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<div class="row"> - <!-- 侧导航æ --> - <div class="col-3 left-nav-container" id="myScrollspy"> - <header class="left-nav" role="banner"> - <nav class="nav" role="navigation"> - <ul class="nav__list"> - <li> - <input id="group-1" type="checkbox" hidden /> - <a href="#s1"><span class="fa fa-angle-right"></span> Overview </a> - </li> - <li> - <input id="group-2" type="checkbox" hidden /> - <label for="group-2"><span class="fa fa-angle-right"></span> Topic Research</label> - <ul class="group-list"> - <li> - <li><a href="#s21">Background Research</a></li> - <li><a href="#s22">Stakeholder Analysis</a></li> - <li><a href="#s23">Public Survey</a></li> - </li></ul> - </li> - <li> - <input id="group-3" type="checkbox" hidden /> - <label for="group-3"><span class="fa fa-angle-right"></span> Exploration</label> - <ul class="group-list"> - <li> - <li><a href="#s31">The Interview of Prof. Ma</a></li> - <li><a href="#s32">The Interview of Prof. Ding</a></li> - <li><a href="#s33">AI Model and Paradigm</a></li> - <li><a href="#s34">Data Source</a></li> - <li><a href="#s35">Yeast Expression System</a></li> - </li></ul> - </li> - <li> - <input id="group-4" type="checkbox" hidden /> - <label for="group-4"><span class="fa fa-angle-right"></span> Application</label> - <ul class="group-list"> - <li> - <li><a href="#s41">The Visit to Nanjing Yiweisen Biotechnology Co., LTD</a></li> - <li><a href="#s42">The visit to Carbon Silicon Institute of Artificial Intelligence Biomedical Research</a></li> - <li><a href="#s43">Enhance LTB Expression</a></li> - <li><a href="#s44">Feedback</a></li> - </li></ul> - <li> - <input id="group-5" type="checkbox" hidden /> - <a href="#s5"><span class="fa fa-angle-right"></span> Ethic </a> - </li> - <li> - <input id="group-6" type="checkbox" hidden /> - <a href="#s6"><span class="fa fa-angle-right"></span> Environment </a> - </li> - <li> - <input id="group-7" type="checkbox" hidden /> - <a href="#s7"><span class="fa fa-angle-right"></span> Entrepreneurship </a> - </li> - </ul> - </li> - - - - </ul> - </nav> - </header> - </div> + <!-- 侧导航æ --> + <div class="col-3 left-nav-container" id="myScrollspy"> + <header class="left-nav" role="banner"> + <nav class="nav" role="navigation"> + <ul class="nav__list"> + <li> + <input id="group-1" type="checkbox" hidden /> + <a href="#s1"><span class="fa fa-angle-right"></span> Overview </a> + </li> + + <li> + <input id="group-2" type="checkbox" hidden /> + <a href="#s2" + ><span class="fa fa-angle-right"></span> School Fair Booth at + Nanjing University + </a> + <ul class="group-list"></ul> + </li> + + <li> + <input id="group-3" type="checkbox" hidden /> + <a href="#s3" + ><span class="fa fa-angle-right"></span> Publicity Lecture at + Nanjing University + </a> + + <ul class="group-list"></ul> + </li> + + <li> + <input id="group-4" type="checkbox" hidden /> + <a href="#s4" + ><span class="fa fa-angle-right"></span> Volunteer Teaching in + Shuangbai County, Yunnan province + </a> + + <ul class="group-list"></ul> + </li> + + <li> + <input id="group-5" type="checkbox" hidden /> + <a href="#s5" + ><span class="fa fa-angle-right"></span> "SynbioRainbow" Picture + book popular science activity + </a> + + <ul class="group-list"></ul> + </li> + + <li> + <input id="group-6" type="checkbox" hidden /> + <a href="#s6" + ><span class="fa fa-angle-right"></span> Ethics and safety + promotion: Debate Competition + </a> + + <ul class="group-list"></ul> + </li> + + <li> + <input id="group-7" type="checkbox" hidden /> + <a href="#s7" + ><span class="fa fa-angle-right"></span> Stage Playabout the + discovery of DNA + </a> + + <ul class="group-list"></ul> + </li> + + <li> + <input id="group-8" type="checkbox" hidden /> + <a href="#s8" + ><span class="fa fa-angle-right"></span> Spread ideas to + public:Popular Science Posts in WeChat Official Account + </a> + + <ul class="group-list"></ul> + </li> + </ul> + </nav> + </header> + </div> -<div class="col-9" style="padding-left: 5%;padding-right: 5%;"> + <div class="col-9" style="padding-left: 5%; padding-right: 5%"> <div style=" width: 100%; height: 100%; @@ -125,369 +299,708 @@ INTEGRATED HP margin-top:60px; border-radius: 15px; "> -<div class="dahe"> -<div class="dabiaotihe" id="s1">Overview</div> -<div style="text-align: center;"><img src="https://static.igem.wiki/teams/4815/wiki/devider.png"></div> -<div class="wenbenkuang"> -<div class="wenbenkuang">NJU-China devotes ourselves to creating an easy-to-use AI model and aparadigm -specifically for synthetic biology research, and then proposes new solutions to the challenge of applying -Artificial Intelligence broadly into synthetic biology. In the Integrated Human Practice page, we show how we -have carefully considered whether our project is responsible and good for the world throughout the whole -lifecycle.During the process, we address both how our project responds to such considerations and how our -proposed solution is implemented responsibly and reflectively.<a style="font-weight: bolder">The public survey</a> gave us an overall picture of -the topic we focus.Through communications with <a style="font-weight: bolder">scholars</a>, we clarified the specific problem to work on and -obtained professional guidance and opinionsfor the design and implementation. We also got inspiration from -<a style="font-weight: bolder">enterprises</a> to take application scenarios, customer needs and expert knowledge on feasibility into -consideration, and we are cheerful to see our model is successfully utilized in their production and -brings benefits. Thanks to these professionals in different fields, our project manages to open a new window -for the future of synthetic biology and gratifying progress to the development of the society.</div> -<div class="dahe"> -<div class="dabiaotihe">Topic Research</div> -<div style="text-align: center;"><img src="https://static.igem.wiki/teams/4815/wiki/devider.png"></div> -<div class="wenbenkuang"> -<p class="xiaobiaoti" id="s21">1. Background Research</p> -<p>Leveraging its immense computational power and intelligent algorithms, AI provides researchers with -unprecedented insights. AI can handle vast amounts of biological data, such as genomes and protein -interaction networks, accelerating drug development and disease diagnosis. The impact is staggering, -with AI speeding up <a style="font-weight: bolder">gene identification and analysis</a> by at least <a style="font-weight: bolder">100 times</a>. In protein folding -prediction, AI achieves an accuracy rate of 90%, greatly reducing the time and resources required -compared to traditional methods. Additionally, AI excels in medical imaging diagnostics, with an -impressive <a style="font-weight: bolder">96%</a> accuracy in breast cancer detection, surpassing human doctors' assessment -capabilities. These remarkable numbers highlight the enormous potential of AI in biology, -revolutionizing medical research and healthcare management, and make our team to think, how can AI -be used generally for synthetic biology?</p> -<p class="xiaobiaoti" id="s22">2. Stakeholder Analysis</p> -<p>We hope to identify the problem together with potential stakeholders, and screen the initial idea -with them. Therefore, our team primarily listed all the actors who could be relevant to our project -in different fields by brainstorming, and determined the order of interaction in order to plan and -design our projects <a style="font-weight: bolder">from the shallower to the deeper</a>.</p> -<img src="https://static.igem.wiki/teams/4815/wiki/ihp/ihp1.png" width="70%" class="imgz"> -<p></p> -<p>Based on the spiral line, we engaged with our stakeholders step by step, and gradually constructed -and improved our project design according to their suggestions and feedback. The process of the -communications and their impact on us will be shown in detail below. At the same time, as clarifying -exactly what project tends to do, we were continuously <a style="font-weight: bolder">adding and refiningour stakeholders list</a> and -manage them through a <a style="font-weight: bolder">power-interest matrix</a>, which helps to prioritize the values of the most -relevant stakeholders. All stakeholders are grouped based on Power (their ability to influence our -project and our strategy) and Interest (how interested they are in our project succeeding). For high -power, high interested group, we <a style="font-weight: bolder">fully engage with them</a> mainly, through discussing all the choices we -make and the progress we book with our project. We also consideredother stakeholdersin respective -ways, and contact them when we require expertise on a specific topic.</p> -<img src="https://static.igem.wiki/teams/4815/wiki/ihp/ihp2.png" width="70%" class="imgz"> -<p class="xiaobiaoti" id="s23">3. Public Survey</p> -<p>Tofully understand the real needs of society and create new value in a targeted manner, public -opinion is very essential, which will determine whether our project can actually benefit society and -what we are supposed to focus on.Therefore, before implementing new technology, we conducted -extensive public questionnaire survey and detailed analyses.In the past year, we have collected <a style="font-weight: bolder">265 -questionnaires</a> from all over the China, covering different kinds of educational background and -occupation, which ensures the universality of our investigation.</p> -<p>Given that the topic of AI for synthetic biology is highly specialized, our questionnaire was divided -into three parts.In the first part we’d like to find out <a style="font-weight: bolder">the public’s awareness and attitude towards -AI application in work and daily life.The results show that about 28% of people never use AI in -daily life and only 7% of them use AI at a high frequency. The reason why some of them <a style="font-weight: bolder">never use AI -or barely use AI</a> including the high threshold for the use of AI, concerns that AI will not meet -individual needs, invade personal privacy or provide false information or there is no need to use -AI.</p> -<img src="https://static.igem.wiki/teams/4815/wiki/ihp/ihp3.png" width="70%" class="imgz"> -<p class="tuzhu">Figure 1. Frequency of using AI in daily life</p> -<br> -<img src="https://static.igem.wiki/teams/4815/wiki/ihp/ihp4.png" width="70%" class="imgz"> -<p class="tuzhu">Figure 2. Reasons for never or less use of AI</p> -<p>When asking about the level of mastery of AI technology, 44% of people only use AI as a tool and 17% -of them know about the principle of AI, which shows that <a style="font-weight: bolder">public’s understanding of AI is very -shallow</a>. Based on the situation, we asked respondents about the obstacles to learning AI, about 60% -of them agreed that it is hard to find AI learning resources and tool resources, and learning AI is -difficult which we need to invest a lot of time in. </p> -<img src="https://static.igem.wiki/teams/4815/wiki/ihp/ihp5.png" width="70%" class="imgz"> -<br> -<p class="tuzhu">Figure 3. Mastery degree of artificial intelligence</p> -<br> -<img src="https://static.igem.wiki/teams/4815/wiki/ihp/ihp6.png" width="70%" class="imgz"> -<p class="tuzhu">Figure 4. Obstacles of learning AI</p> -<p>These results show that <a style="font-weight: bolder">the application of AI is still relatively limited</a>, and further research about -AI technology is needed to effectively solve problems in specific fields, and we believe this is -also true in the field of synthetic biology. In addition, <a style="font-weight: bolder">the high difficulty of professional -knowledge</a> limits people's further study of the application of AI in specific fields, which also -reminds us that it is necessary and helpful to carry out popular science and education activities -about AI for synthetic biology to better promote them to the public.</p> -<p>Then we asked users and developers of AI tools respectively that which aspect of AI they will focus -on. About 70% of them have the request of accuracy, 61% of them pursue ease operation of AI and -about 50% of them expect AI to have data privacy and fast processing speed, which shows that if AI -want to be widespread, it must both to be <a style="font-weight: bolder">accurate and easy to understand</a>, just like web page -technology. Developers concentrated most on the <a style="font-weight: bolder">efficiency and accuracy</a>, as well as their <a style="font-weight: bolder">ability to -transfer to multiple problems</a>, which provides a guidance on our AI model design.