Team:SYSU-Software/Attributions
OVERVIEW
During the period when our main project gradually developed from nothing,
all the team members participated in the project with great enthusiasm, contributing most of their time.
Other organizations and individuals also offered great help on our project,
including fundraising, workplace, experiment materials, software suggestions and technical support.
All of us are very grateful for the contribution of our team members, and acknowledging the support from others.
CONTRIBUTION
Attribution
Summary
YAO, Nan: team leader; established the overall frame of CRAFT and proposed the function of circuit auto-design from the target.
DENG, Kaiwen: team leader; data for database; content for wiki; managing the human practice
ZENG, Ziyi: model selection and establishment; content for wiki; modeling the process of searching and filtering.
LIU, Minxue: PM of validation experiment; communication for experimental support; Interlab project
LIU, Ren: validation experiment; content for Human Practice in wiki; Interlab project
WANG, Baiyu: validation experiment; Interlab project; financial management
ZENG, Dongyu: validation experiment; Interlab project
WANG, Xi: main UI designer of project and Genexplorer; design of team banner, uniform and CCiC poster
NIE, Ziyan: Human Practice participation
SHEN, Zhongyue: Human Practice participation; content for wiki
ZHANG, Zheng: Human Practice participation
LI, Tianqin: Human Practice participation
ZHANG, Zijie: mathematical modeling of project, including optcom, d-optcom, promoter and RBS strength calculation.
CHEN, Fengjie: mathematical modeling of project, including optcom, d-optcom and RBS strength calculation.
WU, Ziming: back-end of project, including searching, filtering and d-optcom realizing; data clean.
LIN, Xiaoya: back-end of project, including promoter and RBS.
LI, Yuzheng: front-end of project.
YANG, Zhanfu: data for database.
YU, Le: wiki programmer, responsible for editing and posting of wiki contents; collaboration project programmer.
ZHONG, Yujie: main UI designer of project and Genexplorer; design of uniform, poster and PPT for presentation.
Attributions
in details
Project
All team members participated in the design and ideas in our project. Nan Yao mainly described the overall framework.
Ziming Wu and Xiaoya Lin were mainly responsible for the back-end of the software. Yuzheng Li was mainly responsible
for the front-end of the software.
CRAFT(Community-based Retro-synthetic Analysis Functional Platform)
Circuit Auto-generation System
[1] Ideas and Designs
Nan Yao and Kaiwen Deng proposed the basic method of traversing circuit and biological filtering standard, including
circuit length, transporters and free energy.
Nan Yao also found the theoretical support on circuit selection, method of promoter and RBS strength calculation.
Fengjie Chen and Zijie Zhang designed and modified the modeling module.
Xi Wang designed the user interface, and Yujie Zhong improved the design, polishing the details.
[2] Database
Kaiwen Deng and Nan Yao found the database for this function in our project.
Baiyu Wang mailed to the official and asked for the development license.
Zhanfu Yang helped retrieve data from these databases.
Ziming Wu, Kaiwen Deng and Nan Yao cleaned these data and determined standard data form.
[3] Implementation
Ziming Wu was responsible for the back-end of this auto-generation system.
Yuzheng Li was responsible for the front-end of this part and improved user interface.
Experimental Scheme System
[1] Ideas and Designs
Nan Yao proposed the main idea.
Dongyu Zeng and Baiyu Wang determined the software standard function flow of this part.
Xi Wang and Yujie Zhong designed user interface, polishing the details.
All team members participated in the improvement of this system.
[2] Database
Dongyu Zeng and Baiyu Wang collected the protocol data from database.
Yuzheng Li found a visual module to exhibit the plasmid.
[3] Implementation
Xiaoya Lin was responsible for the back-end of Experimental Scheme System.
Yuzheng Li was responsible for the front-end of this system, improving the user interface.
User Community
Xi Wang, Yujie Zhong designed the user interface, and Yuzheng Li was responsible for the front-end, implementing
the design; Xiaoya Lin was responsible for the back-end.
Wet-lab Practice
Dongyu Zeng was responsible for Interlab.
Minxue Liu was responsible for the validation experiment.
Minxue Liu, Dongyu Zeng, Baiyu Wang and Ren Liu all participated in Interlab and the validation experiment.
Mathematical modeling
Nan Yao and Ziyi Zeng found the theoretical support of our project.
Fengjie Chen, Zijie Zhang was responsible for altering the model.
Human Practice and Collaboration
Overview: All team members participated in some part of our Human Practice. For more details see (link).
