Difference between revisions of "Team:Edinburgh UG"

 
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                  <a href="https://2016.igem.org/Team:Edinburgh_UG">Home</a></li>
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                      <li><a href="https://2016.igem.org/Team:Edinburgh_UG/Collaborations">Collaboration</a></li>
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                      <li><a href="https://2016.igem.org/Team:Edinburgh_UG/Description">Project</a></li>
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−
                      <li><a href="https://2016.igem.org/Team:Edinburgh_UG/Description">Description</a></li>
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                      <li>
−
                      <li><a href="https://2016.igem.org/Team:Edinburgh_UG/Design">Design</a></li>
+
                          <a href="https://2016.igem.org/Team:Edinburgh_UG">Home</a>
−
                      <li><a href="https://2016.igem.org/Team:Edinburgh_UG/Experiments">Experiments</a></li>
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                      </li>
−
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−
                      <li><a href="https://2016.igem.org/Team:Edinburgh_UG/Demonstrate">Demonstrate</a></li>
+
                        <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">Team<span class="caret"></span></a>
−
                      <li><a href="https://2016.igem.org/Team:Edinburgh_UG/Results">Results</a></li>
+
                        <ul class="dropdown-menu" role="menu">
−
                      <li><a href="https://2016.igem.org/Team:Edinburgh_UG/Notebook">Notebook</a></li>
+
                          <li><a href="https://2016.igem.org/Team:Edinburgh_UG/Team">Team</a></li>
−
                    </ul>
+
                          <li><a href="https://2016.igem.org/Team:Edinburgh_UG/Attribution">Attribution</a></li>
−
                  </li>
+
                        </ul>
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                  <li class="dropdown">
+
                      </li>
−
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+
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−
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+
                        <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">Human Practices<span class="caret"></span></a>
−
                      <li><a href="https://2016.igem.org/Team:Edinburgh_UG/Parts">Team Parts</a></li>
+
                        <ul class="dropdown-menu" role="menu">
−
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                          <li><a href="https://2016.igem.org/Team:Edinburgh_UG/Overview">Overview</a> </li>
−
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+
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−
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+
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−
                    </ul>
+
                          <li><a href="https://2016.igem.org/Team:Edinburgh_UG/Medal_Criteria">Medal Criteria</a> </li>
−
                  </li>
+
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−
                  <li class="dropdown">
+
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+
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−
                    <ul class="dropdown-menu" role="menu">
+
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−
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+
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−
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+
                      </li>
−
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+
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−
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+
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−
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                          <li><a href="https://2016.igem.org/Team:Edinburgh_UG/Description">Description</a></li>
−
                  <li class="dropdown">
+
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−
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−
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+
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−
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+
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−
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+
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−
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+
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−
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+
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+
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−
                      <li><a href="https://2016.igem.org/Team:Edinburgh_UG/Human_Practices">Human Practices</a></li>
+
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−
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−
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−
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−
                       <li><a href="https://2016.igem.org/Team:Edinburgh_UG/Engagement">Engagement</a> </li>
+
                          <li><a href="https://2016.igem.org/Team:Edinburgh_UG/Encryption">Encryption</a></li>
−
                    </ul>
+
                          <li><a href="https://2016.igem.org/Team:Edinburgh_UG/Files">Files</a></li>
−
                  </li>
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−
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−
                      <li><a href="https://2016.igem.org/Team:Edinburgh_UG/Entrepreneurship">Entrepreneurship</a></li>
+
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−
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−
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−
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+
                          <li><a href="https://2016.igem.org/Team:Edinburgh_UG/Part_Collection">Part Collection</a> </li>
−
                      <li><a href="https://2016.igem.org/Team:Edinburgh_UG/Model">Model</a> </li>
+
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−
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+
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−
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+
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−
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−
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−
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   <header class="image-bg-fluid-height">
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   <div class="container-fluid">
 