</p> -<img src="https://static.igem.wiki/teams/4815/wiki/ihp/ihp7.png" class="imgz" width="70%"> -<p class="tuzhu">Figure 5. Focus as a user on aspects of AI models or algorithms</p> -<br> -<img src="https://static.igem.wiki/teams/4815/wiki/ihp/ihp8.png" class="imgz" width="70%"> -<p class="tuzhu">Figure 6. Focus as a developer on aspects of AI models or algorithms</p> -<p>In terms of the function of AI, we found it widely used in various aspects, and nearly <a style="font-weight: bolder">92%</a> of people -believe AI will have <a style="font-weight: bolder">positive effect</a> on the fields they work in. However, it has relatively <a style="font-weight: bolder">few -applications in scientific research</a>, thus we believe it is our value to improve the new application -of AI technology in synthetic biology research.</p> -<img src="https://static.igem.wiki/teams/4815/wiki/ihp/ihp9.png" width="50%" class="imgz"> -<p class="tuzhu">Figure 7. Goals of using AI</p> -<br> -<img src="https://static.igem.wiki/teams/4815/wiki/ihp/ihp10.png" width="70%" class="imgz"> -<p class="tuzhu">Figure 8. The impact AI have on the field you work in</p> -<p>In the next part, we aimed to further explore the public perceptions of the promise of AI for -synthetic biology. We were upset to find that <a style="font-weight: bolder">half</a> the respondents have <a style="font-weight: bolder">never heard of synthetic biology</a> -before, and over <a style="font-weight: bolder">16%</a> of people who know synthetic biology still have <a style="font-weight: bolder">little knowledge about the -application of AI in the field</a>. Obviously, it is necessary for us to introduce and propagate AI for -synthetic biology to the public in a more efficient and suitable way.</p> -<img src="https://static.igem.wiki/teams/4815/wiki/ihp/ihp11.png" width="70%" class="imgz"> -<p class="tuzhu">Figure 9. Degree of understanding of synthetic biology</p> -<br> -<img src="https://static.igem.wiki/teams/4815/wiki/ihp/ihp12.png" width="70%" class="imgz"> -<p class="tuzhu">Figure 10. The extent to which AI is used in the field of synthetic biology</p> -<p>Above all, for those who know the application of AI in the field of synthetic biology, it’s generally -believed that <a style="font-weight: bolder">the application of artificial intelligence in the synthetic biology industry has -bright prospects</a>. As we considered about the specific convenience or revolution that AI can bring to -biology, <a style="font-weight: bolder">improving efficiency and shortening research cycle</a> won the highest score among the few -options we have listed. For the current challenges or constraints which limits the development of AI -for synthetic biology, nearly 70% of them agreed that it lacks uniform standards and specifications -(e.g. data formats, sharing platforms, etc.). About 60% of them believe that the scarce of AI -expertise and skills in biological researchers and lack of synthetic biology data with high quality -and quantity are also main problems.</p> -<img src="https://static.igem.wiki/teams/4815/wiki/ihp/ihp13.png" width="70%" class="imgz"> -<p class="tuzhu">Figure 11. The extent to which AI can help synthetic biology</p> -<br> -<img src="https://static.igem.wiki/teams/4815/wiki/ihp/ihp14.png" width="40%" class="imgz"> -<p class="tuzhu">Figure 12. the application prospect of AI in synthetic biologycompared with other -industries(Assuming an average score of 5) </p> -<br> -<img src="https://static.igem.wiki/teams/4815/wiki/ihp/ihp15.png" width="60%" class="imgz"> -<p class="tuzhu">Figure 13. The importance of the different changes that AI bring to synthetic biology</p> -<br> -<img src="https://static.igem.wiki/teams/4815/wiki/ihp/ihp16.png" width="100%" class="imgz"> -<p class="tuzhu">Figure 14. Challenges of the application of AIin synthetic biology</p> -<p>After anextensive literature research, we chose to <a style="font-weight: bolder">pre-train the AI on existing models and adapt the -parameters to a specific problem</a>. We asked the public for their opinion and were stimulated to find -that most people think this approach <a style="font-weight: bolder">>makes practical sense</a.</p> -<img src="https://static.igem.wiki/teams/4815/wiki/ihp/ihp17.png" width="45%"> -<img src="https://static.igem.wiki/teams/4815/wiki/ihp/ihp18.png" width="45%"> -<p class="tuzhu">Figure 15. (left)the practical value of pre-train and fine-tune AI based on an existing -model(compared with building an AI model from scratch) </p> -<p class="tuzhu">Figure 16. (right)The meaning of applying transfer learning to solvespecific problems in -synthetic biology</p> -<p>In a word, we are glad to find that the public is optimistic about the application of artificial -intelligence in the field of synthetic biology, which gives us great motivation on finding more -possibilities of artificial intelligence applied to synthetic biology on the basis of predecessors. -The survey also provides new ideas on our model design and education activities to improve public -understanding.</p> -</div> -</div> -<div class="dahe"> -<div class="dabiaotihe">Exploration</div> -<div style="text-align: center;"><img src="https://static.igem.wiki/teams/4815/wiki/devider.png"></div> -<div class="wenbenkuang"> -<p class="xiaobiaoti" id="s31">1. The Interview of Prof. Ma</p> -<img src="https://static.igem.wiki/teams/4815/wiki/ihp/ihp19.png" class="tiansuohao2" style="width: 30%;"> -<p>Professor Ma Lijia is currently working at Westlake University, focusing on genomics and systems -biology, and has in-depth research on data mining and AI applications in regulatory sequences.</p> -<p>In the application of biology, what direction is the most significant problem of data limitation? -Keeping this question in mind, we went to Westlake University to have an in-depth exchange with -Professor Ma Lijia. "The regulatory sequence is critical. In fact, 90% of the human genome is -regulatory sequences, and our research group is currently working on the characterization of -regulatory sequences. In my opinion, specific regulatory sequences, such as promoter sequences, are -currently suffering the most data-scarcity, which is mainly limited by experimental techniques for -selecting and characterizing." A crucial keyword in synthetic biology is <a style="font-weight: bolder">expression</a>, which is also -closely related to <a style="font-weight: bolder">regulatory sequences</a>. Building on the important professional insights provided by -Professor Ma Lijia, we finally set our sights on regulating the most direct and ubiquitous -functional regulatory sequences—<a style="font-weight: bolder">promoters</a>, and put it as the specific direction of our project.</p> -<div> -<p class="xiaobiaoti" id="s32">2. The Interview of Prof. Ding</p> -<p>During our communication and promotion efforts with various stakeholders, we have encountered -some <a style="font-weight: bolder">skepticism</a>. Professor Bi Ding from Fudan University questioned the significance of our -project during a discussion, stating that the prevalent use of active learning</a> in the field of -biology and AI suggests that data may not be as limiting as we claim. This has prompted us to -further contemplate the significance of our project and how to convince more people. We have -further confirmed that <a style="font-weight: bolder">the availability of data is not only limited by technical development but -also constrained by costs</a>. In fact, there are instances where obtaining a sufficient amount of -high-quality data is not impossible, but the corresponding high economic and time costs cannot -be justified by the expected output. </p> -<img src="https://static.igem.wiki/teams/4815/wiki/ihp/ihp20.jpg" width="50%" class="imgz"> -<p></p> -<p class="xiaobiaoti" id="s33">3. AI Model and Paradigm</p> -<p>After determining our project direction, choosing the appropriate large-scale model is the most -important problem to consider. We went to Nanjing GenScript Biotechnology Company to conduct an -exchange interview with Sheng Xia, a senior scientist in bioinformatics. Mr. Sheng Xia has been -engaged in biological data mining and analysis for a long time, and has quite mature -professional experience in AI application. After understanding the relevant situation of our -project, Sheng Xia believes that what we need to deal with is <a style="font-weight: bolder">genetic data</a>, which is generally -applicable to language models, the most popular of which are <a style="font-weight: bolder">GPT and Bert models</a>. </p> -<img src="https://static.igem.wiki/teams/4815/wiki/ihp/ihp21.jpg" width="70%" class="imgz"> -<p></p> -<p class="xiaobiaoti" id="s34">4. Data Source</p> -<p>When conducting preliminary dry experiment training with selected 30,000,000-scale dataset, -continuous attempts and optimization of parameters could not obtain good results, and the focus -was on the characteristics of the training data through inter-team communication. The students -of the dry experiment found that the result plotting showed that there was a large number of -data in the complete data whose actual intensity deviated from the reasonable experimental -results, and after communicating with the author of the literature, that is, the data -contributor, and learning his team's method to screen the data, the effect increased -significantly. Since then, we have <a style="font-weight: bolder">maintained communication with the author team</a>, which has -played an important role in promoting the optimization and improvement of our dry lab result. -</p> -<img src="https://static.igem.wiki/teams/4815/wiki/ihp22-24.png" width="70%" class="imgz"> -<p></p> -<p class="xiaobiaoti" id="s35">5. Yeast Expression System</p> -<p>After deciding to use yeast as our expression system, we conducted an exchange interview with -Professor Sheng Xia at Nanjing GenScript Biotechnology Company. Professor Sheng agreed with our -choice and mentioned that <a style="font-weight: bolder">yeast has a slower cultivation speed and it is challenging to achieve -high expression levels</a> compared to some commonly used engineered bacteria in industrial -fermentation processes. He emphasized that if our project could provide a solution to this -issue, it would be extremely helpful. Professor Sheng further advised us that if we plan to -express proteins from prokaryotes or viruses in yeast, it is advisable to optimize the yeast -source. He provided us with <a style="font-weight: bolder">a web platform from GenScript for yeast sequence optimization</a>, which -played a crucial role in facilitating our subsequent project.</p> -<img src="https://static.igem.wiki/teams/4815/wiki/ihp/ihp25.jpg" width="70%" class="imgz"> -<p></p> -<p>The next challenge in protein expression within yeast is how to separate, purify, and quantify -the proteins. In fact, due to the cell wall of yeast, it is relatively difficult to separate and -purify the expressed proteins. Through discussions with Dr. Yiling Hu, a postdoctoral researcher -at the School of Life Sciences, Nanjing University, who specializes in yeast cultivation, Dr. Hu -provided us with a feasible solution. It involves <a style="font-weight: bolder">dding a His-tag to the protein or fusing the -protein with a fluorescent protein</a>a to enable purification and quantification through Western -blot analysis after yeast lysis. Dr. Hu further mentioned that it is worth noting that there is -no precedent for detecting His-tag in yeast, so if our project can <a style="font-weight: bolder">detect His-tag in the yeast -lysate</a>, it would be a significant advancement.</p> -<p>In the process of further exploring our project, we also keep close contact with other iGEM -teams, and shared the progress and challenges with each other. Through these collaborations and -partnerships, we get peer support and review, enhance creativity and advanced our project. For -more information, please click the Partnership link to see how the interaction with other teams -has influenced our project.