Overview

In the past ten months, we went through many twists and turns, but we finally pulled the project off successfully. We would like to sincerely thank the school, team members, other cooperative teams and other aspects for their support and help in this pandemic.

In addition, our project is supported by School of Life Science, Sun Yat-Sen University, both financially and academically. Thus, we especially want to express our gratitude to all these help.
SYSU-Software has always been focusing on interdisciplinary collaboration. This year, our team is well organized and consists of four groups. Everyone is put to their best position.

Following graphs are an overview of our attributions within the team.

division of work	explanation
Search and learn	Mainly refers to looking for literature or results, to learn to support the project
Code	Mainly refers to code writing, program design, program optimization and so on
Publicity	Mainly refers to the Wechat passage, wiki design and writing, posters and video production
HP & Col	Mainly refers to the completion of iGEM requirements of HP, Colla
Lab	Mainly refers to the participation of wet experiment and project verification
Communication	Contact PI and Advisor or the institution to determine information and plans
Finance	Contact reimbursement affairs

	Junli DU	Yue Zeng	Youqi Wang	Xiaoyan Zhang	Musen Lin	Xinyao Zhou	YIfei Zang	Qing Lu	Weining Li	Ruoheng Mo	Shulin Jin
Search and learn	🙋	🙋	🙋	🙋	🙋	🙋	🙋	🙋	🙋	🙋	🙋
Code	🙋		🙋	🙋				🙋
Publicity									🙋
HP&Col	🙋	🙋	🙋		🙋	🙋			🙋		🙋
Lab					🙋			🙋
Communication	🙋	🙋	🙋						🙋	🙋
Finance	🙋	🙋									🙋

Individual Attributions

Biology Group:

Biology Group consists of 11 undergraduates from the School of Life Sciences in Sun Yat-sen University, located in Guangzhou, China. We are enthusiastic about synthetic biology and combining it with Computer Sciences and Mathematics. We are responsible for designing the high-level mechanisms of the program and supervising applications of synthetic biology throughout the process.

1.Junli Du 杜俊利（Student Leader）

Design software functions, Organize the team, seek for new idea, propose implementation methods, arrange experiments, write presentation materials.

2.Yue Zeng 曾玥（Student Leader）

Make overall arrangements for the team, design and evaluate software functions, manage funds, arrange experiments write and design presentation materials.

3.Youqi Wang 王佑琪

design software functions, leader of Image Search module, design and arrange Science Communication, write presentation materials.

4.Xiaoyan Zhang 张笑妍

Leader of Design module, contact with modeling group, write presentation materials.

5.Musen Lin 林沐森

Search database, write presentation materials，make survey about the synthetic biology, conduct wet-lab work.

6.Xinyao Zhou 周欣瑶

carry out human practices, contact with modeling group, write presentation materials.

7.Yifei Zang 臧怡飞

Design genetic circuit expression simulation, write presentation materials.

8.Qing Lu 卢擎

Connect biology group and program group, conduct wet-lab work.

9.Ruoheng Mo 莫若衡

Complete part of Science Communication, write presentation materials.

10.Shulin Jin 金树林

Design and carry out Human Practices, write presentation materials.

11.Weining Li 李蔚苧

Design and carry out Human Practices, write presentation materials.

Modeling group:

Modeling Group consists of 4 undergraduates form the School of Mathematics in Sun Yat-sen University. We learning key algorithms required to implement the project and converting them to functional codes which are later shared with team coding.

1.Bei Zhang 张贝

Exalt the GeneNet algorithm to apply to PDE.

2.Jiahang Cao 曹嘉航

Implement GeneNet algorithm and Bayesian Optimization.

3.Jiahao Cao 田嘉豪

Help to design Bayesian Optimization and write the Moldeling part of Bayesian Optimization.

4.Likun Zhang 张理昆

Help to design Bayesian Optimization.

Programmers:

Programmers consists of 4 undergraduates in the School of Data and Computer Science in Sun Yat-sen University. We are responsible for desgining algorithm for our project, as well as implementing the framework of the software, further encapsulation and optimizations.

1.Yuze Fu 傅禹泽

Design and implemented software user interface. Participated in database data generation.

2.Yongye Su 宿永烨

Design and apply the Yolo, Bayesian Optimization, transfer learning regression algorithm to Image search, Parameter Optimization and TF-BS affinity forecast.

3.Enze He 贺恩泽

Develop image recognition using YOLO and OCR, and mainly responsible for server backend to integrate all non-user-oriented services within one backend application.

4.Yawen Guan 关雅雯

Take responsibility for database construction and implementation of the search algorithms.

Designers:

Designers consists of 4 undergraduates from the School of Communication and Design in Sun Yat-sen University. We are responsible for designing academic posters, promotion video, beautify and customize the wiki pages

1.Jiangyue Yuan 袁江月

Design logos, poster, promotion video, presentation video and wiki interface. Beautify pictures and draw illustrations.

2.Yilin Zhong 钟艺琳

Shoot and design promotion video, Typography of wikis and poster, Processing pictures, Production of presentation video.

3.Yuhou Chen 陈雨后

Shoot and design promotion video, Typography of wikis and poster, Processing pictures, Production of presentation video.

4. Haoxi Zhang 张昊熹

Construct the wiki of our project.

Primary PI:

Jianhua Yang 杨建华

Outstanding academic skills and prior experience supervising multiple iGEM teams. Offered timely advice and instructions throughout the process. He gave us advice on how to plan our schedule, arranging the progress. He also emphasized the creativity in our main project and the standard flow of presentation.
Research interests: disease RNA genomics; functional non-coding RNA and regulatory networks; high-through-put data Informatics.