     <div class="row full-size">
 
     <div class="row full-size">
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        <h3 style="font-size:250%;">By 2040, we will run out of the materials needed to store digital data.</h3>
+
−
        <p style="font-size:180%;">If this happens, there will be no capacity for Twitter, Facebook or iGEM to function online. Last year, data centres worldwide used more electricity than the entire United Kingdom. By 2020, it will cost more than $13.7 billion to power data centres per year.</p>
+
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                      <img src="https://static.igem.org/mediawiki/2016/5/55/EdiGEM16UGdensity.png" class="img-responsive center-block">
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 +
                  </div>
 +
                  <div class="col-xs-3">
 +
                      <h3 style="font-size:200%;" class="text-center">Density</h3>
 +
                      <p class="text-center">DNA has 1000 times the </p>
 +
                      <p class="text-center">density of flash storage</p>
 +
                  </div>
 +
                  <div class="col-xs-3"></div>
 +
              </div>
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          <div class="row">
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              <div class="container">
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                  <div class="col-xs-3"></div>
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 +
                      <div>
 +
                      <img src="https://static.igem.org/mediawiki/2016/2/26/EdiGEM16UGdollar.png" class="img-responsive center-block">
 +
                      </div>
 +
                  </div>
 +
                  <div class="col-xs-3">
 +
                      <h3 style="font-size:200%;" class="text-center">Affordability</h3>
 +
                      <p class="text-center">All our encoding programmes </p>
 +
                      <p class="text-center">are open source and initial </p>
 +
                      <p class="text-center">synthesis of the lexicon is done </p>
 +
                      <p class="text-center">for you providing significant </p>
 +
                      <p class="text-center">cost reductions on existing </p>
 +
                      <p class="text-center">methods</p>
 +
                  </div>
 +
                  <div class="col-xs-3"></div>
 +
              </div>
 +
          </div>
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          <div class="row">
 +
              <div class="container">
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                  <div class="col-xs-3"></div>
 +
                  <div class="col-xs-3">
 +
                      <div>
 +
                      <img src="https://static.igem.org/mediawiki/2016/8/81/EdiGEM16UGhourglass.jpeg" class="img-responsive center-block">
 +
                      </div>
 +
                  </div>
 +
                  <div class="col-xs-3">
 +
                      <h3 style="font-size:200%;" class="text-center">Longevity</h3>
 +
                      <p class="text-center">DNA can last for </p>
 +
                      <p class="text-center">thousands of years </p>
 +
                      <p class="text-center">without consuming </p>
 +
                      <p class="text-center">resources; modern  </p>
 +
                      <p class="text-center">hard drives can only </p>
 +
                      <p class="text-center">last 50</p>
 +
                  </div>
 +
                  <div class="col-xs-3"></div>
 +
              </div>
 +
          </div>
 +
          <div class="row">
 +
              <div class="container">
 +
                  <div class="col-xs-3"></div>
 +
                  <div class="col-xs-3">
 +
                      <div>
 +
                      <img src="https://static.igem.org/mediawiki/2016/e/e0/EdiGEM16UGpuzzle.png" class="img-responsive center-block">
 +
                      </div>
 +
                  </div>
 +
                  <div class="col-xs-3">
 +
                      <h3 style="font-size:200%;" class="text-center">Modularity</h3>
 +
                      <p class="text-center">Assembly of our BabbleBricks </p>
 +
                      <p class="text-center">is unrestricted and completely </p>
 +
                      <p class="text-center">customisable </p>
 +
                  </div>
 +
                  <div class="col-xs-3"></div>
 +
              </div>
 +
          </div>
 
       </div>
 
       </div>
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      <div class="col-sm-8">
 