</p> -</div> -</div> -<div class="dahe"> -<div class="dabiaotihe">Application</div> -<div style="text-align: center;"><img src="https://static.igem.wiki/teams/4815/wiki/devider.png"></div> -<div class="wenbenkuang"> -<p class="xiaobiaoti" id="s41">1. The Visit to Nanjing Yiweisen Biotechnology Co., LTD</p> -<p>After gaining recognition from relevant researchers, we wanted to further explore the industrial significance of our project. We visited Nanjing Yiweisen Biotechnology Co. and had a discussion with Professor Zhongchang Wang. Professor Wang established Nanjing Yiwesen Biotechnology Co., Ltd as the main founder. The company is a high-tech enterprise based on artificial intelligence technology in the field of synthetic biology, incubated by Artificial Intelligence Biomedical Research of Nanjing University. It primarily focuses on microbial genetic modification and downstream industrial applications, researching and developing high-value natural active substances for use in sectors such as food, cosmetics, plant protection, and biopharmaceuticals. Professor Wang acknowledged the significance of our project and pointed out that the current traditional screening methods for selecting target strains from a large number of randomly mutated strains are often costly, time-consuming, and limited in scope. The application of artificial intelligence in synthetic biology has greatly improved the accuracy of mutagenic strains and reduced the cost of screening. Additionally, he provided us with some potential application directions from a business perspective.</p> -<img src="https://static.igem.wiki/teams/4815/wiki/ihp/ihp26.jpg" width="70%" class="imgz"> -<p></p> -<img src="https://static.igem.wiki/teams/4815/wiki/ihp/ihp27.jpg" width="70%" class="imgz"> -<p></p> -<p class="xiaobiaoti" id="s42">2. The visit to Carbon Silicon Institute of Artificial Intelligence Biomedical -Research</p> -<p>We hoped that our project could provide solutions to the most realistic and important human -health or environmental issues, demonstrating responsibility and a positive impact on the world -throughout its entire lifecycle. During our visit and discussions, a possibility that had never -been considered before caught our attention—<a style="font-weight: bolder">the mucosal vaccine</a>. </p> -<img src="https://static.igem.wiki/teams/4815/wiki/ihp/ihp28.jpg" width="70%" class="imgz"> -<p></p> -<p>Professor Chao Yan, from the institute, has extensive experience in drug development and provided -profound insights into using AI for precision drug discovery. He first acknowledged that the -pre-training + fine-tuning model we proposed can not only be applied to synthetic biology but -also to <a style="font-weight: bolder">predictive drug development</a>. He further emphasized that data limitations are not just -technical barriers but are greatly influenced by the spatiotemporal factors of <a style="font-weight: bolder">data generation</a>, -which have high heterogeneity and are difficult to utilize. As an example, he mentioned that AI -image recognition models are trained on datasets in the order of billions, while in the field of -biology, measurements are typically limited to dozens of patients at a time, with only a few -dozen data points per dimension. The disparity between the two is significant. Additionally, he -pointed out the issue of the dimensionality of biological data. Biological data often have <a style="font-weight: bolder">a high -number of dimensions but a low sample size</a>, which is not conducive to leveraging the strengths -of AI. For example, AI excels at image processing with low dimensionality and large sample -sizes, where there are data points in each dimension, resulting in better predictive models. -However, in biology, such as genomics, each gene represents a dimension, but the samples for -each gene are relatively scarce.</p> -<img src="https://static.igem.wiki/teams/4815/wiki/ihp/ihp29.jpg" width="70%" class="imgz"> -<p></p> -<p>Professor Yan's interview deepened our understanding of the significance and value of our project -and made us more fully aware of the multiple aspects of data limitations. Additionally, we -received affirmation and support from him regarding our plans for mucosal vaccine production. -</p> -<img src="https://static.igem.wiki/teams/4815/wiki/ihp/ihp30.jpg" width="70%" class="imgz"> -<p></p> -<p class="xiaobiaoti" id="s43">3. Enhance LTB Expression</p> -<p>After receiving such affirmation, we needed to find suitable mucosal vaccine-related proteins as -the target product for our project. Our attention turned to LTB (Heat-Labile Enterotoxin B -subunit). Through literature review and understanding its production and functions, we -discovered that LTB plays a crucial role in mucosal vaccines and indeed faces expression -limitations. If our project can address the challenges associated with LTB expression, it would -greatly promote the production and dissemination of mucosal vaccines.</p> -<p class="xiaobiaoti" id="s44">4. Feedback</p> -<p>After formulating such a concept, we further engaged in discussions with the aforementioned -researchers. Many of them raised concerns about the <a style="font-weight: bolder">inconsistency between our project's training -data and the downstream product</a>. Specifically, we obtained data from fluorescent protein -expression for training, but intended to use the trained sequences for the production of a -different protein. As they pointed out, the strength of the promoter is highly likely to be -influenced by downstream genes. This prompted us to consider <a style="font-weight: bolder">providing feedback from wet lab -experiments</a>, specifically the expression data obtained for LTB, to the AI involved in dry lab -experiments. This feedback would facilitate the development of a more targeted model for LTB -expression.</p> -</div> -</div> -<div class="dahe"> -<div class="dabiaotihe" id="s5">Ethic</div> -<div style="text-align: center;"><img src="https://static.igem.wiki/teams/4815/wiki/devider.png"></div> -<div class="wenbenkuang"> -<p>We believe that the use and training of AI models must adhere to <a style="font-weight: bolder">ethical guidelines for data</a>, -meaning that only <a style="font-weight: bolder">publicly available datasets</a> should be used for training. It is important to -respect the owners' rights and avoid using private data without permission. When it comes to the -pre-training and fine-tuning paradigms, copyright issues pertaining to pre-trained models must -be taken into consideration. It is advisable to utilize <a style="font-weight: bolder">publicly available pre-trained models</a>. -Moreover, during the AI for Synbio Seminar, we engaged in discussions with other teams and -reached a consensus that <a style="font-weight: bolder">data transparency and sharing of AI model algorithms</a> are essential, -particularly for our iGEM team. Other teams should also ensure that they make use of publicly -available datasets when collecting data.</p> -<p>In addition, one of the primary concerns related to AI safety is that the training of AI models -should be focused on tasks that are beneficial to humans and compliant with legal regulations -within that specific domain.</p> -</div> -</div> -<div class="dahe"> -<div class="dabiaotihe" id="s6">Environment</div> -<div style="text-align: center;"><img src="https://static.igem.wiki/teams/4815/wiki/devider.png"></div> -<div class="wenbenkuang"> -<p>After achieving some experimental results, we engaged in discussions with AI pharmaceutical -companies to seek guidance on the subsequent industrialization process. They recognized the -potential utility of our model in industrial production but also highlighted certain -considerations. Firstly, for yeast production and larger-scale experiments, it is crucial to pay -special attention to <a style="font-weight: bolder">preventing biological contamination</a>. Secondly, due to the high level of -pollution associated with yeast production, <a style="font-weight: bolder">wastewater treatment</a> should be prioritized. In fact, -the production of <a style="font-weight: bolder">1 ton</a> of dry yeast can generate <a style="font-weight: bolder">150 tons</a> of wastewater. Building upon these -considerations, Zhang Xiaotong, the supervisor of the wet lab experiments, guided the innovative -development of a <a style="font-weight: bolder">biological wastewater treatment device</a> (Patent No: CN215886592U) and a -<a style="font-weight: bolder">bioreactor</a> to prevent contamination from miscellaneous bacteria (Patent No: CN216141527U). These -developments have prepared us for the industrial production phase of our project. </p> -<img src="https://static.igem.wiki/teams/4815/wiki/ihp31.png" width="50%" class="imgz"> -</div> -</div> -<div class="dahe"> - <div class="dabiaotihe" id="s7">Entrepreneurship</div> - <div style="text-align: center;"><img src="https://static.igem.wiki/teams/4815/wiki/devider.png"></div> - <div class="wenbenkuang"> - <p>Based on Pymaker, we plan to develop <a style="font-weight: bolder">a software for designing cis-regulatory elements in yeast promoter regions based on deep learning</a>. We have already reached intentions for collaboration and signed agreements with Nanjing LianDu Biological Technology Co., Ltd. and Nanjing YiWeiSen Biological Technology Co., Ltd. Through the collaboration, our research results and developed models can be used to <a style="font-weight: bolder">guide the design and optimization of yeast fermentation production lines</a>, significantly reducing the cost of industrial production screening and validation, and ultimately bringing high-quality products to the market. </p> - <img - src="https://static.igem.wiki/teams/4815/wiki/contribution/liandu1.jpg" - width="49%" - alt="" - /> - <img - src="https://static.igem.wiki/teams/4815/wiki/contribution/liandu2.jpg" - width="49%" - alt="" - /> - <img - src="https://static.igem.wiki/teams/4815/wiki/contribution/yiwei1.jpg"" - width="49%" - alt="" - /> - <img - src="https://static.igem.wiki/teams/4815/wiki/contribution/liandu2.jpg" - width="49%" - alt="" - /> -</div> -</div> -</div> -</div> -</div> -</div> -</div> -</div> -</div> + <div class="dahe"> + <div class="wenbenkuang"> + <div class="dabiaotihe" id="s1">Overview</div> + <div style="text-align: center"> + <img src="https://static.igem.wiki/teams/4815/wiki/devider.png" /> + </div> + <p> + In recent years, advances in <a style="font-weight: bolder">synthetic biology and artificial intelligence</a> have brought about significant changes in people's lives, which arouses great public interest. However, due to the high threshold of professional knowledge and the lack of access to learning resources, it is difficult for people to learn more about the crossing field of synthetic biology and AI. Therefore, we carry out a series of science popularization activities to impart related knowledge to the public. In order to maximize the influence of our activities, we deeply reflected on the target audience, form and content of the activities before conducting communication and education, aiming to convey the messages to various groups in the most appropriate way. To use an ancient Chinese saying, we hope to <a style="font-weight: bolder">spread knowledge according to individual's characteristics</a>. Therefore, we designed a series of online and offline popular science activities after brainstorming, with a wide range of diverse forms including forms, with a wide range of <a style="font-weight: bolder">lectures, teaching, debate competitions, stage plays, booth displays, hand drawn and so on</a>. + </p> + <p> + To achieve the above objectives, we have created the following table to show our <a style="font-weight: bolder">offline activity</a> plan: + </p> + <img + class="imgz" + src="https://static.igem.wiki/teams/4815/wiki/education-table.png" + width="80%" + /> + <p> + In addition, we have also utilized WeChat official account to publish + a series of popular science posts, with the intention of broadening + the reach of our publicity efforts and introducing synthetic biology + to a wider audience. + </p> + <p> + Concurrently, we have established the following process to serve as a + guide for all our educational activities: + </p> + <img + class="imgz" + src="https://static.igem.wiki/teams/4815/wiki/edchain.png" + width="40%" + /> + </div> + </div> + + <div class="dahe"> + <div class="dabiaotihe" id="s2"> + School Fair Booth at Nanjing University + </div> + <div style="text-align: center"> + <img src="https://static.igem.wiki/teams/4815/wiki/devider.png" /> + </div> + <div class="wenbenkuang"> + <p class="xiaobiaoti" id="s21">Target group</p> + <p>Nanjing University students</p> + </div> + + <div class="wenbenkuang" style="position: relative"> + <p class="xiaobiaoti" id="s31">Why</p> + <p class="tiansuohao2" style="width: 90%"> + <img + class="tiansuohao4" + style="width: 40%" + style="padding: 