Difference between revisions of "Team:UESTC-software/Description"

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                         <li><a href="https://2016.igem.org/Team:UESTC-software/Design">Design</a></li>
 
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     <p class="title">Description</p>
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     <p class="title">Attributions</p>
 
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    <h2 id="Background">Background</h2>
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                 <p> In the past summer, fifteen members of the iGEM UESTC-Software team worked together to achieve our goal, to develop a biological information storage system. During the process, every one made an effort to go beyond the set goal. Moreover, the team’s success is not only a result of the concerted contribution of all members and but also due to the generous help from many other people.</p>
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                 <p>Living in an information explosion era, digital production, transmission and storage have not only revolutionized the way information is accessed and used, but also made information archiving an increasingly complex task <sup>[1]</sup>. Have you been perplexed by vast quantity of information? And have you ever imagined if there exists a practical, high-capacity, low-maintenance, and even self-copy information storage medium which would be still readable after thousands of years? It is not just a dreamy illusion anymore because of the appearance of DNA storage technology.</p>
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                 <h2 id="Member Attributions">Member Attributions</h2>
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                 <p class="img-p" style="font-size:13px;"><img src="https://static.igem.org/mediawiki/2016/a/a4/Uestc_software-description_development_1.png" /><br/><B>Fig.1.</B> Genome controls the growth and development of human being.</p>
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                <strong>Projects</strong>
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                 <p>DNA, one of the most miraculous masterpiece created by Nature as the stable genetic material, holds a great promise for high-density, long-term and massive information storage. For example, human genome, just 3 billion base pairs, encodes all of the complex biology information of human being, including appearance, metabolism, growth, development, production and many other delicate functions <B>(Fig.1)</B>.</p>
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                 <p>Why do not we utilize DNA to store information? Researches indicate that it is extremely dense, and spectacularly high-capacity with a raw storage density limit of 1 exabyte/mm<sup>3</sup>(10<sup>9</sup> GB/mm<sup>3</sup>)<sup>[2]</sup>. In other words, every gram of DNA is equivalent to 14 thousand 50 GB blue-ray discs or 233 x 3 TB hard-disks which weighs more than 151 kg. Meanwhile, compared with current routinely used information storage media, DNA can be stored up to centuries<B>(Fig.2)</B><sup>[2]</sup>.  Grass et al developed an innovative preservation of digital information on DNA which presumably can last 1 million years in silica<sup>[3]</sup>.In conclusion, a great number of virtues makes DNA makes it an ideal archival material for information storage. </p>
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                <strong style="font-style: italic;">Bio101 design</strong>
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                 <p class="img-p" style="font-size:13px;"><img src="https://static.igem.org/mediawiki/2016/a/a8/Uestc_software-description_storage_2.png" /><br/><B>Fig.2.</B>DNA storage as the bottom level of the storage hierarchy.<sup>[2]</sup></p>
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                <p class="one-line" style="margin-bottom:0;">Back-end and Webpage Framework: Dongkai Pu, Jianwei Xu</p>
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                 <h2 id="Biotechnology Availability">Biotechnology Availability</h2>
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                <p class="one-line" style="margin:0;">Front-end: Jianwei Xu, Jun Li, Meng Liu</p>
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                 <p>You may wonder how a piece of arbitrary information is stored into DNA molecules. On the physical reading side, it depends on the DNA sequencing technology <B>(Fig.3)</B>. In 1977, Frederick Sanger adopted primer-extension strategy to develop the DNA sequencing method "DNA sequencing with chain-terminating inhibitors"<sup>[4]</sup>, and it directly facilitated human genome project <B>(HGP)</B>.But Sanger method is too expensive and takes too long time, such that HGP project spent 3 billion dollars over fifteen years<sup>[5]</sup>. Until next-generation sequencing <B>(NGS)</B>, also named high-throughput sequencing, technologies generated, the cost of vast sequencing became comprehensive and really acceptable. 454 pyrosequencing<sup>[6]</sup>, illumina (Solexa) sequencing<sup>[7]</sup>, SOLiD sequencing<sup>[8]</sup> are three mainly applied popular methods. Meanwhile the third generation nanopore DNA sequencing has appeared<sup>[9]</sup>.Owing to technology development, sequencing cost per genome exponential decrease from 1 million dollars in 2008 to just 1 thousand now<sup>[10]</sup>. Encouragingly, the cost will keep dropping, and sequencing would become as simple as reading information from a hard disk or compact optical disk.</p>