−
        <p></p>
 
−
        <h3 style="font-size:250%;">We have a solution: DNA Text Encoding</h3>
 
−
      </div>
 
−
    </div>
 
 
   </div>
 
   </div>
−
 
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     <div id="prev" class="col-xs-2 col-xs-offset-4 well ">previous</div>
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        <img src="https://static.igem.org/mediawiki/2016/5/55/EdiGEM16UGdensity.png" class="img-responsive center-block">
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+
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        <p></p>
+
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+
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+
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      <div class="col-sm-3">
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        <p></p>
+
−
        <h3 style="font-size:200%;" class="text-center">Density</h3>
+
−
        <p class="text-center">DNA has 1000 times</p>
+
−
        <p class="text-center">greater storage density</p>
+
−
        <p class="text-center">than flash memory</p>
+
−
      </div>
+
−
      <div class="col-sm-3">
+
−
        <p></p>
+
−
        <h3 style="font-size:200%;" class="text-center">Affordability</h3>
+
−
        <p class="text-center">All our encoding programmes </p>
+
−
        <p class="text-center">are open source and initial </p>
+
−
        <p class="text-center">synthesis of the lexicon is done </p>
+
−
        <p class="text-center">for you providing significant </p>
+
−
        <p class="text-center">cost reductions on existing </p>
+
−
        <p class="text-center">methods</p>
+
−
      </div>
+
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      <div class="col-sm-3">
+
−
        <p></p>
+
−
        <h3 style="font-size:200%;" class="text-center">Longevity</h3>
+
−
        <p class="text-center">DNA can last for </p>
+
−
        <p class="text-center">thousands of years </p>
+
−
        <p class="text-center">without consuming </p>
+
−
        <p class="text-center">resources; modern </p>
+
−
        <p class="text-center">hard drives can only </p>
+
−
        <p class="text-center">last 50</p>
+
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      </div>
+
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      <div class="col-sm-3">
+
−
        <p></p>
+
−
        <h3 style="font-size:200%;" class="text-center">Modularity</h3>
+
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        <p class="text-center">Assembly of our BabbleBricks </p>
+
−
        <p class="text-center">is unrestricted and completely </p>
+
−
        <p class="text-center">customisable </p>
+
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+
 
   </div>
 
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           <p></p>
 
           <p></p>
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           <h3 style="font-size:250%;" class="text-center">Abstract</h3>
+
           <h3 style="font-size:400%;" class="text-center">Abstract</h3>
−
           <p>The last decade has seen an exponential increase in data and information
+
           <br>
−
            generation, creating a storage demand that will soon outweigh supply.
+
          <h2>
−
            By 2040, global data storage demand will reach 3×10^24 (3 million billion billion)
+
In 2014, over 10 sextillion bits of data were digitally stored worldwide. To put this in context, there are only 1 sextillion grains of sand on this entire Earth. According to IBM, we generate over 2.5 billion gigabytes daily through tweets, emails and Facebook posts! The University of Edinburgh’s undergraduate team has designed a DNA storage system that is a sustainable, dense and long-lasting alternative to magnetic tape data storage. The storage system relies on modular DNA fragments that can flexibly and cost effectively store any type of data. Modularity makes BabblED the cheapest and most accessible DNA storage system available. The system also boasts new and novel techniques to incorporate error-correcting and encryption in DNA storage. In fact, this ‘DNA Typewriter’ has already been implemented by the National Library of Scotland to archive one of their most precious manuscripts: the last letter of Mary Queen of Scots.
−
            bits1.. Considering the amount of energy required to run a data centre
+
</h2>
−
            (about 2% of global energy consumption2.) and the limited supply of raw materials
+
    </div>
−
            like silicon for manufacturing memory devices, it is clear that novel storage
+
    <div class="col-sm-2">
−
            methods are of the utmost importance in meeting demand and providing a
+
−
            sustainable, long term solution to the data storage problem. The University
+
−
            of Edinburgh 2016 undergraduate iGEM team held these considerations in mind
+
−
            when we set out to create a new DNA-based storage system.</p>
+
−
          <p>Over the course of weeks 1 and 2 our team explored and researched ideas
+
−
            for a project utilising DNA as an information storage device. Our
+
−
            brainstorming process evolved through discussions about the advantages
+
−
            and disadvantages of DNA synthesis and encoding digital information into
+
−
            nucleotide sequences. Major points of debate were cost, fidelity and efficiency
+
−
            of data storage. Following some constructive feedback from our supervisors,
+
−
            our team focused on developing a method that is accessible, sustainable
+
−
            and fits the iGEM format.</p>
+
−
          <p>Our project, given the name BabblED, is based on a simple idea: develop
+
−
            a modular system for encoding text, or any other unit of information,
+
−
            into DNA. We will prove the validity of our concept by encoding Ogden’s
+
−
            Basic English (a collection of 850-1,000 words that can be used to express
+
−
            most concepts in the English language). Each encoded word a BabbleBrick
+
−
            will be stored in a different PhytoBrick. Sentence assembly and unidirectionality
+
−
            is ensured by the stepwise addition of BabbleBricks that have alternating types
+
−
            of sticky ends; this also prevents repeats and minimizes the occurrence of missing
+
−
            words. The whole sentence construct can be melted off for easy retrieval and
+
−
            assembled back into a PhytoBrick for storage. Since the value that is
+
−
            assigned to each BabbleBrick is arbitrary, each one can be reused with
+
−
            any library or language. In this way, our encoding and assembly method
+
−
            can be optimized for many types of data. Furthermore, using tools such
+
−
            as checksums, optimal rectangular codes and, when appropriate, natural
+
−
            language processing techniques, we are able to ensure that each BabbleBrick
+
−
            sentence can be decoded with 100% accuracy.</p>
+
−
          <p>As of week 4, we have developed the computer program that converts
+
−
              our vocabulary to BabbleBrick sequences. We have designed the DNA sequences
+
−
              for error-correcting codes and researched the benefits and potential ways
+
−
              to utilize encryption in our method. We are in the process of ordering our
+
−
              first BabbleBricks in the form of gBlocks from IDT and testing our
+
−
              assembly method for efficiency. We have commenced the 2016 Interlab
+
−
              study and are pursuing another exciting project on bacterial growth-based
+
−
              logic. We have already had some fascinating discussions with data specialists
+
−
              and librarians; their feedback and expertise are vital to how we are shaping
+
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              our project. We have also been in touch with other iGEM teams, such
+
−
              as Newcastle and Dundee, and are hosting a Scottish team meet-up in
+
−
              the beginning of July.</p>
+
−
            <p>References:</p>
+
−
            <p>1.http://www.nature.com/nmat/journal/v15/n4/full/nmat4594.html#supplementary-information</p>
+
−
            <p>2.http://www.greenpeace.org/international/Global/international/publications/climate/2011/
+
−
            Cool%20IT/dirty-data-report-greenpeace.pdf/</p>
+
 
