.png" alt=""/></a></center>
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<h3>Gallery </h3>
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<p>Spy on our cells or join the Heidelberg Team in the lab with our <a href="https://2009.igem.org/Team:Heidelberg/Gallery">gallery tour</a>.</p></div>
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<p>
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<div id="sponsors_box"> <center><a href="https://2009.igem.org/Team:Heidelberg/Sponsors"><img src="https://static.igem.org/mediawiki/2009/9/91/Handschlag.png" alt=""/></a></center>
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</p>
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<h3>Sponsors</h3>
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<p>We thank our great sponsors, who supported us financially and made this project a success. <a href="https://2009.igem.org/Team:Heidelberg/Sponsors">Go here </a> to find out more about them.</p> </div>  
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<embed src="http://www.oneplusyou.com/bb/files/countdown/countdown.swf?co=8fc332&bgcolor=FFFFFF&date_month=10&date_day=30&date_year=0&un=IGEM JAMBOREE 2009&size=normal&mo=10&da=31&yr=2009" type="application/x-shockwave-flash" pluginspage="http://www.macromedia.com/go/getflashplayer" width="240" height="80" wmode="transparent"></embed>
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==News==
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''28 Aug. 2009,''    '''Generous Donation by Klaus Tschira Foundation'''
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<div id="news">
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[[image:HD09_kts-logo.jpg|center|100px|http://www.klaus-tschira-stiftung.de/english/index.html]]
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<h3>The Team</h3>
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<br>
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<center><img src="https://static.igem.org/mediawiki/2009/8/89/Team_verySmall.jpg" alt=""/></center>
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<p>This year 13 students started the Heidelberg iGEM team.</p>
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<center><embed src="http://www.oneplusyou.com/bb/files/countdown/countdown.swf?co=8fc332&bgcolor=FFFFFF&date_month=11&date_day=09&date_year=0&un=IGEM JAMBOREE 2009&size=normal&mo=10&da=31&yr=2009" type="application/x-shockwave-flash" pluginspage="http://www.macromedia.com/go/getflashplayer" width="240" height="80" wmode="transparent"></embed></center>
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<h3> Heidelberg Jamboree Blog</h3>
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<p>
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We will report all important news during the jamboree right away from Cambridge <a href="http://www.bioquant.uni-heidelberg.de/igem/jamboree-blog"> here</a>.</p>
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The Klaus Tschira Foundation GmbH is a non-profit organization and supports research in informatics, the natural sciences, and mathematics; at the same time it promotes a public understanding in these sciences. With this combination the Klaus Tschira foundation is our ideal partner in this competition.  
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<h3> The iGEM idea </h3>
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<br>
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<p>iGEM (international genetically engineered machines competition) is an international competition in synthetic biology, hosted by the MIT in Boston. The aim of this competition is to answer a basic question that Randy Rettberg, the director of iGEM, once described as follows: "Can simple biological systems be built from standard, interchangeable parts and operated in living cells? Or is biology just too complicated to be engineered in this way?"
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<br>
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The iGEM-approach to answer that question is to actually try to engineer biological systems with a proper function. To this end, more than 100 interdisciplinary student teams from all over the world, mainly consisting of undergraduate students in biology, biochemistry, engineering, informatics and mathematics, carry out different projects during the Summer. These projects reach from medical applications, i.e. genetically modified bacteria used in cancer-treatment to environmental and manufacturing projects, i.e. the construction of a watch-like counter consisting of living cells. In contrast to classical genetic engineering where only one gene is transferred from organism A to organism B, synthetic biology goes forward into the construction of whole new systems with a completely new function. Therefore, all iGEM-Teams get access to a gene- Database called registry, where hundreds of different genetic parts with characterized functions are available in a “plug-and-play” –like format. These parts can be simply stuck together to build functional systems.
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The rising number of iGEM-Teams over the last years as well as the upcoming public interest in iGEM, the iGEM-Teams’ projects and synthetic biology in general shows, that synthetic biology will for sure have a great impact in many different fields of both scientific research and every-day life.</p>
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''25 Aug. 2009,'' '''LANGE + PFLANZ becomes Gold Sponsor'''
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<p>The contents and design of this wiki are published under the <a href="http://commons.wikimedia.org/wiki/Commons:GNU_Free_Documentation_License">GNU Free Documentation License</a> You are granted the right to copy and modify our work, but you must publish your work under the same type of license while recognizing us the authors.</p>
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[[image:HD09_Lange_pflanz.gif|center|120px|http://www.lpsp.de/werbeagentur]]
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<br>  
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LANGE + PFLANZ Werbeagentur GmbH (www.lpsp.de) have just declared the sponsorship of our team by designing a team logo, a team shirt, a website, and power-point slides for the Championship Jamboree at MIT. This positions the company - an established marketing and design company which successfully designed the corporate identiy for our Bioquant Institute - right into the sponsorship Gold category. You will find soon the first results on this page!
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''Sep 2009,''  '''iGEM Team Heidelberg wins Gold Medal'''
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[[image:HD09_ValenciaGoldMetal.jpg|center|100px|https://2009.igem.org/Team:Valencia/Human]]
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<br>
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The iGEM Team Heidelberg won the Collaboration Gold Medal in the Survey
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on Synthetic Biology and by this successfully helped iGEM [https://2009.igem.org/Team:Valencia Team Valencia]
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by their work on Human Practice!
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[[http://igem.bioquant.uni-heidelberg.de/mediawiki/index.php/News See more]]
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Latest revision as of 10:13, 25 October 2010