0px" + src="https://static.igem.wiki/teams/4815/wiki/ed1.png" + />Booth is a platform that enables interactive education, actively + engaging participants in the dissemination of knowledge and making + complex topics such as synthetic biology and AI more accessible. By + engaging in gaming activities, participants gain practical experience + with these concepts, which in turn enhances their comprehension and + retention. Games serve as stimuli for creativity and imagination, + prompting participants to apply their knowledge practically and engage + in problem-solving activities. This approach has the potential to + attract younger audiences, fostering interest and nurturing potential + talent in the fields of synthetic biology and AI. The provision of + real-time feedback during gaming activities contributes to + participants' learning and improvement process. Simultaneously, the + entertainment value of the games enhances participant engagement, + making it an enjoyable and effective method of promoting synthetic + biology and AI. + </p> + </div> + <div class="clear"></div> + <div class="wenbenkuang"> + <p class="xiaobiaoti" id="s41">Process</p> + <p> + On the evening of May 19, 2023, as a part of Nanjing University's + 121st anniversary celebration, the Anniversary School Fair took place + on the campus. NJU-China organized a diverse range of activities at + our booth, focused on AI and synthetic biologyto encourage + participation from students of all grades and disciplines. + </p> + <p> + The activities for the event comprised several components aimed at + educating students about synthetic biology and generating interest in + the field. These components included: + </p> + <p> + 1) Award-winning Quiz: This activity involves a quiz that tested + students' knowledge of the basics of synthetic biology and artificial + intelligence, providing an interactive learning experience. + </p> + <p> + 2) Creative Merchandise and Exquisite Posters: Pre-designed merchandise + with creative features related to synthetic biology, iGEM, and + NJU-China were prepared for distribution at the event. These items, + along with promotional posters, help create a visual representation of + the concepts and generate interest in the field. + </p> + <p> + 3) Imagination Doodles: This activity encourages students to express + their creativity by drawing patterns representing biology in a + graffiti book.It allows students to engage with the subject in a + creative and interactive way. + </p> + <img + width="28%" + class="imgl" + src="https://static.igem.wiki/teams/4815/wiki/ed2.jpg" + /> + + <img + width="41.6%" + class="imgr" + src="https://static.igem.wiki/teams/4815/wiki/ed3.jpg" + /> + <p> + After the activities, we conducted questionnaire survey to gauge + public awareness, interest, and opinions about synthetic biology, + iGEM, and our project, as well as get feedback on our science + popularization activities from participants. A total of 121 valid + questionnaires were collected, with 14.88% of the survey group + majoring in life sciences, 19.83% related to AI and computer science. + It can be seen that most students had little knowledge of synthetic + biology before participating in our activities, with more than half of + the population completely unaware and only 12.4% of the population + relatively aware. As for the iGEM Competition, there was even less + awareness of it among students. + </p> + <img + src="https://static.igem.wiki/teams/4815/wiki/ed4.png" + width="100%" + alt="" + /> + <p style="text-align: center"> + Figure 1 Overall Cognitive Degree of Synthetic Biology + </p> + <img + src="https://static.igem.wiki/teams/4815/wiki/ed5.png" + width="100%" + alt="" + /> + <p style="text-align: center"> + Figure 2 whether heard of iGEM Competition or not + </p> + <p> + We were delighted to find that after our promotion, most of the + participants were very interested in learning more about synthetic + biology, and has high expectations for the future of synthetic biology + combined with AI, scoring a high average of 4.23. It is believed that + AI will bring changes to synthetic biology in many aspects, such as + improving efficiency, shortening research cycles, and enhancing + product quality. + </p> + <img + src="https://static.igem.wiki/teams/4815/wiki/ed6.png" + width="100%" + alt="" + /> + <p style="text-align: center"> + Figure 3 Willingness to learn more about synthetic biology + </p> + <img + src="https://static.igem.wiki/teams/4815/wiki/ed7.png" + width="100%" + alt="" + /> + <p style="text-align: center"> + Figure 4 Opinions about the prospect of Synthetic Biology×AI(full + score is 5) + </p> + <p> + Through our publicity, many students expressed their willingness to + participate in IGEM and contribute to the solution of global issues + such as the environment and healthcare. + </p> + <img + src="https://static.igem.wiki/teams/4815/wiki/ed8.png" + width="100%" + alt="" + /> + + <p style="text-align: center"> + Figure 5 The convenience AI brings to synthetic biology + </p> + <img + src="https://static.igem.wiki/teams/4815/wiki/ed9.png" + width="100%" + alt="" + /> + <p style="text-align: center"> + Figure 6 Reasons to participate in the competition if possible + </p> + </div> + <div class="wenbenkuang"> + <p class="xiaobiaoti" id="s51">Learn</p> + <p> + At our booth, we not only serve as ambassadors but also offer detailed + explanations and introductions to classmates who may not be + well-versed in these fields. We have observed that the majority of + students display strong interest and curiosity towards the emerging + technologies of synthetic biology and AI that we have introduced. They + have expressed the view that opportunities to access relevant + knowledge often require a high level of professional expertise, such + as attending professional lectures, with limited availability of + science popularization materials covering basic concepts and + principles. We are pleased to see that our award-winning quiz, doodle, + and creative merchandise have proven to be effective methods, and + moving forward, we aim to incorporate more interactive and interesting + formats in our follow-up activities to further increase public + acceptance. + </p> + </div> + </div> + <div class="dahe"> + <div class="dabiaotihe" id="s3"> + Publicity Lecture at Nanjing University + </div> + <div style="text-align: center"> + <img src="https://static.igem.wiki/teams/4815/wiki/devider.png" /> + </div> + <div class="wenbenkuang"> + <p class="xiaobiaoti" id="s22">Target group</p> + <p>Nanjing University freshmen</p> + </div> -{% endblock %} \ No newline at end of file + <div class="wenbenkuang"> + <p class="xiaobiaoti" id="s32">Why</p> + <p> + The utilization of lectures as a method of science popularization can + effectively engage and resonate with individuals, particularly college + students, enabling them to comprehend our projects and gain a swift + and efficient understanding of synthetic biology. + </p> + </div> + <div class="wenbenkuang"> + <p class="xiaobiaoti" id="s42">Process</p> + <p> + In July, NJU China and the Red Cross Society of Nanjing University + jointly held the "Caring for Youth - Life and Health Education on + Campus" event, introducing students to the popular science knowledge + of synthetic biology related to the epidemic and vaccines, and + introducing the content of NJU China's project. Especially since most + of these students are majoring in biology or chemistry, we have + provided them with a detailed introduction to the IGEM competition, + hoping that they can also participate in the promotion of synthetic + biology. The lecture received a warm response from the students. Many + students have raised questions related to synthetic biology with our + team members and expressed their willingness to participate in iGEM. + </p> + <img + src="https://static.igem.wiki/teams/4815/wiki/ed10.jpg" + width="49%" + alt="" + /> + <img + src="https://static.igem.wiki/teams/4815/wiki/ed11.jpg" + width="49%" + alt="" + /> + </div> + <div class="wenbenkuang"> + <p class="xiaobiaoti" id="s52">Learn</p> + <p> + During our interactions with freshmen, we recognized the importance of + generating daring ideas and embracing the perspectives of various + stakeholders. The iGEM competition serves as a prominent platform that + fosters innovation and integration, enabling the realization of + numerous ideas that are beyond the scope of any single discipline. + Initially, we wholeheartedly dedicated ourselves to exploring + cutting-edge research achievements within the academic community, + inadvertently neglecting our own circumstances. However, through the + exchange, we have learned to shift our focus towards our immediate + surroundings and strive to create a model that is well-suited for + practical problem in synthetic biology. + </p> + <img + class="imgz" + src="https://static.igem.wiki/teams/4815/wiki/ed12.jpg" + width="50%" + alt="" + /> + </div> + </div> + <div class="dahe"> + <div class="dabiaotihe" id="s4"> + Volunteer Teaching in Shuangbai County, Yunnan province + </div> + <div style="text-align: center"> + <img src="https://static.igem.wiki/teams/4815/wiki/devider.png" /> + </div> + <div class="wenbenkuang"> + <p class="xiaobiaoti" id="s23">Target group</p> + <p> + First and third year students of Tuodian Middle School in Shuangbai + County, Chuxiong Prefecture, Yunnan Province + </p> + <p class="xiaobiaoti" id="s33">Why</p> + <p> + Teaching provides us with the opportunity to visit impoverished + regions and gain insights into the lives of our classmates. Moreover, + it allows us to develop a deeper understanding of the specific + knowledge they seek. Volunteer teaching encompasses a wide range of + formats, enabling us to not only provide indoor instruction but also + engage in outdoor experiential learning. + </p> + <p class="xiaobiaoti" id="s43">Process</p> + <p> + From July 27th to July 31st, NJU China collaborated with the Nanyue + Rural Teaching Team of Nanjing University to carry out teaching + support activities at Tuodian Middle School in Shuangbai County, + Chuxiong Prefecture, Yunnan Province. After interacting with the + children, we found that their understanding of biology and artificial + intelligence was limited, and many children had never heard of + synthetic biology. In view of this, we have launched a series of + scientific courses to popularize the benefits of artificial + intelligence, synthetic biology, and the combination of artificial + intelligence and synthetic biology in our daily lives. We hope to open + up new knowledge and fields for them, and stimulate their independent + thinking, interest, and creativity. + </p> + <img + class="imgz" + src="https://static.igem.wiki/teams/4815/wiki/ed13.jpg" + width="60%" + /> + <p> + Our team's teaching in this program primarily targeted first-year and + third-year junior high school students and was divided into three + sessions. Inthe first session, we provided a brief introduction to + artificial intelligence (AI) and allowed students to experience AI + drawing and ChatGPT. In the second session, we discussed "AI and + Phenological Observation" and led students to identify various plants + on campus with the help of AI.Finally, we shared basic knowledge and + application of synthetic biology and its intersection with AI. + </p> + <img + style="position: relative; left: 30%; transform: translateX(-50%)" + src="https://static.igem.wiki/teams/4815/wiki/ed14.jpg" + width="28%" + /> + <img + style="position: relative; left: 35%; transform: translateX(-50%)" + src="https://static.igem.wiki/teams/4815/wiki/ed15.jpg" + width="37%" + /> + <p> + We got cheerful feedback of our courses from students. The children + were still excited and wanted to continue experimenting with AI tools + after class. They were also very involved in participating in + phenological observation and offered to go to the lusher parts of the + campus for further observation and identification. We were surprised + to receive dandelions from them, which symbolized their yearning for + the wider world and a better life. During the interactions, we also + presented various cultural and creative products we designed about + synthetic biology to the students. + </p> + <img + style="position: relative; left: 30%; transform: translateX(-50%)" + src="https://static.igem.wiki/teams/4815/wiki/ed16.jpg" + width="38%" + /> + <img + style="position: relative; left: 30%; transform: translateX(-50%)" + src="https://static.igem.wiki/teams/4815/wiki/ed17.jpg" + width="38%" + /> + <p