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                   <hr>
 
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                   <h2 class="intro-text text-center">Contact
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                   <h2 class="intro-text text-center">Follow
 
                       <strong>Us</strong>
 
                       <strong>Us</strong>
 
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                   </h2>
 
                   <hr>
 
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                   <div class="intro-text text-center">
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                      <p><a href="mailto:edinburgh.igem2016@gmail.com">edinburgh.igem2016@gmail.com</a>
 
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                               <a href="https://twitter.com/EdiGEM2016"><img src="https://static.igem.org/mediawiki/2016/9/94/Edinburgh2_t2.jpg"></img></a>
 
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                               <a href="https://www.instagram.com/edigem2016/"><img src="https://static.igem.org/mediawiki/2016/6/64/Edinburgh2_insta2.png"></img></a>
 
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Latest revision as of 23:43, 19 October 2016

The University of Edinburgh Undergraduate iGEM team 2016 presents:

The Next Generation of Information Storage

Density

DNA has 1000 times the

density of flash storage

Affordability

All our encoding programmes

are open source and initial

synthesis of the lexicon is done

for you providing significant

cost reductions on existing

methods

Longevity

DNA can last for

thousands of years

without consuming

resources; modern

hard drives can only

last 50

Modularity

Assembly of our BabbleBricks

is unrestricted and completely

customisable

Abstract


In 2014, over 10 sextillion bits of data were digitally stored worldwide. To put this in context, there are only 1 sextillion grains of sand on this entire Earth. According to IBM, we generate over 2.5 billion gigabytes daily through tweets, emails and Facebook posts! The University of Edinburgh’s undergraduate team has designed a DNA storage system that is a sustainable, dense and long-lasting alternative to magnetic tape data storage. The storage system relies on modular DNA fragments that can flexibly and cost effectively store any type of data. Modularity makes BabblED the cheapest and most accessible DNA storage system available. The system also boasts new and novel techniques to incorporate error-correcting and encryption in DNA storage. In fact, this ‘DNA Typewriter’ has already been implemented by the National Library of Scotland to archive one of their most precious manuscripts: the last letter of Mary Queen of Scots.

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