Collaboration

Since the beginning of our project, we have been searching for collaborations for realization of HEATMAP. We systematically classified our collaboration into 6 parts, respectively cooperations with researchers&laboratories, teams, schools, enterprises, and public organizations.

The State Key Laboratory of Microbial Metabolism (Shanghai Jiao Tong University) was approved by the Ministry of Science and Technology in 2011. Facing the frontier of microbial metabolism science and major industrial needs, the laboratory explores the mechanism of microbial synthesis and catabolism, reveals the physiological function, regulatory network and interaction mode of microbial metabolic activities, and strives to scientifically explore the inner driving force of microbial cell factories, serving the transformation and upgrading of modern biological industry, and realizing the optimal release of microbial metabolic potential.

At the beginning of our project when we were looking for reasons that lead to low purity and unit yield of spinosad, we went to State Key Laboratory of Microbial Metabolism-Bai group. Professor Bai Linquan mentioned that improving the production efficiency of spinosad is of far-reaching significance for agricultural development, which can create a virtuous circle that will improve the overall efficiency and sustainability of agricultural production, bringing economic benefits to farmers and environmental benefits to society. After a series of research we did later, as you can see in Integrated Human Practice section, we eventually comfirmed our topic, which is enhancing the production efficiency of spinosad by optimizing the metabolic pathways within Saccharopolyspora spinosa.

After we constructed HEATMAP-AI, we consulted with professor Bai Linquan and did wet experiments at State Key Laboratory of Microbial Metabolism-Bai group to verify the accuracy of our model.

On the one hand, based on these data, we did another circle of model improvement and build up etcGEM model as well. On the other hand, after the optimization of HEATMAP-AI, Bai group can use precise optimal temperature forecasted by our model to have a better and more conprehensive understanding of the metabolic pathway within any other bacterial strain, and transform it to give higher purity and unit yield.

Shanghai Jiao Tong University's Center for High Performance Computing platform is a university-level computing public service platform. The network information Center is responsible for the construction and daily management, and fully supports the teaching, scientific research, management and other computing needs of the whole school.

Thanks to this HPC, we can get high-performance HEATMAP-AI after we input 6090 initial datas of protein sequences and the corresponding optimal tempetature that is already known.

To promote synthetic biology knowledge to younger audiences, we collaborated with Fudan University, Zhejiang University, ShanghaiTech University, and other colleges to create a science picture book. The book use comic-style illustrations and simple language to introduce basic concepts of synthetic biology to young children. This approach aims to spark children's interest in science early, encouraging their curiosity and desire to explore. The science picture book designed for children has also received high praise from parents and educators, being regarded as a valuable tool for early science education. We plan to further promote the book for broader use in educational settings.

Our team actively participated in the "AI and Biosafety" online bioethics roundtable forum hosted by the Xi'an Jiaotong-Liverpool University iGEM team, where we collaborated with several other iGEM teams to explore the applications and challenges of AI technology in synthetic biology and related fields. The forum covered a wide range of topics, including AI applications in gene editing (such as CRISPR technology), biomedical research, public health monitoring, and agriculture, as well as the ethical issues that arise from these applications, such as genetic discrimination, privacy protection, and ecosystem balance.

The success of this forum not only facilitated interdisciplinary scientific discussions but also provided valuable experience and resources for incorporating AI and biosafety topics into our team's future science education work, promoting interdisciplinary collaboration and advancing public education.

Later, we will cooperate together to write a “Whitebook” focused on the safety in AI engineering, hoping to promote a safer biology environment.

University of Science and Technology (ECUST) at Shanghai Jiao Tong University. Both teams engaged in in-depth discussions and shared experiences on project content and Human Practice work. We benefited greatly from the insights and perspectives of ECUST, which broadened our understanding of project design and implementation and inspired creative thinking for future work. Additionally, we provided ECUST team with a guided tour of our campus, including its history, culture, and our laboratory facilities. This exchange deepened the cooperation between the two universities, laying a solid foundation for future inter-school exchanges and collaboration.

In September, we held an online exchange event with Tongji-Software in the purpose of exchanging problems we met and methods we used in the construction of AI model. Since we are both teams in Software&AI, we gained quite a few helps about how to optimize our project from the communication. Simultaneously, we talked about how to expand our project to society, promote the project into practice to ecentually solve worldwide problems.

Despite the challenge of time zone differences, we conducted an online meeting with the iGEM team from Imperial College London. During the meeting, both teams presented their respective projects and shared experiences and insights from their Human Practice work. Team members actively posed questions, provided suggestions, and discussed potential improvements and innovative ideas. This international collaboration not only fostered camaraderie between the teams but also offered new inspiration and opportunities for enhancing both projects. Following the meeting, both teams continued to stay in contact, planning for further collaboration and exchange in the future.

In July, we participated in the 11th China iGEM Community (CCiC) event held at Xi'an Jiaotong-Liverpool University. CCiC is a national conference initiated by iGEM teams in China and has now become one of the largest academic conferences for university students in the country. The theme of this year's CCiC conference is "SynBio Nexus." This significant exchange platform allowed us to share and present our research project with iGEM teams from across China, discussing the latest developments and prospects in synthetic biology. We also engaged in productive exchanges with experts from academia and industry, providing new insights and inspiration for our project.

To better promote our project, we created tri-fold brochures and displayed team posters. Thanks to the unique creativity and exquisite design, our posters won the "Most Popular Poster Award," which not only boosted our team's cohesion but also expanded our social impact.

During SJTUers' Day, we received Shanghai Shixi High School with designed cartoon character representing spinosad, which illustrated stories involving spinosad and various microorganisms in the form of a series of engaging memory cards. These cards were used in games to help participants learn relevant biological knowledge in a relaxed and enjoyable environment. Additionally, we created various merchandise, including keychains, phone stands, stamp booklets, and stamp sets featuring these cartoon elements, which were displayed and sold at our event booth.

