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{% extends "layout.html" %}
{% block title %}HP-Overview{% endblock %}
{% block title %}Human Practices{% endblock %}
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<div class="bannertt">
HP OVERVIEW
INTEGRATED HP
<p class="bannertt2">responsible and good for the world</p>
</div>
</div>
......@@ -155,23 +62,53 @@ HP OVERVIEW
</li>
<li>
<input id="group-2" type="checkbox" hidden />
<a href="#s2"><span class="fa fa-angle-right"></span> Timeline </a>
<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 />
<a href="#s3"><span class="fa fa-angle-right"></span> Integrated HP </a>
<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 />
<a href="#s4"><span class="fa fa-angle-right"></span> Partnership </a>
</li>
<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> Education </a>
<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>
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<a href="#s7"><span class="fa fa-angle-right"></span> Entrepreneurship </a>
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......@@ -189,152 +126,364 @@ HP OVERVIEW
border-radius: 15px;
">
<div class="dahe">
<div class="dabiaotihe" id="s1">
Overview
<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 style="text-align: center;">
<img src="https://static.igem.wiki/teams/4815/wiki/devider.png">
</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>We focus on utilizing AI to address a critical issue in synthetic biology: expression, with the
ultimate goal of further validating the practicality and scalability of the proposed learning
paradigm of transfer learning and AI models in the field of synthetic biology.
To assess whether Pymaker could bridge the data gap, which represents the final frontier of AI
in the field of biology, and finally benefit synthetic biology, it is critical to <a style="font-weight: bolder">engage all
stakeholders</a> who may be affected by our solutions and those who may influence our solutions. We
also participate in meetups extensively to <a style="font-weight: bolder">communicate with various teams</a>, getting suggestions
for our projects. Our interactions with these stakeholders and kindred spirits have taught us
more about the intersection of the two frontiers of AI and synthetic biology, and have shaped
our project. Additionally, we are committed to <a style="font-weight: bolder">impart synthetic biology knowledge and ideas to
the wider community</a> to bring positive impact on the society.
This page provides an overview of all the work of our Human Practices. Be sure to click on each link to see how Human Practices are benefiting and
shaping our project.
<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" id="s2">
Timeline
</div>
<div style="text-align: center;">
<img src="https://static.igem.wiki/teams/4815/wiki/devider.png">
<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 class="timeline">
<div class="timeline-item">
<div class="date">May</div>
<div class="content">
<h2 class="wenbenkuang">Pre-survey questionnaire (about perspectives and perceptions of synthetic biology and iGEM)</h2>
<h2 class="wenbenkuang">School fair booth (synthetic biology knowledge popularization and team project publicity)</h2>
<h2 class="wenbenkuang">NIA meetup (exchange project design and progress with other 8 teams from Nanjing)</h2>
</div>
</div>
<div class="timeline-item">
<div class="date">June</div>
<div class="content">
<h2 class="wenbenkuang">Discussion with experts of synthetic biology and AI (about the shortcomings of the current design and arrange for the
planning of upcoming experiments)</h2>
<h2 class="wenbenkuang">Questionnaire (about the application, evaluation and future of AI in working and research)</h2>
</div>
</div>
<div class="timeline-item">
<div class="date">July</div>
<div class="content">
<h2 class="wenbenkuang">10th CCiC (share our project and communicate with over 80 teams)</h2>
<h2 class="wenbenkuang">University education lecture in Nanjing University (themed on AI for Biology)</h2>
<h2 class="wenbenkuang">Volunteer teaching in secondary school in Yunnan</h2>
<h2 class="wenbenkuang">Publish science promoting articles on official accounts (about Mucosal vaccine, AI for synbio and transfer learning)</h2>
</div>
</div>
<div class="timeline-item">
<div class="date">August</div>
<div class="content">
<h2 class="wenbenkuang">Seminar discussion on AI for synbio (share ideas about the application of AI in synthetic biology with other iGEM teams)</h2>
