Difference between revisions of "Team:Edinburgh UG/Description"

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<h3>★  ALERT! </h3>
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<a href="http://www.wysiwygwebbuilder.com" target="_blank"><img src="images/builtwithwwb11.png" alt="WYSIWYG Web Builder" style="position:absolute;left:656px;top:2897px;border-width:0;z-index:250"></a>
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<p>This page is used by the judges to evaluate your team for the<a href="https://2016.igem.org/Judging/Medals"> improve a previous part or project gold medal criterion</a>. </p>
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<p> Delete this box in order to be evaluated for this medal. See more information at <a href="https://2016.igem.org/Judging/Pages_for_Awards/Instructions"> Instructions for Pages for awards</a>.</p>
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<span style="color:#000000;font-family:Arial;font-size:8px;">ProjectD</span></div>
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<span style="color:#000000;font-family:Verdana;font-size:75px;">Project Discription</span></div>
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<p>Tell us about your project, describe what moves you and why this is something important for your team.</p>
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<span style="color:#000000;font-family:Verdana;font-size:19px;">The last decade has seen an exponential increase in data and information generation, creating a storage demand that will soon outweigh supply. By 2040, global data storage demand will reach 3×10^24 (3 million billion billion) bits<sup>1.</sup>. Considering the amount of energy required to run a data centre (about 2% of global energy consumption<sup>2.</sup>) and the limited supply of raw materials like silicon for manufacturing memory devices, it is clear that novel storage methods are of the utmost importance in meeting demand and providing a sustainable, long term solution to the data storage</span><span style="color:#000000;font-family:Arial;font-size:19px;"> </span><span style="color:#000000;font-family:Verdana;font-size:19px;">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. <br><br></span></div>
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<h5>What should this page contain?</h5>
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<li> A clear and concise description of your project.</li>
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<li>A detailed explanation of why your team chose to work on this particular project.</li>
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<li>References and sources to document your research.</li>
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<li>Use illustrations and other visual resources to explain your project.</li>
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<span style="color:#000000;font-family:Verdana;font-size:19px;">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.</span></div>
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<span style="color:#000000;font-family:Verdana;font-size:19px;">Our project, given the name <strong>BabblED</strong>, 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 sequence, termed a BabbleBrick, will be stored in a different PhytoBrick. Sentence assembly and directionality is ensured with stepwise addition of ‘DNA words’ 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 <strong>BabbleBrick </strong>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. </span></div>
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<h5>Advice on writing your Project Description</h5>
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We encourage you to put up a lot of information and content on your wiki, but we also encourage you to include summaries as much as possible. If you think of the sections in your project description as the sections in a publication, you should try to be consist, accurate and unambiguous in your achievements.  
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<span style="color:#000000;font-family:Verdana;font-size:19px;">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 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. </span></div>
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Judges like to read your wiki and know exactly what you have achieved. This is how you should think about these sections; from the point of view of the judge evaluating you at the end of the year.
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<span style="color:#000000;font-family:Verdana;font-size:19px;">References:<br>1.http://www.nature.com/nmat/journal/v15/n4/full/nmat4594.html#supplementary-information<br>2.http://www.greenpeace.org/international/Global/international/publications/climate/2011/Cool%20IT/dirty-data-report-greenpeace.pdf/</span></div>
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<p>See how other teams have described and presented their projects: </p>
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<li><a href="https://2014.igem.org/Team:Imperial/Project"> Imperial</a></li>
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<li><a href="https://2014.igem.org/Team:UC_Davis/Project_Overview"> UC Davis</a></li>
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<li><a href="https://2014.igem.org/Team:SYSU-Software/Overview">SYSU Software</a></li>
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Revision as of 10:50, 30 June 2016

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ProjectD
Project Discription
The last decade has seen an exponential increase in data and information generation, creating a storage demand that will soon outweigh supply. By 2040, global data storage demand will reach 3×10^24 (3 million billion billion) bits1.. Considering the amount of energy required to run a data centre (about 2% of global energy consumption2.) and the limited supply of raw materials like silicon for manufacturing memory devices, it is clear that novel storage 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.

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.
 
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 sequence, termed a BabbleBrick, will be stored in a different PhytoBrick. Sentence assembly and directionality is ensured with stepwise addition of ‘DNA words’ 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.
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 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.
References:
1.http://www.nature.com/nmat/journal/v15/n4/full/nmat4594.html#supplementary-information
2.http://www.greenpeace.org/international/Global/international/publications/climate/2011/Cool%20IT/dirty-data-report-greenpeace.pdf/