class="xiaobiaoti" id="s53">Learn</p> + <p> + In the process of teaching support, not only do we bring some new + knowledge to our classmates, but it is also the process of students + giving us feedback on their ideas. After introducing our project, we + were amazed by the students' talents. They not only raised pertinent + questions related to the project itself but also highlighted ethical + and safety concerns associated with it. Prior to this, we had not + extensively explored the intersection between AI and synthetic + biology. Consequently, we have now paid more attention towards + addressing these safety and ethical issues. + </p> + </div> + </div> + <div class="dahe"> + <div class="dabiaotihe" id="s5"> + "SynbioRainbow" Picture book popular science activity + </div> + <div style="text-align: center"> + <img src="https://static.igem.wiki/teams/4815/wiki/devider.png" /> + </div> + <div class="wenbenkuang"> + <p class="xiaobiaoti" id="s24">Target group</p> + <p> + Children aged 6-12 with Asperger's Syndrome Asperger's Syndrome (AS) + falls under the Autism Spectrum Disorder (ASD) or Pervasive + Developmental Disorder (PPD) umbrella, characterized by social + interaction difficulties, restricted interests, repetitive behaviors, + and attention deficits similar to autism. AS children are like free + spirits, wandering in their own imaginative worlds. + </p> + <p class="xiaobiaoti" id="s34">Why</p> + <p> + The utilization of picture books for disseminating knowledge to AS + children offers numerous distinctive benefits and advantages. + Precisely, picture books present information through visuals, such as + images and illustrations, thus assisting AS children in better + comprehending knowledge due to their heightened visual sensitivity. + Moreover, pictures often possess well-defined narrative structures, + contributing to the effective organization and comprehension of + information for them. + </p> + <p class="xiaobiaoti" id="s44">Process</p> + <p> + Content: Introduction to Biology and Synthetic Biology Considering the + young age, limited prior knowledge, and challenges in maintaining + focus among the target audience, we adopted a logical progression, + starting from simpler concepts and gradually delving into biology, + then synthetic biology. We adjusted the content based on feedback from + AS children. + </p> + <img + style="position: relative; left: 28%; transform: translateX(-50%)" + src="https://static.igem.wiki/teams/4815/wiki/ed18.jpg" + width="50%" + /> + <img + style="position: relative; left: 24%; transform: translateX(-50%)" + src="https://static.igem.wiki/teams/4815/wiki/ed19.jpg" + width="41%" + /> + <p> + Approach: telling stories + Coloring picture books We prepared two + engaging and visually appealing synthetic biology cartoon stories to + captivate the attention of AS children during the lessons. After the + knowledge presentation, black-and-white line drawings of the cartoon + stories were distributed, and the children were encouraged to color + them according to their preferences. + </p> + <img + class="imgz" + src="https://static.igem.wiki/teams/4815/wiki/ed20.jpg" + width="50%" + /> + <p> + These "children from the stars" displayed varying levels of + receptivity to different subjects. During the activity, we observed + some children who had a keen interest in biology and possessed + excellent prior knowledge. Others, surprisingly, maintained high + levels of concentration during coloring. Their feedback highlighted + the significance of this science outreach activity: (1) We effectively + used the engaging synthetic biology cartoon stories to help AS + children improve their ability to focus, potentially aiding their + integration into society. (2) Based on the feedback from different AS + children, we planted the seeds of synthetic biology in the hearts of + those with a great interest in biology. In their small worlds, biology + might become their guiding light. + </p> + <img + class="imgz" + src="https://static.igem.wiki/teams/4815/wiki/ed21.jpg" + width="50%" + /> + <p> + Furthermore, during the promotion of this activity, NJU-China + collaborated with over ten iGEM teams, including OUC-China and + SZU-China, in knowledge exchange and sharing of coloring storybooks. + </p> + <p class="xiaobiaoti" id="s54">Learn</p> + <p> + During the picture book science outreach event, we acquired a fresh + perspective on children with AS, debunking common misconceptions that + they are difficult to interact with or understand. On the contrary, we + discovered that they are open to sharing their thoughts, expressing + their emotions, and attentively listening to our messages. Moreover, + their distinctive viewpoint as children may even offer novel insights + into our comprehension of synthetic biology. This experience + highlighted the importance of not overlooking these children in + educational settings. Moving forward, we aspire for more collective + efforts to prioritize their needs and enrich their lives. + </p> + </div> + </div> + <div class="dahe"> + <div class="dabiaotihe" id="s6"> + Ethics and safety promotion: Debate Competition + </div> + <div style="text-align: center"> + <img src="https://static.igem.wiki/teams/4815/wiki/devider.png" /> + </div> + <div class="wenbenkuang"> + <p class="xiaobiaoti" id="s25">Target group</p> + <p>the general public</p> + <p class="xiaobiaoti" id="s35">Why</p> + <p> + Debate competition has a significant potential to stimulate critical + thinking and create a resonance among the public. The competition + represents a relatively new and captivating form of popular science + that is readily embraced by the general population. + </p> + <p class="xiaobiaoti" id="s45">Process</p> + <p> + In order to disseminate knowledge about generative AI to the public + and help university students form relatively accurate and objective + views on generative AI, the NJU-China group has organized and hosted a + debate with the theme "Is Generative AI a Friend or Foe in Research + and Education?" + </p> + <p> + The affirmative side argues that "we should base our attitude towards + AI on its current state in order to promote social progress." The + first speaker for the affirmative side primarily argues from three + perspectives: the imperfection of AI itself, the questionable + reliability of its data sources, and the detrimental effects of + excessive reliance on AI on creativity development and academic + progress. They express the viewpoint that caution should be exercised + when dealing with AI. + </p> + <p> + The negative side provides a more objective interpretation of AI + applications. As a technology, artificial intelligence is undoubtedly + successful and beneficial. The purpose of research and education is + not solely to acquire specific knowledge because knowledge is always + evolving. What's important in research and education is the subjective + experience and self-fulfillment of individuals. If we divide research + and education into basic tasks and exploratory, creative work, we will + find that AI can be highly beneficial for both. Firstly, in the field + of educational research, there is a significant amount of repetitive + mechanical work, such as translating PPTs and creating lesson plans. + Using generative AI can eliminate much of the preparatory work, + providing basic support services and improving scholars' learning + efficiency. In more exploratory fields, AI can complement the + shortcomings of human exploration. Artificial intelligence, combined + with high-performance computing, can validate scientists' hypotheses + in areas with high experimental costs and difficulties, speeding up + research output, such as digital simulations of nuclear experiments, + which can reduce costs and increase safety. + </p> + <img + class="imgz" + src="https://static.igem.wiki/teams/4815/wiki/ed22.jpg" + width="50%" + /> + <p> + Our approach to technology should always be one of not being afraid. + Throughout human history, technology has always had slightly more + benefits than drawbacks because people always have the ability to + refine and correct it as they develop alongside technology. While the + application of artificial intelligence is still in its early stages, + it undoubtedly shows tremendous potential and future development. Why + not attempt to use AI to address the various challenges facing + synthetic biology and empower its rapid development? It is worth + mentioning that we should always pay attention to and continuously + consider the ethical and safety issues of AI in its use, and use it in + a responsible and appropriate manner. + </p> + <p class="xiaobiaoti" id="s55">Learn</p> + <p> + Throughout this debate competition, we have acquired valuable insights + into the safety and ethical considerations surrounding our project. + Initially, we viewed artificial intelligence (AI) solely as a means to + advance synthetic biology. However, engaging in debates and listening + to different perspectives has broadened our comprehension of AI. We + now recognize that our stance should not merely be in favor of or + against AI, but rather advocating for its responsible and mindful + implementation. We understand the significance of using AI cautiously + and appropriately, prioritizing the control and containment of its + impact within our project to avert potential adverse consequences. + </p> + </div> + </div> + <div class="dahe"> + <div class="dabiaotihe" id="s7">Stage Playabout the discovery of DNA</div> + <div style="text-align: center"> + <img src="https://static.igem.wiki/teams/4815/wiki/devider.png" /> + </div> + <div class="wenbenkuang"> + <p class="xiaobiaoti" id="s26">Target group</p> + <p>well-educated high school students</p> + <p class="xiaobiaoti" id="s36">Why</p> + <p> + Utilizing a stage play as a medium for introducing the life and + scientific journey of Rosalind Franklin to high school students + provides a dynamic and captivating approach to fostering scientific + literacy, inspiring budding scientists, and delving into pertinent + themes concerning science and society. Compared to other storytelling + methods, stage theater offers a vivid and emotionally resonant + experience. + </p> + <p class="xiaobiaoti" id="s46">Process</p> + <p>"Franklin, the Scientific Rose"</p> + + <div class="wenbenkuang" style="position: relative"> + <p class="tiansuohao2" style="width: 90%"> + <img + class="tiansuohao4" + style="width: 40%" + style="padding: 0px" + src="https://static.igem.wiki/teams/4815/wiki/ed23.png" + />Synopsis: The stage play focuses on the brief yet thrilling life + of Rosalind Franklin. Female scientist Rosalind Franklin, who + suffered from ovarian cancer due to excessive exposure to radiation, + left this world prematurely at the age of 38. However, the clear + photograph she took, known as Photograph 51, has circulated widely + and is printed in every genetics or biology textbook, silently + recounting the hardships and quests of the unknown photographer. + Without the data support it provided, Watson and Crick's double + helix model might have remained a castle in the air.To introduce the + discovery history hidden behind the DNA double helix structure to + high school students and commemorate the 70th anniversary of the + unveiling of the DNA double helix structure while honoring the + female scientist Rosalind Franklin, we planned this stage play + activity. + <br /> + This stage play is aimed at high school students with a significant + level of biological knowledge. We held a stage performance in the + School of Science of Nanjing University, and invited visiting + students from Nanjing Foreign Languages University to come and + watch. After the play's exhibition, it received a great response, + and many high school students expressed a deeper understanding of + the history of the discovery of the DNA double helix. + </p> + <img + class="imgz" + src="https://static.igem.wiki/teams/4815/wiki/education/education1.png" + width="60%" + /> + + <p class="xiaobiaoti" id="s56">Learn</p> + <p> + Through the process of preparing the play, we gained a deeper + understanding of the historical context surrounding DNA discovery, + including the dedicated efforts and inevitable setbacks encountered + along the way. Crucially, our current project resides on the cutting + edge of synthetic biology research, and the stories we encountered + throughout this endeavor have fueled our determination to strive for + excellence in our own endeavors. We also