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                 <p class="one-line" style="margin:0;">Modeling: Dongkai Pu, Meng Liu, Chenxiang Zheng, Hao Xu, Wei Zhao</p>
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                 <p class="img-p" style="font-size:13px;"><img src="https://static.igem.org/mediawiki/2016/6/6a/Uestc_software-description_sequence_3.png" /><br/><B>Fig.3.</B>  The history of DNA sequencing technology progress.</p>
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                 <p class="one-line" style="margin:0;">Test and Validation: Zhongtian Ma, Jianwei Xu</p>  
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                 <p>On the other hand, writing information physically into DNA molecules depends on the chemical synthesis of artificial DNA sequences. Currently, oligonucleotide synthesis is used for preparing primers, gene probes, etc. The process is implemented as solid-phase synthesis using phosphoramidite method<sup>[11]</sup> and phosphoramidite building blocks derived from protected 2’-deoxynucleosides (dA, dC, dG, and T), ribonucleosides (A, C, G, and U), or chemically modified nucleosides. <B>(Fig.4)</B>.  Unfortunately, we still cannot synthesize any DNA molecules as we wish, for example long DNA segments or some possessing special second structures or high GC-content now are still hard or impossible to synthesize chemically. Although oligonucleotide synthesis has been proposed as early as in 1955<sup>[12]</sup>, the technique is still very expensive, comparing the synthesis cost 0.04 US cent per base (add reference here.) with just 1 cent in reading 1 million bases. Therefore, it is not surprising to find the writing of one megabyte of information cost $12,400 while the reading only costs $220 in a recent DNA storage experiment<sup>[14]</sup>.</p>
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                <p class="one-line" style="margin:0;">Art Design: Xin Ma, Zining Wu</p>
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                 <p class="img-p" style="font-size:13px;"><img src="https://static.igem.org/mediawiki/2016/7/75/Uestc_software-description_synthesis_4.png" /><br/><B>Fig.4.</B>  Synthetic cycle for preparation of oligonucleotides by phosphoramidite method<sup>[13]</sup>.</p>
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                <p class="one-line" style="margin:0;">Documentation: Meng Liu, Jun Li, Yuening Yan, Caixi Xi</p>
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                 <p>However, we believe as the rapid development of biotechnology the DNA synthesis will become cheap enough for the information storage usage. What remains to be solved is how to encode an arbitrary computer file into DNA sequences and decode the DNA sequencing information. There needs a bridge to connect today’s electronic based information world with the future biotechnology based information world. </p>
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                <strong style="font-style: italic;">Bio2048 design</strong>
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                 <h2 id="Project abstract">Project abstract</h2>
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                <p class="one-line" style="margin-bottom:0;">User Interface: Xin Ma</p>
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                 <p>Towards creating a platform for information storage in artificial DNA, our team built a user-friendly web-based tool Bio101 to encode and decode information in DNA sequences. Through a five-step process, compression, encryption, bit-to-nt conversion, indexing and validation, Bio101 can be used to encode conventional electronic computer files into nucleotide sequences which are ready for chemical synthesis and decode the sequencing results of a DNA sample reversely. In addition, we proposed a solution for DNA-based file editing.</p>
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                 <p class="one-line" style="margin:0;">Programming: Xin Ma</p>
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                 <p class="img-p" style="font-size:13px;"><img src="https://static.igem.org/mediawiki/2016/f/fb/Uestc_software-description_project_5.png" /><br/><B>Fig.5.</B>  The design of Bio101 for transformation between DNA sequences and computer files.</p>
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                <p class="one-line" style="margin:0;">Icon Degisn：Haobo Zhou</p>