Design your own promoter

Here we present a new approach to synthesize synthetic promoters using a database that predicts the position of conserved promoter binding sequences. We coded an easy to use interface that is available for public use.

HEARTBEAT: Start Design

Mammalian biobricks

Mammalian synthetic biology has huge potential, but it is in need of new standards and of systematic construction of comprehensive part libraries. Learn more about our new mission on the project page.

Go To Project Page

Mission accomplished

We developed two novel, in silico guided methods for the rational construction of synthetic promoters and experimentally validated the predicted results. View our graphical abstract and get an overview of the achievements of our team.

Download Graphical Abstract

iGEM Team Heidelberg 2009: First Runner-Up, Winner of the PoPS Prize, Finalist, Best Wiki, Best New Standard

Mission: Spybricks

The Heidelberg 2009 team attempts to take Synthetic Biology a step further by introducing novel concepts for the work with mammalian cells, defining Synthetic Mammalian Biology (SMB). We are the first-ever team at iGEM trying to systematically develop a BioBrick library for use in mammalian cells. Being the first team of Heidelberg's "SMB initiative", we emphasize the central position of gene regulation. Our team's work therefore focused on synthetic mammalian promoters. We provide the foundations of a methodical library of such promoters, together with novel standards for their characterization. We have developed an avant-garde method for the synthesis of mammalian promoters, and a bioinformatical model predicting such promoters which we test in vivo. Go to Project Abstract

Team

Thirteen students and nine advisors are working on this four month project. We split up into several subgroups whose focus and results you can follow on the Notebook and Project pages. If you want to know more about the subgroups and the people involved, meet us on our Team page and let's get to know each other better at the Jamboree in Boston.

HEARTBEAT

Our team worked on a computational approach for the rational design of promoter libraries. Similar to existing methods which predict spatial preferences of transcription factor binding sites (TFBS) by detecting statistically overrepresented motives we used Promotersweep to analyze and process the information of over 4000 human promoter sequences.

Eukaryopedia

You are working in bacteria and never heard of U2-OS, SREBP or CYP1A1? Don't worry! Browse our Eukaryopedia and enter the world of mammalian BioBricks.

Parts

Our team submits a library of thoroughly characterized and standardized parts. Therefore contributing towards the establishment of a new standard for eukaryotic cells in the iGEM context.

Sponsors

We thank our great sponsors, who supported us financially and made this project a success. Go here to find out more about them.

The Team

This year 13 students started the Heidelberg iGEM team.

Heidelberg Jamboree Blog

We will report all important news during the jamboree right away from Cambridge here.

The iGEM idea

iGEM (international genetically engineered machines competition) is an international competition in synthetic biology, hosted by the MIT in Boston. The aim of this competition is to answer a basic question that Randy Rettberg, the director of iGEM, once described as follows: "Can simple biological systems be built from standard, interchangeable parts and operated in living cells? Or is biology just too complicated to be engineered in this way?" The iGEM-approach to answer that question is to actually try to engineer biological systems with a proper function. To this end, more than 100 interdisciplinary student teams from all over the world, mainly consisting of undergraduate students in biology, biochemistry, engineering, informatics and mathematics, carry out different projects during the Summer. These projects reach from medical applications, i.e. genetically modified bacteria used in cancer-treatment to environmental and manufacturing projects, i.e. the construction of a watch-like counter consisting of living cells. In contrast to classical genetic engineering where only one gene is transferred from organism A to organism B, synthetic biology goes forward into the construction of whole new systems with a completely new function. Therefore, all iGEM-Teams get access to a gene- Database called registry, where hundreds of different genetic parts with characterized functions are available in a “plug-and-play” –like format. These parts can be simply stuck together to build functional systems. The rising number of iGEM-Teams over the last years as well as the upcoming public interest in iGEM, the iGEM-Teams’ projects and synthetic biology in general shows, that synthetic biology will for sure have a great impact in many different fields of both scientific research and every-day life.

The contents and design of this wiki are published under the GNU Free Documentation License You are granted the right to copy and modify our work, but you must publish your work under the same type of license while recognizing us the authors.

Retrieved from "http://2009.igem.org/Team:Heidelberg"