took the opportunity to + share our experiences and harvests with the high school students who + attended the performance, aiming to inspire and encourage them to + contribute to the future development of synthetic biology. + </p> + </div> + </div> + <div class="dahe"> + <div class="dabiaotihe" id="s8"> + Spread ideas to public:Popular Science Posts in WeChat Official + Account + </div> + <div style="text-align: center"> + <img src="https://static.igem.wiki/teams/4815/wiki/devider.png" /> + </div> + <div class="wenbenkuang"> + <p class="xiaobiaoti" id="s27">Target group</p> + <p>the general public</p> + <p class="xiaobiaoti" id="s37">Why</p> + <p> + Offline activities often have limitations in terms of participant + numbers and groups, whereas the Internet has increasingly become a + crucial avenue for individuals of all ages, backgrounds, and + locations to access information. Recognizing this, we utilize a + WeChat official account to disseminate popular science articles and + interview transcripts. This approach enables us to reach a wider + range of individuals, transcending geographical boundaries and + engaging diverse individuals from various walks of life. + </p> + <p class="xiaobiaoti" id="s47">Process</p> + <p> + We created the team's public account "Pymaker" topopularize AI and + synthetic biology knowledge among the public, wherescience promoting + articles, interviews, and records of our education activitieswere + published. We have published tweets theme on mucosal vaccines, LTB + expressed in yeast, deep learning in synthetic biology and transfer + Learning. Our public account currently has over 110 followers, with + over 2,400 readings. In the future, we will continue to publish + relevant popular science articles, bringing cutting-edge and + life-related AI and synthetic biology knowledge to the public. + </p> + <p class="xiaobiaoti" id="s57">Learn</p> + <p> + To ensure the dissemination of the most advanced and valuable + knowledge to the public, we have conducted extensive research, + delving into numerous literature and reports. Through this process, + we meticulously curated the essential contents, acquiring profound + insights into the respective fields and drawing inspiration for our + project design. Furthermore, as we share this knowledge with the + public, we deepen our own understanding of these concepts, affirming + that education is indeed a reciprocal learning process. + </p> + <img + class="imgz" + src="https://static.igem.wiki/teams/4815/wiki/education/education12.png" + width="40%" + /> + </div> + </div> + </div> + </div> + </div> + </div> + </div> + + <!-- è°ƒaos库 --> + <!--<script src="https://cdnjs.cloudflare.com/ajax/libs/aos/2.3.4/aos.js"></script> + <script> + AOS.init(); + </script>--> +</div> +{% endblock %} diff --git a/wiki/pages/human-practices.html b/wiki/pages/human-practices.html index 3a15dae8c52464deb1458cc53fdb258fafb9198b..addc5df1ce5619b701dafa9c921badd0baf832f5 100644 --- a/wiki/pages/human-practices.html +++ b/wiki/pages/human-practices.html @@ -1,3 +1,493 @@ -{% extends "layout.html" %} {% block page_content %} -<p>adcacwd</p> -{% endblock %} +{% extends "layout.html" %} +{% block title %}Human Practices{% endblock %} +{% block page_content %} + + +<meta charset="UTF-8"> +<link rel="stylesheet" href="{{ url_for('static', filename = 'style.css') }}"> +<link rel="stylesheet" href="{{ url_for('static', filename = 'reset.min.css') }}"> +<link rel="stylesheet" href="{{ url_for('static', filename = 'css/des.css') }}"> +<link rel="stylesheet" href="{{ url_for('static', filename = 'css/ft.css') }}"> + +<meta charset="UTF-8"> + + +<style>.tuzhu{text-align:center;}.tiansuohao2{width:50%;float:left;box-sizing:border-box;border:0px solid #000;padding:2.5%;margin:0;}.bannertt { + position: absolute; 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+ left: 50%; + transform: translateX(-50%); + }</style> +<style>@keyframes zoom { + 0% {background-size: 100%;} + 50% {background-size: 140%;} + 100% {background-size: 100%;} +}</style> +<div + style=" + background-image: url('https://static.igem.wiki/teams/4815/wiki/test33.png'); + background-attachment: fixed; + background-position: left; + background-repeat: no-repeat; + padding-bottom: 100px; + animation: zoom 4s infinite; + " +> +<div style="position: relative;height: 60vh;width: 100%;background-image: url(https://static.igem.wiki/teams/4815/wiki/hpbanner.png);background-size: 100% auto;background-position: center;"> +<div class="bannertt"> +INTEGRATED HP +<p class="bannertt2">responsible and good for the world</p> +</div> +</div> + +<div class="row"> + <!-- 侧导航æ --> + <div class="col-3 left-nav-container" id="myScrollspy"> + <header class="left-nav" role="banner"> + <nav class="nav" role="navigation"> + <ul class="nav__list"> + <li> + <input id="group-1" type="checkbox" hidden /> + <a href="#s1"><span class="fa fa-angle-right"></span> Overview </a> + </li> + <li> + <input id="group-2" type="checkbox" hidden /> + <label for="group-2"><span class="fa fa-angle-right"></span> Topic Research</label> + <ul class="group-list"> + <li> + <li><a href="#s21">Background Research</a></li> + <li><a href="#s22">Stakeholder Analysis</a></li> + <li><a href="#s23">Public Survey</a></li> + </li></ul> + </li> + <li> + <input id="group-3" type="checkbox" hidden /> + <label for="group-3"><span class="fa fa-angle-right"></span> Exploration</label> + <ul class="group-list"> + <li> + <li><a href="#s31">The Interview of Prof. Ma</a></li> + <li><a href="#s32">The Interview of Prof. Ding</a></li> + <li><a href="#s33">AI Model and Paradigm</a></li> + <li><a href="#s34">Data Source</a></li> + <li><a href="#s35">Yeast Expression System</a></li> + </li></ul> + </li> + <li> + <input id="group-4" type="checkbox" hidden /> + <label for="group-4"><span class="fa fa-angle-right"></span> Application</label> + <ul class="group-list"> + <li> + <li><a href="#s41">The Visit to Nanjing Yiweisen Biotechnology Co., LTD</a></li> + <li><a href="#s42">The visit to Carbon Silicon Institute of Artificial Intelligence Biomedical Research</a></li> + <li><a href="#s43">Enhance LTB Expression</a></li> + <li><a href="#s44">Feedback</a></li> + </li></ul> + <li> + <input id="group-5" type="checkbox" hidden /> + <a href="#s5"><span class="fa fa-angle-right"></span> Ethic </a> + </li> + <li> + <input id="group-6" type="checkbox" hidden /> + <a href="#s6"><span class="fa fa-angle-right"></span> Environment </a> + </li> + <li> + <input id="group-7" type="checkbox" hidden /> + <a href="#s7"><span class="fa fa-angle-right"></span> Entrepreneurship </a> + </li> + </ul> + </li> + + + + </ul> + </nav> + </header> + </div> + +<div class="col-9" style="padding-left: 5%;padding-right: 5%;"> + <div style=" + width: 100%; + height: 100%; + background-color: #fff; + box-shadow: 0px 0px 10px rgba(255, 0, 0, 0.5); + padding-left:40px; + padding-right:40px; + margin-top:60px; + border-radius: 15px; + "> +<div class="dahe"> +<div class="dabiaotihe" id="s1">Overview</div> +<div style="text-align: center;"><img src="https://static.igem.wiki/teams/4815/wiki/devider.png"></div> +<div class="wenbenkuang"> +<div class="wenbenkuang">NJU-China devotes ourselves to creating an easy-to-use AI model and aparadigm +specifically for synthetic biology research, and then proposes new solutions to the challenge of applying +Artificial Intelligence broadly into synthetic biology. In the Integrated Human Practice page, we show how we +have carefully considered whether our project is responsible and good for the world throughout the whole +lifecycle.During the process, we address both how our project responds to such considerations and how our +proposed solution is implemented responsibly and reflectively.<a style="font-weight: bolder">The public survey</a> gave us an overall picture of +the topic we focus.Through communications with <a style="font-weight: bolder">scholars</a>, we clarified the specific problem to work on and +obtained professional guidance and opinionsfor the design and implementation. We also got inspiration from +<a style="font-weight: bolder">enterprises</a> to take application scenarios, customer needs and expert knowledge on feasibility into +consideration, and we are cheerful to see our model is successfully utilized in their production and +brings benefits. Thanks to these professionals in different fields, our project manages to open a new window +for the future of synthetic biology and gratifying progress to the development of the society.</div> +<div class="dahe"> +<div class="dabiaotihe">Topic Research</div> +<div style="text-align: center;"><img src="https://static.igem.wiki/teams/4815/wiki/devider.png"></div> +<div class="wenbenkuang"> +<p class="xiaobiaoti" id="s21">1. Background Research</p> +<p>Leveraging its immense computational power and intelligent algorithms, AI provides researchers with +unprecedented insights. AI can handle vast amounts of biological data, such as genomes and protein +interaction networks, accelerating drug development and disease diagnosis. The impact is staggering, +with AI speeding up <a style="font-weight: bolder">gene identification and analysis</a> by at least <a style="font-weight: bolder">100 times</a>. In protein folding +prediction, AI achieves an accuracy rate of 90%, greatly reducing the time and resources required +compared to traditional methods. Additionally, AI excels in medical imaging diagnostics, with an +impressive <a style="font-weight: bolder">96%</a> accuracy in breast cancer detection, surpassing human doctors' assessment +capabilities. These remarkable numbers highlight the enormous potential of AI in biology, +revolutionizing medical research and healthcare management, and make our team to think, how can AI +be used generally for synthetic biology?</p> +<p class="xiaobiaoti" id="s22">2. Stakeholder Analysis</p> +<p>We hope to identify the problem together with potential stakeholders, and screen the initial idea +with them. Therefore, our team primarily listed all the actors who could be relevant to our project +in different fields by brainstorming, and determined the order of interaction in order to plan and +design our projects <a style="font-weight: bolder">from the shallower to the deeper</a>.</p> +<img src="https://static.igem.wiki/teams/4815/wiki/ihp/ihp1.png" width="70%" class="imgz"> +<p></p> +<p>Based on the spiral line, we engaged with our stakeholders step by step, and gradually constructed +and improved our project design according to their suggestions and feedback. The process of the +communications and their impact on us will be shown in detail below. At the same time, as clarifying +exactly what project tends to do, we were continuously <a style="font-weight: bolder">adding and refiningour stakeholders list</a> and +manage them through a <a style="font-weight: bolder">power-interest matrix</a>, which helps to prioritize the values of the most +relevant stakeholders. All stakeholders are grouped based on Power (their ability to influence our +project and our strategy) and Interest (how interested they are in our project succeeding). For high +power, high interested group, we <a style="font-weight: bolder">fully engage with them</a> mainly, through discussing all the choices we +make and the progress we book with our project. We also consideredother stakeholdersin respective +ways, and contact them when we require expertise on a specific topic.</p> +<img src="https://static.igem.wiki/teams/4815/wiki/ihp/ihp2.png" width="70%" class="imgz"> +<p class="xiaobiaoti" id="s23">3. Public Survey</p> +<p>Tofully understand the real needs of society and create new value in a targeted manner, public +opinion is very essential, which will determine whether our project can actually benefit society and +what we are supposed to focus on.Therefore, before implementing new technology, we conducted +extensive public questionnaire survey and detailed analyses.In the past year, we have collected <a style="font-weight: bolder">265 +questionnaires</a> from all over the China, covering different kinds of educational background and +occupation, which ensures the universality of our investigation.</p> +<p>Given that the topic of AI for synthetic biology is highly specialized, our questionnaire was divided +into three parts.In the first part we’d like to find out <a style="font-weight: bolder">the public’s awareness and attitude towards +AI application in work and daily life.The results show that about 28% of people never use AI in +daily life and only 7% of them use AI at a high frequency. The reason why some of them <a style="font-weight: bolder">never use AI +or barely use AI</a> including the high threshold for the use of AI, concerns that AI will not meet +individual needs, invade personal privacy or provide false information or there is no need to use +AI.