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                 <p>TThere are five steps in this process including compression, encryption, bit-to-nt conversion, indexing and validation. <B>(Fig.5)</B> This coding tool can create a convenient DNA information workflow, so researchers can choose any files they want and focus on synthesizing DNA. The surprisingly simple idea has the potential to reshape the global face of data storage in the not-too-distant future, and our work contributes to practical areas can accelerate the step to success.</p>
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                <p class="one-line" style="margin:0;">Hierarchical Concept: Zhongtian Ma</p>  
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                 <h2 id="References">References</h2>
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                <br>   
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                <strong>Human Practices and Collaborations</strong>
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                 <ul>
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                <br>
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                <li style="font-size:13px;">[1] Goldman N, Bertone P, Chen S, et al. Towards practical, high-capacity, low-maintenance information storage in synthesized DNA[J]. Nature, 2013, 494(7435): 77-80.</li>  
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                 <strong style="font-style: italic;">Development of Data-Processing Tool for UESTC-China</strong>
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                 <li style="font-size:13px;">[2] Bornholt J, Lopez R, Carmean D M, et al. A DNA-based archival storage system[C]//Proceedings of the Twenty-First International Conference on Architectural Support for Programming Languages and Operating Systems. ACM, 2016: 637-649.</li>  
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                 <p class="one-line" style="margin-bottom:0;">Programming and Documentation: Jianwei Xu, Dongkai Pu, Xin Ma</p>  
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                 <li style="font-size:13px;">[3] Grass R N, Heckel R, Puddu M, et al. Robust Chemical Preservation of Digital Information on DNA in Silica with Error‐Correcting Codes[J]. Angewandte Chemie International Edition, 2015, 54(8): 2552-2555. </li>  
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                <strong style="font-style: italic;">Support for TMMU_China</strong>
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                 <li style="font-size:13px;">[4] Sanger F, Nicklen S, Coulson A R. DNA sequencing with chain-terminating inhibitors[J]. Proceedings of the National Academy of Sciences, 1977, 74(12): 5463-5467. </li>  
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                <p class="one-line" style="margin-bottom:0;">Programming and Documentation: Meng Liu</p>  
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                 <li style="font-size:13px;">[5] Lander E S, Linton L M, Birren B, et al. Initial sequencing and analysis of the human genome[J]. Nature, 2001, 409(6822): 860-921. </li>  
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                <strong style="font-style: italic;">Collaboration with AHUT_ China</strong>
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                 <li style="font-size:13px;">[6] Margulies M, Egholm M, Altman W E, et al. Genome sequencing in microfabricated high-density picolitre reactors[J]. Nature, 2005, 437(7057): 376-380. </li>  
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                <p class="one-line" style="margin-bottom:0;">Video Meeting: Jianwei Xu, Hao Xu</p>
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                <li style="font-size:13px;">[7] Bentley D R, Balasubramanian S, Swerdlow H P, et al. Accurate whole human genome sequencing using reversible terminator chemistry[J]. nature, 2008, 456(7218): 53-59. </li>  
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                <li style="font-size:13px;">[8] Valouev A, Ichikawa J, Tonthat T, et al. A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning[J]. Genome research, 2008, 18(7): 1051-1063. </li>  
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                <strong style="font-style: italic;">iGEM Southwest China Union Meetup</strong>
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                <li style="font-size:13px;">[9] Clarke J, Wu H C, Jayasinghe L, et al. Continuous base identification for single-molecule nanopore DNA sequencing[J]. Nature nanotechnology, 2009, 4(4): 265-270. </li>  
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                <li style="font-size:13px;">[10] Kedes L, Liu E T. The Archon Genomics X PRIZE for whole human genome sequencing[J]. Nature genetics, 2010, 42(11): 917-918. </li>  
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                 <p class="one-line" style="margin-bottom:0;">Presentation: Chenxiang Zheng</p>
