Difference between revisions of "Team:Heidelberg/Software"

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<p>In order to be considered for the <a href="https://2015.igem.org/Judging/Awards#SpecialPrizes">Best Software Tool award</a>, you must fill out this page.</p>
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<h3 class="basicheader"> Software </h3>
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Nowadays detection of new aptamers is dependent on systematic evolution of ligands by exponential enrichment (SELEX)<x-ref>Ellington1990</x-ref><x-ref>Tuerk1990</x-ref><x-ref>Bartel1993</x-ref>. This process involves numerous cycles to select potential candidates from a random pool. These selected sequences have to be further mutated over and over again in order to generate an aptamer with a high affinity.
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To substitute this very time consuming and expensive SELEX we developed a new software with different featuressoftware <b>M</b>aking <b>A</b>patmers <b>W</b>ithout <b>S</b>ELEX (MAWS), which enables us to efficiently generate new aptamers within less than a day compared. Thus we were able to predict many aptamers by MAWS and validated them in different assay during the summer. If we had been restricted to use the existing methods this would not have been possible.
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Every aptamer bears the potential to be used as module in order to generate switchable aptazymes.<x-ref>Soukup1999</x-ref> In order to obtain the best possible fusion of an aptamer with a ribozyme or DNAzyme another SELEX with several cycles would have been needed. In order to bypass this second time-cosuming SELEX we developed <b>J</b>oining <b>A</b>patmers <b>W</b>ithout <b>S</b>ELEX (JAWS). We are able to optimize the transition element to create a bistable system where either one conformation is favored in presence of the ligand while the other one is in absence of the ligand.
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MAWS enables the scientific community the possibility to generate aptamers for any ligand <i>in silico</i>. The JAWS generated modules can be fused to a ribozyme or DNAzyme to create ligand-dependent tools. JAWS thus bypasses the requirement for SELEX and, in conjunction with MAWS, enables rapid design-prototype-test cycles, drastically improving the stardardization and modularization of nucleic acid-based devices!
  
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<p>Regardless of the topic, iGEM projects often create or adapt computational tools to move the project forward. Because they are born out of a direct practical need, these software tools (or new computational methods) can be surprisingly useful for other teams. Without necessarily being big or complex, they can make the crucial difference to a project's success. This award tries to find and honour such "nuggets" of computational work.</p>
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Get further information about <a href="software/maws">MAWS</a>
  
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or about <a href="software/jaws">JAWS</a>
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If you are working on software as your main project, please join the software track. If you are creating software as an addition to your main project, please apply for this award.
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Here are a few examples from previous teams:
 
 
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<li><a href="https://2013.igem.org/Team:TU-Munich/Results/Software">TU Munich 2013</a></li>
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<li><a href="https://2014.igem.org/Team:Heidelberg/Software">Heidelberg 2014</a></li>
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<li><a href="https://2014.igem.org/Team:Aachen/Project/Measurement_Device#Software">Aachen 2014</a></li>
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Latest revision as of 09:18, 2 December 2015

Software

Nowadays detection of new aptamers is dependent on systematic evolution of ligands by exponential enrichment (SELEX)Ellington1990Tuerk1990Bartel1993. This process involves numerous cycles to select potential candidates from a random pool. These selected sequences have to be further mutated over and over again in order to generate an aptamer with a high affinity. To substitute this very time consuming and expensive SELEX we developed a new software with different featuressoftware Making Apatmers Without SELEX (MAWS), which enables us to efficiently generate new aptamers within less than a day compared. Thus we were able to predict many aptamers by MAWS and validated them in different assay during the summer. If we had been restricted to use the existing methods this would not have been possible. Every aptamer bears the potential to be used as module in order to generate switchable aptazymes.Soukup1999 In order to obtain the best possible fusion of an aptamer with a ribozyme or DNAzyme another SELEX with several cycles would have been needed. In order to bypass this second time-cosuming SELEX we developed Joining Apatmers Without SELEX (JAWS). We are able to optimize the transition element to create a bistable system where either one conformation is favored in presence of the ligand while the other one is in absence of the ligand. MAWS enables the scientific community the possibility to generate aptamers for any ligand in silico. The JAWS generated modules can be fused to a ribozyme or DNAzyme to create ligand-dependent tools. JAWS thus bypasses the requirement for SELEX and, in conjunction with MAWS, enables rapid design-prototype-test cycles, drastically improving the stardardization and modularization of nucleic acid-based devices!

Get further information about MAWS or about JAWS

References