</p> +<img src="https://static.igem.wiki/teams/4815/wiki/ihp/ihp3.png" width="70%" class="imgz"> +<p class="tuzhu">Figure 1. Frequency of using AI in daily life</p> +<br> +<img src="https://static.igem.wiki/teams/4815/wiki/ihp/ihp4.png" width="70%" class="imgz"> +<p class="tuzhu">Figure 2. Reasons for never or less use of AI</p> +<p>When asking about the level of mastery of AI technology, 44% of people only use AI as a tool and 17% +of them know about the principle of AI, which shows that <a style="font-weight: bolder">public’s understanding of AI is very +shallow</a>. Based on the situation, we asked respondents about the obstacles to learning AI, about 60% +of them agreed that it is hard to find AI learning resources and tool resources, and learning AI is +difficult which we need to invest a lot of time in. </p> +<img src="https://static.igem.wiki/teams/4815/wiki/ihp/ihp5.png" width="70%" class="imgz"> +<br> +<p class="tuzhu">Figure 3. Mastery degree of artificial intelligence</p> +<br> +<img src="https://static.igem.wiki/teams/4815/wiki/ihp/ihp6.png" width="70%" class="imgz"> +<p class="tuzhu">Figure 4. Obstacles of learning AI</p> +<p>These results show that <a style="font-weight: bolder">the application of AI is still relatively limited</a>, and further research about +AI technology is needed to effectively solve problems in specific fields, and we believe this is +also true in the field of synthetic biology. In addition, <a style="font-weight: bolder">the high difficulty of professional +knowledge</a> limits people's further study of the application of AI in specific fields, which also +reminds us that it is necessary and helpful to carry out popular science and education activities +about AI for synthetic biology to better promote them to the public.</p> +<p>Then we asked users and developers of AI tools respectively that which aspect of AI they will focus +on. About 70% of them have the request of accuracy, 61% of them pursue ease operation of AI and +about 50% of them expect AI to have data privacy and fast processing speed, which shows that if AI +want to be widespread, it must both to be <a style="font-weight: bolder">accurate and easy to understand</a>, just like web page +technology. Developers concentrated most on the <a style="font-weight: bolder">efficiency and accuracy</a>, as well as their <a style="font-weight: bolder">ability to +transfer to multiple problems</a>, which provides a guidance on our AI model design.</p> +<img src="https://static.igem.wiki/teams/4815/wiki/ihp/ihp7.png" class="imgz" width="70%"> +<p class="tuzhu">Figure 5. Focus as a user on aspects of AI models or algorithms</p> +<br> +<img src="https://static.igem.wiki/teams/4815/wiki/ihp/ihp8.png" class="imgz" width="70%"> +<p class="tuzhu">Figure 6. Focus as a developer on aspects of AI models or algorithms</p> +<p>In terms of the function of AI, we found it widely used in various aspects, and nearly <a style="font-weight: bolder">92%</a> of people +believe AI will have <a style="font-weight: bolder">positive effect</a> on the fields they work in. However, it has relatively <a style="font-weight: bolder">few +applications in scientific research</a>, thus we believe it is our value to improve the new application +of AI technology in synthetic biology research.</p> +<img src="https://static.igem.wiki/teams/4815/wiki/ihp/ihp9.png" width="50%" class="imgz"> +<p class="tuzhu">Figure 7. Goals of using AI</p> +<br> +<img src="https://static.igem.wiki/teams/4815/wiki/ihp/ihp10.png" width="70%" class="imgz"> +<p class="tuzhu">Figure 8. The impact AI have on the field you work in</p> +<p>In the next part, we aimed to further explore the public perceptions of the promise of AI for +synthetic biology. We were upset to find that <a style="font-weight: bolder">half</a> the respondents have <a style="font-weight: bolder">never heard of synthetic biology</a> +before, and over <a style="font-weight: bolder">16%</a> of people who know synthetic biology still have <a style="font-weight: bolder">little knowledge about the +application of AI in the field</a>. Obviously, it is necessary for us to introduce and propagate AI for +synthetic biology to the public in a more efficient and suitable way.</p> +<img src="https://static.igem.wiki/teams/4815/wiki/ihp/ihp11.png" width="70%" class="imgz"> +<p class="tuzhu">Figure 9. Degree of understanding of synthetic biology</p> +<br> +<img src="https://static.igem.wiki/teams/4815/wiki/ihp/ihp12.png" width="70%" class="imgz"> +<p class="tuzhu">Figure 10. The extent to which AI is used in the field of synthetic biology</p> +<p>Above all, for those who know the application of AI in the field of synthetic biology, it’s generally +believed that <a style="font-weight: bolder">the application of artificial intelligence in the synthetic biology industry has +bright prospects</a>. As we considered about the specific convenience or revolution that AI can bring to +biology, <a style="font-weight: bolder">improving efficiency and shortening research cycle</a> won the highest score among the few +options we have listed. For the current challenges or constraints which limits the development of AI +for synthetic biology, nearly 70% of them agreed that it lacks uniform standards and specifications +(e.g. data formats, sharing platforms, etc.). About 60% of them believe that the scarce of AI +expertise and skills in biological researchers and lack of synthetic biology data with high quality +and quantity are also main problems.</p> +<img src="https://static.igem.wiki/teams/4815/wiki/ihp/ihp13.png" width="70%" class="imgz"> +<p class="tuzhu">Figure 11. The extent to which AI can help synthetic biology</p> +<br> +<img src="https://static.igem.wiki/teams/4815/wiki/ihp/ihp14.png" width="40%" class="imgz"> +<p class="tuzhu">Figure 12. the application prospect of AI in synthetic biologycompared with other +industries(Assuming an average score of 5) </p> +<br> +<img src="https://static.igem.wiki/teams/4815/wiki/ihp/ihp15.png" width="60%" class="imgz"> +<p class="tuzhu">Figure 13. The importance of the different changes that AI bring to synthetic biology</p> +<br> +<img src="https://static.igem.wiki/teams/4815/wiki/ihp/ihp16.png" width="100%" class="imgz"> +<p class="tuzhu">Figure 14. Challenges of the application of AIin synthetic biology</p> +<p>After anextensive literature research, we chose to <a style="font-weight: bolder">pre-train the AI on existing models and adapt the +parameters to a specific problem</a>. We asked the public for their opinion and were stimulated to find +that most people think this approach <a style="font-weight: bolder">>makes practical sense</a.</p> +<img src="https://static.igem.wiki/teams/4815/wiki/ihp/ihp17.png" width="45%"> +<img src="https://static.igem.wiki/teams/4815/wiki/ihp/ihp18.png" width="45%"> +<p class="tuzhu">Figure 15. (left)the practical value of pre-train and fine-tune AI based on an existing +model(compared with building an AI model from scratch) </p> +<p class="tuzhu">Figure 16. (right)The meaning of applying transfer learning to solvespecific problems in +synthetic biology</p> +<p>In a word, we are glad to find that the public is optimistic about the application of artificial +intelligence in the field of synthetic biology, which gives us great motivation on finding more +possibilities of artificial intelligence applied to synthetic biology on the basis of predecessors. +The survey also provides new ideas on our model design and education activities to improve public +understanding.</p> +</div> +</div> +<div class="dahe"> +<div class="dabiaotihe">Exploration</div> +<div style="text-align: center;"><img src="https://static.igem.wiki/teams/4815/wiki/devider.png"></div> +<div class="wenbenkuang"> +<p class="xiaobiaoti" id="s31">1. The Interview of Prof. Ma</p> +<img src="https://static.igem.wiki/teams/4815/wiki/ihp/ihp19.png" class="tiansuohao2" style="width: 30%;"> +<p>Professor Ma Lijia is currently working at Westlake University, focusing on genomics and systems +biology, and has in-depth research on data mining and AI applications in regulatory sequences.</p> +<p>In the application of biology, what direction is the most significant problem of data limitation? +Keeping this question in mind, we went to Westlake University to have an in-depth exchange with +Professor Ma Lijia. "The regulatory sequence is critical. In fact, 90% of the human genome is +regulatory sequences, and our research group is currently working on the characterization of +regulatory sequences. In my opinion, specific regulatory sequences, such as promoter sequences, are +currently suffering the most data-scarcity, which is mainly limited by experimental techniques for +selecting and characterizing." A crucial keyword in synthetic biology is <a style="font-weight: bolder">expression</a>, which is also +closely related to <a style="font-weight: bolder">regulatory sequences</a>. Building on the important professional insights provided by +Professor Ma Lijia, we finally set our sights on regulating the most direct and ubiquitous +functional regulatory sequences—<a style="font-weight: bolder">promoters</a>, and put it as the specific direction of our project.</p> +<div> +<p class="xiaobiaoti" id="s32">2. The Interview of Prof. Ding</p> +<p>During our communication and promotion efforts with various stakeholders, we have encountered +some <a style="font-weight: bolder">skepticism</a>. Professor Bi Ding from Fudan University questioned the significance of our +project during a discussion, stating that the prevalent use of active learning</a> in the field of +biology and AI suggests that data may not be as limiting as we claim. This has prompted us to +further contemplate the significance of our project and how to convince more people. We have +further confirmed that <a style="font-weight: bolder">the availability of data is not only limited by technical development but +also constrained by costs</a>. In fact, there are instances where obtaining a sufficient amount of +high-quality data is not impossible, but the corresponding high economic and time costs cannot +be justified by the expected output. </p> +<img src="https://static.igem.wiki/teams/4815/wiki/ihp/ihp20.jpg" width="50%" class="imgz"> +<p></p> +<p class="xiaobiaoti" id="s33">3. AI Model and Paradigm</p> +<p>After determining our project direction, choosing the appropriate large-scale model is the most +important problem to consider. We went to Nanjing GenScript Biotechnology Company to conduct an +exchange interview with Sheng Xia, a senior scientist in bioinformatics. Mr. Sheng Xia has been +engaged in biological data mining and analysis for a long time, and has quite mature +professional experience in AI application. After understanding the relevant situation of our +project, Sheng Xia believes that what we need to deal with is <a style="font-weight: bolder">genetic data</a>, which is generally +applicable to language models, the most popular of which are <a style="font-weight: bolder">GPT and Bert models</a>. </p> +<img src="https://static.igem.wiki/teams/4815/wiki/ihp/ihp21.jpg" width="70%" class="imgz"> +<p></p> +<p class="xiaobiaoti" id="s34">4. Data Source</p> +<p>When conducting preliminary dry experiment training with selected 30,000,000-scale dataset, +continuous attempts and optimization of parameters could not obtain good results, and the focus +was on the characteristics of the training data through inter-team communication. The students +of the dry experiment found that the result plotting showed that there was a large number of +data in the complete data whose actual intensity deviated from the reasonable experimental +results, and after communicating with the author of the literature, that is, the data +contributor, and learning his team's method to screen the data, the effect increased +significantly. Since then, we have <a style="font-weight: bolder">maintained communication with the author team</a>, which has +played an important role in promoting the optimization and improvement of our dry lab result. +</p> +<img src="https://static.igem.wiki/teams/4815/wiki/ihp22-24.png" width="70%" class="imgz"> +<p></p> +<p class="xiaobiaoti" id="s35">5. Yeast Expression System</p> +<p>After deciding to use yeast as our expression system, we conducted an exchange interview with +Professor Sheng Xia at Nanjing GenScript Biotechnology Company. Professor Sheng agreed with our +choice and mentioned that <a style="font-weight: bolder">yeast has a slower cultivation speed and it is challenging to achieve +high expression levels</a> compared to some commonly used engineered bacteria in industrial +fermentation processes. He emphasized that if our project could provide a solution to this +issue, it would be extremely helpful. Professor Sheng further advised us that if we plan to +express proteins from prokaryotes or viruses in yeast, it is advisable to optimize the yeast +source. He provided us with <a style="font-weight: bolder">a web platform from GenScript for yeast sequence optimization</a>, which +played a crucial role in facilitating our subsequent project.