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                <li style="font-size:13px;">[11] Reese C B. Oligo-and poly-nucleotides: 50 years of chemical synthesis[J]. Organic & biomolecular chemistry, 2005, 3(21): 3851-3868. </li>  
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                <p class="one-line" style="margin:0;">Poster: Zining Wu</p>
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                <li style="font-size:13px;">[12] Michelson A M, Todd A R. Nucleotides part XXXII. Synthesis of a dithymidine dinucleotide containing a 3′: 5′-internucleotidic linkage[J]. Journal of the Chemical Society (Resumed), 1955: 2632-2638. </li>  
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                <p class="one-line" style="margin:0;">Brief Introduction: Hui Che</p>
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                <li style="font-size:13px;">[13] https://commons.wikimedia.org/wiki/File%3AOligocycle1.png </li>  
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                 <li style="font-size:13px;">[14] Goldman N, Bertone P, Chen S, et al. Towards practical, high-capacity, low-maintenance information storage in synthesized DNA[J]. Nature, 2013, 494(7435): 77-80. </li>  
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                 <strong style="font-style: italic;">Meet-up with TMMU_China and Nanjing-China</strong>
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                 </ul>
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                <p class="one-line" style="margin-bottom:0;">Presentation: Hui Che, Haobo Zhou</p>  
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                 <p class="one-line" style="margin:0;">Poster: Zining Wu</p>
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                 <p class="one-line" style="margin:0;">Brief Introduction: Jianwei Xu</p>  
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                 <strong style="font-style: italic;">Science Lecture</strong>
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                 <p class="one-line" style="margin-bottom:0;">Material Preparation: Caixi Xi, Hao Xu</p>  
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                 <p class="one-line" style="margin:0;">Presentation: Yuening Yan, Hui Che</p>
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                <p class="one-line" style="margin:0;">PowerPoint Slides Design: Zining Wu</p>
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                 <p class="one-line" style="margin:0;">Photo: Haobo Zhou</p>
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                 <p class="one-line" style="margin:0;">Documentation: Yuening Yan, Hui Che</p>
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                 <strong style="font-style: italic;">Lab-Open Day Event</strong>
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                 <p class="one-line" style="margin-bottom:0;">Design, Planning and Implementation: Hao Xu, Caixi Xi</p>
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                 <strong style="font-style: italic;">Sina Microblog Public Account</strong>
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                 <p class="one-line" style="margin-bottom:0;">Management: Zhongtian Ma</p>
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                 <strong style="font-style: italic;">Community Propaganda</strong>
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                 <p class="one-line" style="margin-bottom:0;">Design and Plan: Caixi Xi, Haobo Zhou</p>  
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              <strong>Art and design</strong>
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              <strong style="font-style: italic;">Wiki</strong>
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              <p class="one-line" style="margin-bottom:0;">Programming: Meng Liu, Jun Li</p>
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              <p class="one-line" style="margin-bottom:0;">Design: Haobo Zhou</p>
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              <p class="one-line" style="margin-bottom:0;">Copywriting: Hui Che, Yuening Yan, Meng Liu, Caixi Xi, Wei Zhao, Zhongtian Ma, Chenxiang Zheng</p>
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              <strong style="font-style: italic;">Team sign and uniform</strong>
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              <p class="one-line" style="margin-bottom:0;">Inspiration: Haobo Zhou</p>
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              <p class="one-line" style="margin-bottom:0;">Design and Draw: Zining Wu, Xin Ma</p>
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                 <h2 id="Special Thanks" >Special Thanks</h2>
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                 <strong>Professor Xianlong Wang, Primary PI</strong>
 