Advisors:

1.Tianqin Li 李天钦

Graduate student at Carnegie Mellon University, School of Computer Science. Interested in Deep Learning, Computer Vision, Computational Biology, Computational neuroscience
Give advice on software design, presentation, Human Practices and Collaborations.

2.Tianlun Lei 雷天伦

Graduate student at Carnegie Mellon University, School of Computer Science. Interested in Deep Learning, Computer Vision, Computational Biology, Computational neuroscience
Graduate student at Sun Yat-sen University, School of Life Science. Give adive to our software design and help us to conduct the wet-lab work.

Instructors:

1.Zhumei He 贺竹梅

Prof.He gave us suggestions on biosafety regulations and safety problems of our software.
Research interest：Molecular mechanism of aflatoxin anabolism regulation and biological control technology of aflatoxin.

2.Jian Ren 任间

Prof.Ren gave us suggestion on program design and presentation skills.
Research interest: proteome Informatics; genome Informatics; cancer Informatics; supercomputing

3.Jianzhong Liu 刘建忠

Prof.Liu gave us suggestion on lab work and experiment design to validate our software.
Research interest: Microbial metabolic engineering and synthetic Biology

4.Zeng Kun 曾坤

Prof. Zeng Kun gave us advice on machine learning and biomedical research.

Database

IGEM Registry

https://synbiohub.org/public/igem/igem_collection/1

RegulonDB

RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12.
Alberto Santos-Zavaleta, Heladia Salgado, Socorro Gama-Castro, Mishael Sánchez-Pérez, Laura Gómez-Romero, Daniela Ledezma-Tejeida, Jair Santiago García-Sotelo, Kevin Alquicira-Hernández, Luis José Muñiz-Rascado, Pablo Peña-Loredo, Cecilia Ishida-Gutiérrez, David A Velázquez-Ramírez, Víctor Del Moral-Chávez, César Bonavides-Martínez, Carlos-Francisco Méndez-Cruz, James Galagan, Julio Collado-Vides
Nucleic Acids Research, Volume 47, Issue D1, 08 January 2019, Pages D212?D220, doi: https://doi.org/10.1093/nar/gky1077.
PMID: 30395280 PMC: PMC6324031

Uniport

The UniProt Consortium, UniProt: a worldwide hub of protein knowledge, Nucleic Acids Research, Volume 47, Issue D1, 08 January 2019, Pages D506–D515, https://doi.org/10.1093/nar/gky1049.

Acknowledgements

Sun Yat-sen University

School of Life Sciences, Sun Yat-Sen University

School of Communication and Design, Sun Yat-Sen University

School of Data and Computer Science, Sun Yat-Sen University

School of Mathematics, Sun Yat-Sen University

KingMed Diagnotics，Guangzhou headquarters

Project support and advice:

  • Prof. Yang Jianhua gave us advice on how to plan our schedule, arranging the progress of every member. He also emphasized the creativity in our main project and the standard flow of presentation.
  • Prof. Ren Jian gave us advice on our main project, suggesting some improvements software.
  • Prof. He Zhumei gave advice on the biosafety.
  • Prof. Liu Jianzhong gave advice on Biosafety and how to conduct our wet-lab validation.
  • Prof. Zeng Kun gave us advice on machine learning and biomedical research.
  • Guang Dong Ying Zun Law Firm gave advice on intellectual property and other legal issues.
  • Ms Xiao Dongqi from KingMed Diagnotics gave us an introduction of the application of biotechnology in the dianotics industry. She also answered our questions on softwares and the application of synthetic biology in this field.

Fund raising help and advice

• School of Life Sciences, Yat-sen School covered the fees of flights, accommodation and also Team Registration Fee and Jamboree Attendance Fee, which greatly reduced our burden.
• Prof. Cui Jun, Ms He Sumin helped us a lot on registering for the 2020 iGEM Giant Jamboree and paying the fees.

Wet-Lab Support

• Prof. Yang Jianhua kindly provided us with the lab and experiment materials and related equipments, which guarantee our success of the experiments.
• Mr. Li Bin kindly gave us directions and advice in the wet-lab.

Project advisor support

  • Mr. Li Tianqin gave us suggestions on our project goals and ideas and gave us instructions on computer algorithms.
  • Mr. Lei Tianlun guided us through the wet-lab validations.
  • Mr. Feng Xiao gave us advice on project goals and ideas.
  • Ms. Shi Huili gave us advice on collaboration and wiki writing

Presentation Coaching

• Prof. Yang Jianhua trained us on how to organized the presentation clearly and logically.
• Prof. Ren Jian gave some important advice on the persentation.

Human Practice and Science Communication Support

• The Student Union of School of Life Sciences of Sun Yat-Sen University gave us support on the mini class and the speech to freshmen and sophomores.
• The Promoter Club in the School of Life Sciences of Sun Yat-Sen University gave us support by co-hosting the mini class with us.

Collaboration Support

  • We sincerely thank all the 55 interviewee inside and outside iGEM for helping us fill out our questionnaire.
  • School of Life Sciences of Sun Yat-Sen University gave us support for holding the first Conference of China Software iGEMer Community (CCSiC)
  • Prof. Yang Jianhua and Mr. Li Tianqin have gave us comments and instructions on the CCSiC.
  • We sincerely thank the 7th iGEM CCiC for inviting us to the conference and helped us hold a workshop.
  • We sincerely thank Tongji-Software for co-hosting the CCSiC and CCiC workshop with us and provide us with software support.

Team:SYSU-Software/Attributions