Team:Freiburg software

From 2009.igem.org

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Universal Endonuclease &ndash; Cutting Edge Technology</b>
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SynBioWave</b>
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<p>Gene technology is driven by the use of restriction
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<p>Synthetic Biology aims at constructing whole new genomes. Such an effort is pushed forward by many users and relies on modular combination of genetic elements. The genetic elements represent an increasing complexity by assembling parts to devices and then systems. The construction process needs to be transparent and even at final stages control at the basepair level is required. We propose to build a user environment able to analyze and construct genetic parts and ultimately genomes.
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endonucleases.
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Yet, constraints of limited sequence length and variation recognized by
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We will build the software suite on the Google-Wave format, which is currently in beta testing, and add molecular biology tools mainly from the BioJava library. The first goal is to provide basic molecular biology cloning functionality which appeals to the wet bench scientist. On top of that, we would like to add specific synthetic biology functionality such as biobrick database access and part annotation. The software for the Jamboree will not be feature complete, but demonstrate the principle use, with some molecular biology standard tasks, as well as the power of the wave approach for a distributed collaborative synthetic biology effort. Many wave-robots with a manageable set of capabilities will divide and conquer the complex task of creating a genome in silico.
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available restriction enzymes pose a major roadblock for synthetic
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biology. We developed the basis for universal restriction enzymes,
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The first developments of 'SynBioWave' will lay the ground for a useful grouping of functionality for wave-robots, how the calling of robots and their functions is managed, how robots act on DNA or protein sequences, how intermediate results are stored, etc... The process should be open and clear so that users can add and share robots useful for synthetic biology.  
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primarily for routine cloning but also with potential for in vivo
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applications. We use a nucleotide cleavage domain fused to a binding
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domain, which recognizes a programmable adapter that mediates binding
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to DNA and thus cleavage. As adapter we use readily available modified
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oligonucleotides, as binding domain anticalins and as cleavage domain
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FokI moieties engineered for heterodimerization and activity. For
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cloning, this universal enzyme has merely to be mixed with the sequence
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specific oligonucleotide and the target DNA. Binding and release are
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addressed with thermocycling. Additionally, we provide concepts for in
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vivo applications by external adapter delivery, activity regulation by
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photo-switching, as well as for modifying an argonaute protein towards
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a DNA endonuclease.
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Revision as of 13:37, 13 October 2009

FREiGEM 2009

an image

Team Freiburg Software


The first German team ever to participate in iGEM is back again and after last year's second place we're highly motivated  to make some good piece of synthetic biology in 2009. In this year we want to create an universal restriction enzyme to facilitate labwork and enable new techniques.

We're looking forward to meeting you on this year's jamboree!



SynBioWave

Synthetic Biology aims at constructing whole new genomes. Such an effort is pushed forward by many users and relies on modular combination of genetic elements. The genetic elements represent an increasing complexity by assembling parts to devices and then systems. The construction process needs to be transparent and even at final stages control at the basepair level is required. We propose to build a user environment able to analyze and construct genetic parts and ultimately genomes. We will build the software suite on the Google-Wave format, which is currently in beta testing, and add molecular biology tools mainly from the BioJava library. The first goal is to provide basic molecular biology cloning functionality which appeals to the wet bench scientist. On top of that, we would like to add specific synthetic biology functionality such as biobrick database access and part annotation. The software for the Jamboree will not be feature complete, but demonstrate the principle use, with some molecular biology standard tasks, as well as the power of the wave approach for a distributed collaborative synthetic biology effort. Many wave-robots with a manageable set of capabilities will divide and conquer the complex task of creating a genome in silico. The first developments of 'SynBioWave' will lay the ground for a useful grouping of functionality for wave-robots, how the calling of robots and their functions is managed, how robots act on DNA or protein sequences, how intermediate results are stored, etc... The process should be open and clear so that users can add and share robots useful for synthetic biology.

FREiGEM 2009

Team
The Team
In 2009 our team consists of  14 undergraduates and 4 advisors.
Read more...

bioss
Bioss

We want to thank our main sponsor Bioss for supporting our project.
Read more...

Visitors