                  
 
                  
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                <p>Helping the team design and plan the project. His guidance to all 15 members is greatly appreciated.  </p>
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                <strong>Professor Fengbiao Guo, Secondary PI</strong>
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                <p>Giving the team precious advice on the presentation and wiki design.  </p>
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                <strong>Ling Quan and Qiong Zhang, Instructors</strong>
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                <p>Their leadership and directions on how to build a successful team is worth mentioning. They taught us how to become more friendly and united. Also, they gave us advice on issues regarding travelling to Boston and the contents of our presentation.</p>
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                <strong>Kaiyue Zhang, the team leader of 2015 UESTC-China, and Yaocong Duan, the team leader of 2015 UESTC-Software.</strong>
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                <p>For giving us advice on building our team and disciplines, providing support outside of training, which encouraged us to be focused and produce a perfect project.</p>
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                <strong>Xu Wang, System Administrator at Xingchen Studio</strong>
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                <p>For building the server and helping us set up backstage when we had problem during visualization design.</p>
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                <strong>Bohan Li, Ziyun Guan, Jingyi Wang, Huanghao Yang, Wei Liu, the Preliminary Team Members (sophomores of UESTC).</strong>
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                <p>For helping us with human practices including the implementation of the open-day visiting activity “To Be Scientists Tomorrow” and Community Advocacy. Their help is especially appreciated for taking photos, shooting videos and preparing materials.  </p>
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                <strong>Other teams taking part in the competition</strong>
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                <br>
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                <p><a href="https://2016.igem.org/Team:SCU-China" style="color:#3C9CD3;text-indent:28px;font-size:15px;" target="_blank"> <b>·SCU-China</b></a>,<a href="https://2016.igem.org/Team:Nanjing-China" style="color:#3C9CD3;text-indent:28px;font-size:15px;" target="_blank"><b>Nanjing-China</b></a>,<a href="https://2016.igem.org/Team:TMMU_China" style="color:#3C9CD3;text-indent:28px;font-size:15px;" target="_blank"> <b>TMMU_China</b></a>,<a href="https://2016.igem.org/Team:UESTC-China" style="color:#3C9CD3;text-indent:28px;font-size:15px;" target="_blank"> <b>UESTC-China</b></a>,<a href="https://2016.igem.org/Team:AHUT_China" style="color:#3C9CD3;text-indent:28px;font-size:15px;" target="_blank"><b>AHUT_China</b></a></p>
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                <p>For discussing our projects with us and putting forward some views and suggestions to improve our task. </p>
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                <p><a href="https://2016.igem.org/Team:UESTC-China" style="color:#3C9CD3;text-indent:28px;font-size:15px;" target="_blank"><b>·UESTC-China</b></a></p>
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                <p>For mentoring us to do wet-lab experiment and assisting us with two human practices, the lab-open day “To Be Scientists Tomorrow” and the science lecture in Puyang Middle School. </p>
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                <p><a href="https://2016.igem.org/Team:AHUT_China" style="color:#3C9CD3;text-indent:28px;font-size:15px;" target="_blank"> <b>·AHUT_China</b></a></p>
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                <p>For doing dry-lab testing and offering testing report for our project.  </p>
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                <strong>Developers of the Following Open-Source Libraries and Packages</strong>
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                <p>Django, Owl-Carousel, Bootstrap, JQuery and ISAAC.</p>
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                <strong>Dean’s Office of University of Electronic Science and Technology of China</strong>
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                <p>It’s a great deal for us that the Dean’s Office provided our funds during the competition. The Dean’s Office covered the flight fees, accommodation, also Team Registration Fees and the Jamboree Attendance Fee, which greatly reduced our financial burden and motivated us to focus on the competition.</p>
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                <strong>Thanks again to all the people who helped us during the summer. With your support, we become a successful iGEM team. </strong>
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                <img src="https://static.igem.org/mediawiki/2016/7/7d/Uestc_software-mingxie1.PNG" style="width:50%;margin-left:200px;"></img>
 