</p> +<img src="https://static.igem.wiki/teams/4815/wiki/ihp/ihp25.jpg" width="70%" class="imgz"> +<p></p> +<p>The next challenge in protein expression within yeast is how to separate, purify, and quantify +the proteins. In fact, due to the cell wall of yeast, it is relatively difficult to separate and +purify the expressed proteins. Through discussions with Dr. Yiling Hu, a postdoctoral researcher +at the School of Life Sciences, Nanjing University, who specializes in yeast cultivation, Dr. Hu +provided us with a feasible solution. It involves <a style="font-weight: bolder">dding a His-tag to the protein or fusing the +protein with a fluorescent protein</a>a to enable purification and quantification through Western +blot analysis after yeast lysis. Dr. Hu further mentioned that it is worth noting that there is +no precedent for detecting His-tag in yeast, so if our project can <a style="font-weight: bolder">detect His-tag in the yeast +lysate</a>, it would be a significant advancement.</p> +<p>In the process of further exploring our project, we also keep close contact with other iGEM +teams, and shared the progress and challenges with each other. Through these collaborations and +partnerships, we get peer support and review, enhance creativity and advanced our project. For +more information, please click the Partnership link to see how the interaction with other teams +has influenced our project.</p> +</div> +</div> +<div class="dahe"> +<div class="dabiaotihe">Application</div> +<div style="text-align: center;"><img src="https://static.igem.wiki/teams/4815/wiki/devider.png"></div> +<div class="wenbenkuang"> +<p class="xiaobiaoti" id="s41">1. The Visit to Nanjing Yiweisen Biotechnology Co., LTD</p> +<p>After gaining recognition from relevant researchers, we wanted to further explore the industrial significance of our project. We visited Nanjing Yiweisen Biotechnology Co. and had a discussion with Professor Zhongchang Wang. Professor Wang established Nanjing Yiwesen Biotechnology Co., Ltd as the main founder. The company is a high-tech enterprise based on artificial intelligence technology in the field of synthetic biology, incubated by Artificial Intelligence Biomedical Research of Nanjing University. It primarily focuses on microbial genetic modification and downstream industrial applications, researching and developing high-value natural active substances for use in sectors such as food, cosmetics, plant protection, and biopharmaceuticals. Professor Wang acknowledged the significance of our project and pointed out that the current traditional screening methods for selecting target strains from a large number of randomly mutated strains are often costly, time-consuming, and limited in scope. The application of artificial intelligence in synthetic biology has greatly improved the accuracy of mutagenic strains and reduced the cost of screening. Additionally, he provided us with some potential application directions from a business perspective.</p> +<img src="https://static.igem.wiki/teams/4815/wiki/ihp/ihp26.jpg" width="70%" class="imgz"> +<p></p> +<img src="https://static.igem.wiki/teams/4815/wiki/ihp/ihp27.jpg" width="70%" class="imgz"> +<p></p> +<p class="xiaobiaoti" id="s42">2. The visit to Carbon Silicon Institute of Artificial Intelligence Biomedical +Research</p> +<p>We hoped that our project could provide solutions to the most realistic and important human +health or environmental issues, demonstrating responsibility and a positive impact on the world +throughout its entire lifecycle. During our visit and discussions, a possibility that had never +been considered before caught our attention—<a style="font-weight: bolder">the mucosal vaccine</a>. </p> +<img src="https://static.igem.wiki/teams/4815/wiki/ihp/ihp28.jpg" width="70%" class="imgz"> +<p></p> +<p>Professor Chao Yan, from the institute, has extensive experience in drug development and provided +profound insights into using AI for precision drug discovery. He first acknowledged that the +pre-training + fine-tuning model we proposed can not only be applied to synthetic biology but +also to <a style="font-weight: bolder">predictive drug development</a>. He further emphasized that data limitations are not just +technical barriers but are greatly influenced by the spatiotemporal factors of <a style="font-weight: bolder">data generation</a>, +which have high heterogeneity and are difficult to utilize. As an example, he mentioned that AI +image recognition models are trained on datasets in the order of billions, while in the field of +biology, measurements are typically limited to dozens of patients at a time, with only a few +dozen data points per dimension. The disparity between the two is significant. Additionally, he +pointed out the issue of the dimensionality of biological data. Biological data often have <a style="font-weight: bolder">a high +number of dimensions but a low sample size</a>, which is not conducive to leveraging the strengths +of AI. For example, AI excels at image processing with low dimensionality and large sample +sizes, where there are data points in each dimension, resulting in better predictive models. +However, in biology, such as genomics, each gene represents a dimension, but the samples for +each gene are relatively scarce.</p> +<img src="https://static.igem.wiki/teams/4815/wiki/ihp/ihp29.jpg" width="70%" class="imgz"> +<p></p> +<p>Professor Yan's interview deepened our understanding of the significance and value of our project +and made us more fully aware of the multiple aspects of data limitations. Additionally, we +received affirmation and support from him regarding our plans for mucosal vaccine production. +</p> +<img src="https://static.igem.wiki/teams/4815/wiki/ihp/ihp30.jpg" width="70%" class="imgz"> +<p></p> +<p class="xiaobiaoti" id="s43">3. Enhance LTB Expression</p> +<p>After receiving such affirmation, we needed to find suitable mucosal vaccine-related proteins as +the target product for our project. Our attention turned to LTB (Heat-Labile Enterotoxin B +subunit). Through literature review and understanding its production and functions, we +discovered that LTB plays a crucial role in mucosal vaccines and indeed faces expression +limitations. If our project can address the challenges associated with LTB expression, it would +greatly promote the production and dissemination of mucosal vaccines.</p> +<p class="xiaobiaoti" id="s44">4. Feedback</p> +<p>After formulating such a concept, we further engaged in discussions with the aforementioned +researchers. Many of them raised concerns about the <a style="font-weight: bolder">inconsistency between our project's training +data and the downstream product</a>. Specifically, we obtained data from fluorescent protein +expression for training, but intended to use the trained sequences for the production of a +different protein. As they pointed out, the strength of the promoter is highly likely to be +influenced by downstream genes. This prompted us to consider <a style="font-weight: bolder">providing feedback from wet lab +experiments</a>, specifically the expression data obtained for LTB, to the AI involved in dry lab +experiments. This feedback would facilitate the development of a more targeted model for LTB +expression.</p> +</div> +</div> +<div class="dahe"> +<div class="dabiaotihe" id="s5">Ethic</div> +<div style="text-align: center;"><img src="https://static.igem.wiki/teams/4815/wiki/devider.png"></div> +<div class="wenbenkuang"> +<p>We believe that the use and training of AI models must adhere to <a style="font-weight: bolder">ethical guidelines for data</a>, +meaning that only <a style="font-weight: bolder">publicly available datasets</a> should be used for training. It is important to +respect the owners' rights and avoid using private data without permission. When it comes to the +pre-training and fine-tuning paradigms, copyright issues pertaining to pre-trained models must +be taken into consideration. It is advisable to utilize <a style="font-weight: bolder">publicly available pre-trained models</a>. +Moreover, during the AI for Synbio Seminar, we engaged in discussions with other teams and +reached a consensus that <a style="font-weight: bolder">data transparency and sharing of AI model algorithms</a> are essential, +particularly for our iGEM team. Other teams should also ensure that they make use of publicly +available datasets when collecting data.</p> +<p>In addition, one of the primary concerns related to AI safety is that the training of AI models +should be focused on tasks that are beneficial to humans and compliant with legal regulations +within that specific domain.</p> +</div> +</div> +<div class="dahe"> +<div class="dabiaotihe" id="s6">Environment</div> +<div style="text-align: center;"><img src="https://static.igem.wiki/teams/4815/wiki/devider.png"></div> +<div class="wenbenkuang"> +<p>After achieving some experimental results, we engaged in discussions with AI pharmaceutical +companies to seek guidance on the subsequent industrialization process. They recognized the +potential utility of our model in industrial production but also highlighted certain +considerations. Firstly, for yeast production and larger-scale experiments, it is crucial to pay +special attention to <a style="font-weight: bolder">preventing biological contamination</a>. Secondly, due to the high level of +pollution associated with yeast production, <a style="font-weight: bolder">wastewater treatment</a> should be prioritized. In fact, +the production of <a style="font-weight: bolder">1 ton</a> of dry yeast can generate <a style="font-weight: bolder">150 tons</a> of wastewater. Building upon these +considerations, Zhang Xiaotong, the supervisor of the wet lab experiments, guided the innovative +development of a <a style="font-weight: bolder">biological wastewater treatment device</a> (Patent No: CN215886592U) and a +<a style="font-weight: bolder">bioreactor</a> to prevent contamination from miscellaneous bacteria (Patent No: CN216141527U). These +developments have prepared us for the industrial production phase of our project. </p> +<img src="https://static.igem.wiki/teams/4815/wiki/ihp31.png" width="50%" class="imgz"> +</div> +</div> +<div class="dahe"> + <div class="dabiaotihe" id="s7">Entrepreneurship</div> + <div style="text-align: center;"><img src="https://static.igem.wiki/teams/4815/wiki/devider.png"></div> + <div class="wenbenkuang"> + <p>Based on Pymaker, we plan to develop <a style="font-weight: bolder">a software for designing cis-regulatory elements in yeast promoter regions based on deep learning</a>. We have already reached intentions for collaboration and signed agreements with Nanjing LianDu Biological Technology Co., Ltd. and Nanjing YiWeiSen Biological Technology Co., Ltd. Through the collaboration, our research results and developed models can be used to <a style="font-weight: bolder">guide the design and optimization of yeast fermentation production lines</a>, significantly reducing the cost of industrial production screening and validation, and ultimately bringing high-quality products to the market. </p> + <img + src="https://static.igem.wiki/teams/4815/wiki/contribution/liandu1.jpg" + width="49%" + alt="" + /> + <img + src="https://static.igem.wiki/teams/4815/wiki/contribution/liandu2.jpg" + width="49%" + alt="" + /> + <img + src="https://static.igem.wiki/teams/4815/wiki/contribution/yiwei1.jpg"" + width="49%" + alt="" + /> + <img + src="https://static.igem.wiki/teams/4815/wiki/contribution/liandu2.jpg" + width="49%" + alt="" + /> +</div> +</div> +</div> +</div> +</div> +</div> +</div> +</div> +</div> + +{% endblock %} \ No newline at end of file