<h2 class="wenbenkuang">Visit to Carbon Silicon Institute of Artificial Intelligence Biomedical Research and interview the principal</h2>
<h2 class="wenbenkuang">Visit to Nanjing Yiweisen Biotechnology Co., LTD and interview the principal</h2>
<h2 class="wenbenkuang">Visit to Genscript Biotech Corporation. and interview the bioinformatics senior engineer</h2>
<h2 class="wenbenkuang">
Color the picture book about synthetic biology with AS children and introduce synthetic biology</h2>
</div>
</div>
<div class="timeline-item">
<div class="date">September</div>
<div class="content">
<h2 class="wenbenkuang">Debate competition (about the pros and cons of AI application in education and Scientific research)</h2>
<h2 class="wenbenkuang">
Stage play for senior high school students ( about the discovery of DNA and our project)</h2>
</div>
</div>
</div>
<div class="dahe">
<div class="dabiaotihe" id="s3">Integrated HP</div>
<div style="text-align: center;">
<img src="https://static.igem.wiki/teams/4815/wiki/devider.png">
</div>
<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">
<img src="https://static.igem.wiki/teams/4815/wiki/ihp.png" class="tiansuohao2" style="width: 60%">
<p>On the integrated Human Practices page we explain the problem we face and how we came to
the solution to the problem. To validate the problem and the solution, we involved the
stakeholders and their requirements in project, and managed them as efficiently as
possible through a power-interest matrix. We worked with our stakeholders to examine the
needs, technical, corporate, social, safety and ethical considerations of the project.
To do this, we have communicated with various stakeholders, including <a style="font-weight: bolder">synthetic
biologists, AI experts, AI pharmaceutical companies and others</a> through online and
face-to-face interviews, as well as on-site surveys. Based on the feedbacks, we closed
the loop between what was designed and what is desired.<br>
Please click the <a href="{{ url_for('pages', page='human-practices') }}" style="color:#5271FF">integrated HP
link</a>&nbsp;
to read the complete Human Practices journey we went through with our partners.</p>
<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="clear"></div>
<div class="dahe">
<div class="dabiaotihe" id="s4">Partnership</div>
<div style="text-align: center;">
<img src="https://static.igem.wiki/teams/4815/wiki/devider.png">
</div>
<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">
<img src="https://static.igem.wiki/teams/4815/wiki/part.png" width="100%" class="tiansuohao2">
<p>We are pleasant to work with several different iGEM teams on various kinds of collaborations,
which we benefit a lot and they can also learn something from us. Through collaborations, we
provide and get peer support and review, enhance creativity and advanced our project.<br>
Please click the <a href="{{ url_for('pages', page='partnership') }}" style="color:#5271FF">partnership
link</a>&nbsp;
to learn more about our communications and collaborations with other teams.
</p>
<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="clear"></div>
<div class="dahe">
<div class="dabiaotihe" id="s5">Education</div>
<div style="text-align: center;">
<img src="https://static.igem.wiki/teams/4815/wiki/devider.png">
<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 class="wenbenkuang">
<img src="https://static.igem.wiki/teams/4815/wiki/edu.png" width="130%" class="tiansuohao2">
<p>It's interesting and meaningful to communicate and share knowledge around our project, and
expand the boundaries of our work. We believe that, on the one hand, more efforts are needed
to promote the field and iGEM competition by making the public aware of the many real-world
problems that synthetic biology can solve. On the other hand, we hope to share how AI has
helped us in solving problems using synthetic biology methods, and how it is easier than we
thought for non-AI professionals to use AI tools to assist their work and life, ranging from
pupils to professors.AI for synbio in general and all the jobs that are part of this field
deserve to be put under the spotlight and we wanted to contribute to that. <br>
Please click the <a href="{{ url_for('pages', page='education') }}" style="color:#5271FF">education link </a>to
read the convivial moments of discovery, sharing and exchanges of scientific interests.</p>
</div>
</div>
<div class="clear"></div>
</div>
</div>
</div>
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