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Revision as of 08:04, 19 October 2016

三级页面

Attributions

In the past summer, fifteen members of the iGEM UESTC-Software team worked together to achieve our goal, to develop a biological information storage system. During the process, every one made an effort to go beyond the set goal. Moreover, the team’s success is not only a result of the concerted contribution of all members and but also due to the generous help from many other people.

Member Attributions

Projects
Bio101 design

Back-end and Webpage Framework: Dongkai Pu, Jianwei Xu

Front-end: Jianwei Xu, Jun Li, Meng Liu

Modeling: Dongkai Pu, Meng Liu, Chenxiang Zheng, Hao Xu, Wei Zhao

Test and Validation: Zhongtian Ma, Jianwei Xu

Art Design: Xin Ma, Zining Wu

Documentation: Meng Liu, Jun Li, Yuening Yan, Caixi Xi

Bio2048 design

User Interface: Xin Ma

Programming: Xin Ma

Icon Degisn：Haobo Zhou

Hierarchical Concept: Zhongtian Ma

Human Practices and Collaborations
Development of Data-Processing Tool for UESTC-China

Programming and Documentation: Jianwei Xu, Dongkai Pu, Xin Ma

Support for TMMU_China

Programming and Documentation: Meng Liu

Collaboration with AHUT_ China

Video Meeting: Jianwei Xu, Hao Xu

iGEM Southwest China Union Meetup

Presentation: Chenxiang Zheng

Poster: Zining Wu

Brief Introduction: Hui Che

Meet-up with TMMU_China and Nanjing-China

Presentation: Hui Che, Haobo Zhou

Poster: Zining Wu

Brief Introduction: Jianwei Xu

Science Lecture

Material Preparation: Caixi Xi, Hao Xu

Presentation: Yuening Yan, Hui Che

PowerPoint Slides Design: Zining Wu

Photo: Haobo Zhou

Documentation: Yuening Yan, Hui Che

Lab-Open Day Event

Design, Planning and Implementation: Hao Xu, Caixi Xi

Sina Microblog Public Account

Management: Zhongtian Ma

Community Propaganda

Design and Plan: Caixi Xi, Haobo Zhou

Art and design
Wiki

Programming: Meng Liu, Jun Li

Design: Haobo Zhou

Copywriting: Hui Che, Yuening Yan, Meng Liu, Caixi Xi, Wei Zhao, Zhongtian Ma, Chenxiang Zheng

Team sign and uniform

Inspiration: Haobo Zhou

Design and Draw: Zining Wu, Xin Ma

Special Thanks

Professor Xianlong Wang, Primary PI

Helping the team design and plan the project. His guidance to all 15 members is greatly appreciated.

Professor Fengbiao Guo, Secondary PI

Giving the team precious advice on the presentation and wiki design.

Ling Quan and Qiong Zhang, Instructors

Their leadership and directions on how to build a successful team is worth mentioning. They taught us how to become more friendly and united. Also, they gave us advice on issues regarding travelling to Boston and the contents of our presentation.

Kaiyue Zhang, the team leader of 2015 UESTC-China, and Yaocong Duan, the team leader of 2015 UESTC-Software.

For giving us advice on building our team and disciplines, providing support outside of training, which encouraged us to be focused and produce a perfect project.

Xu Wang, System Administrator at Xingchen Studio

For building the server and helping us set up backstage when we had problem during visualization design.

Bohan Li, Ziyun Guan, Jingyi Wang, Huanghao Yang, Wei Liu, the Preliminary Team Members (sophomores of UESTC).

For helping us with human practices including the implementation of the open-day visiting activity “To Be Scientists Tomorrow” and Community Advocacy. Their help is especially appreciated for taking photos, shooting videos and preparing materials.

Other teams taking part in the competition

·SCU-China,Nanjing-China, TMMU_China, UESTC-China,AHUT_China

For discussing our projects with us and putting forward some views and suggestions to improve our task.

·UESTC-China

For mentoring us to do wet-lab experiment and assisting us with two human practices, the lab-open day “To Be Scientists Tomorrow” and the science lecture in Puyang Middle School.

·AHUT_China

For doing dry-lab testing and offering testing report for our project.

Developers of the Following Open-Source Libraries and Packages

Django, Owl-Carousel, Bootstrap, JQuery and ISAAC.

Dean’s Office of University of Electronic Science and Technology of China

It’s a great deal for us that the Dean’s Office provided our funds during the competition. The Dean’s Office covered the flight fees, accommodation, also Team Registration Fees and the Jamboree Attendance Fee, which greatly reduced our financial burden and motivated us to focus on the competition.

Thanks again to all the people who helped us during the summer. With your support, we become a successful iGEM team.

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