Meanwhile, we also asked high school students about their conprehension of synthetic biology. Although they haven’t get accessed to classes related to synthetic biology, most of them had unique views about this subject. Hearing their thinking and questions, we understood most teenagers confusion and acknowledgment of synthetic biology, which promoted out later work in Education section.

Qilu Pharmaceutical Group is a large-scale comprehensive modern pharmaceutical enterprise in China, who takes maintaining human health as its purpose and meeting social needs as its responsibility. Relying on advanced science and technology, Qilu Pharma develops drugs for the treatment of common diseases, frequently-occurring diseases and many other diseases that seriously endanger human health. Qilu Pharmaceutical (Inner Mongolia) Co., Ltd. Hulunbuir Branch Arongqi Base Biopharmaceutical Industry Project has a total investment of 10 billion yuan to build high-end biological pesticides, biological veterinary drugs, high-end human drugs and other products and their research and development bases.

Concerning our project HEATMAP which focused on the problem of low purity and unit yield of spinosad, Qilu Pharma shared problems they met in the actual producing process to suggest that we can infer the cause from effect in the research process, and explore the mechanism after discovering a certain factor to increase the yield. Meanwhile, they supported us in applying AI model to the project, focusing their research on the optimization of optimal temperature and fermentation conditions in the early stage.

Qilu Pharma put a premium on HEATMAP, strenghening the significance of our project, which can play an irreplaceable role in bringing economic benefits to farmers and environmental benefits to society if we realize and industrialize this project. They reached a cooperation with us and gave us financial support for the realization.

Care for life, maintain health. As a leader in green pharmaceutical innovation technology, Jiuzhou Pharmaceutical has mastered in cutting-edge green pharmaceutical technology with independent intellectual property rights, providing customers with industry-leading technical solutions, improving research and development efficiency and success rate, and reducing research and development costs.

Given that Jiuzhou Pharmaceutical Company is one of the best enterprises in green pharmaceutical innovation technology, it is the first company that we got in touch with after we confirmed our topic: Harmonizing Enzymatic Activity and Temperature in Metabolic Pathways. We sent our project plan to Jiuzhou’s board officer Lin Huilu, who soon paid high attention and expectation to our plan. After several online meeting, director Lin approved for further discussion and possible cooperation.

Subsequently, We contacted with engineers in thier biocatalytic platform, introducing our project and exchanging ideas about the prospect of synthetic biology. The engineers spoke highly of HEATMAP and gave us quite a few valuable suggestions on how to realize it. After several weeks’ heated discussion, we signed a contract in April, for the realization of this project.

Chengdu Yunlian Technology Co., Ltd. 's business scope includes communication equipment maintenance and technical consulting, computer technology consulting, computer hardware and software, business management consulting and so on.

At the beginning of this project, we consulted them for common problems we may be faced with during frontend developing, who gave us comprehensive feedback and completed summery of the difficulty and relevant solutions in fronend development.

Hearing the content and schedule of HEATMAP, Chengdu Yunzhiliansheng Science and Technology Company praised our creative idea and gave us financial support to fully realize this project.

Vincent Hawk is a institution that have always adhered to the brand concept of high quality service and private customization. Through Vincent Hawk, we communited with some graduates who used to participate in iGEM. They enthusiastically shared their experience, expressed their affinity for iGEM competition and told us to enjoy the game.

Through Global Graduates’ Union, we also get aquaintance to some graduates who used to participate in iGEM. They enthusiastically shared their experience, expressed their affinity for iGEM competition and told us to enjoy the game.

MGI Tech Company is a subsidiary of BGI Genomics Co.,Ltd., the latter of whom is one of the world's leading life science and genomics organizations, with the mission to use genomics to benefit mankind and to be a leader in the era of life sciences.

At very start of our project, we luckily got contact with MGI Tech Company, asking about the problems they met in synthetic biology field. In August, we gave a mid-term presentation to them, and got really precious advice from the general manager, Wu Li. He emphasized that in the presentation, it is of great significant to present the importance and urgancy of our project, or others who are not quite familiar with HEATMAP may can’t catch and follow out points. We learned a lot from these meeings and continued to improve our team.

Mengniu focuses on providing nutritious, healthy and delicious dairy products to Chinese and global consumers, forming a rich product matrix including liquid milk, ice cream, milk powder, cheese and other categories.

First of all, we consulted about the problems we may met during the directly opimization of metabolic pathways through wet lab. Mengniu Diary shared real producing progress and insisted that this straight optimization is too difficult and troublesome to realize, which confirmed us that we need to use drt lab, the etcGEM, to find out key enzymes in the first step and mutate them through experiment later.

Our team also discussed the social acceptance and safety of synthetic biology products with two PhDs from Mengniu. Dr. Huang first said that the products of synthetic biology have been around for a long time, and there are also a large number of experiences from developed countries that can be used as references in the formulation of relevant domestic regulations, and the approval process is complete and reliable. In addition, synthetic biology-based R&D products will also be less expensive, which can help increase their popularity in society. Dr. Zhao added that synthetic biology products can exclude allergens such as antibiotics and are safer than traditional dairy products for special populations such as lactose intolerance. Therefore, synthetic biology has great application potential in the fields of food, medicine, and chemical products.

Chengdu Zijie Xingqiu Technology Company develops the ABC medical digital platform, the largest primary-level medical digital platform in China, providing a new generation of Internet smart medical products for clinics, medical libraries, community hospitals and grade hospitals.

We consulted with them about works in both frontend and backend, heared their experience and learned the methods they used.