Genexplorer
Dongyu Zeng proposed the idea of the game, and Ziming Wu, Xiaoya Lin, Yuzheng Li helped improve its rules and implement the game.
Xi Wang mainly designed the elements in this game.
Biology Festival
Kaiwen Deng was responsible for planning the activity.
Xi Wang designed the banner to advertise our activity and took pictures for us.
Ren Liu bought the materials for this activity.
All team members participated to some extent in the Festival.
Bio-5-Talk
Kaiwen Deng was responsible for the model design and bought the materials for constructing this model.
Kaiwen Deng, Ziming Wu, Tianqin Li and Zhongyue Shen participated in this activity.
Senior High School Summer Camp
Kaiwen Deng and Tianqin Li organized the presentation, and Baiyu Wang helped make PPT for this presentation; Xi Wang took photos when presenting.
CCiC held in Sun Yat-sen University
Baiyu Wang, Xi Wang, Minxue Liu, Tianqin Li, Zhongyue Shen, Ren Liu and Zheng Zhang participated in or contributed to CCiC organization collaborating with SYSU-CHINA.
Kaiwen Deng and Nan Yao organized our presentation, and Xi Wang took photos for us.
Person of the Year in Sun Yat-sen University
Xiao Feng and Zhengyang Wen made presentation in this ceremony.
All team members participated in this ceremony as audience or photographer.
Collaboration with NJU-China
Le Yu designed a tool to generate and select siRNAs based on given mRNA sequences. For more details see link.
Speaking to Freshmen
Zhongyue Shen, Ziyan Nie, Zheng Zhang, Tianqin Li organized and made the presentation for freshmen.
Weilin Xu advised this presentation and took photograph for them.
Consult to the Professor
Zhongyue Shen, Ziyan Nie, Tianqin Li, Zheng Zhang and Kaiwen Deng contacted and communicated with the teacher
Teacher Jie Zhang gave us suggestions on biosafety regulations and safety problems of our software.
Annotation the Promoter in iGEM Registry
Ziyi Zeng, Zijie Zhang found related methods for calculating strength from sequences
Xiaoya Lin implemented this method.
Documentation, Art and Design
Wiki
Contents
Kaiwen Deng, Ren Liu were mainly responsible for the contents of the wiki. All other team members also participated in or contributed to the contents of the wiki.
Designs
Yujie Zhong and Xi Wang were responsible for the design of wiki.
Programming
Le Yu was responsible of implementing the design and representing all the completed work on the web.
Uniform
Yujie Zhong and Xi Wang were responsible for the designs of uniforms.
Team Banner, Poster and PPT
Yujie Zhong and Xi Wang were responsible for the designs of these art works.
Financing and Planning of the Journey to Boston
Kaiwen Deng and Xi Wang was responsible for planning the journey to Boston, booking tickets and hotels.
Our advisor Xiangwan Lu helped us with the financial work, applying financial support.
ACKNOWLEDGEMENTS
Project support and advice:
Prof. Xionglei He gave us advice on our project, figuring out the meanings and applications of our idea.
Prof. Wensheng Shu supported our project with theories about microorganism communities.
Prof. Jianhua Yang 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. Jian Ren provided us a working place, also gave us advice on our main project, suggesting some improvements of our software.
Prof. Yan Zhang supported us on fundraising and working place application strongly, relieving out burden and motivating us to work harder.
Prof. Yongjun Lu gave advice on the biosafety and guided us on safe experiment operation.
Fundraising 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. Yan Zhang and Xiangwan Lu helped us a lot on registering for the 2016 iGEM Giant Jamboree and paying the fees.
Prof. Yan Zhang, Prof. Yongjun Lu and Prof. Jianhua Yang helped us raise the funds for wet lab validation.
Lab Support:
Wet-lab Support
Prof. Yongjun Lu and Prof. Yikang Rong kindly provided us with the lab spaces as well as materials needed to do our validation experiment and Interlab during our project. Ph.D. student Dongni Chen, a member in Prof. Yongjun Lu’s lab, selflessly guided us how to operate our experiment.
Prof. Xinhui Xing, Chong Zhang, Mei Li, from School of Life Sciences, Tsinghua University, kindly provided us with their plasmid, relieving us from constructing new vectors.
Dry-lab Support
Prof. Jian Ren and Prof. Yan Zhang offered us classroom and lab where we can work on our project during summer vacation.
Microsoft Student Technology Club of Sun Yat-sen University kindly offered us the space where we worked on our project during the new semester. Club members also helped us solve some problems when using computers.
Project advisor support
Xiao Feng gave us suggestions on describing our main ideas and reminded us the importance of following basic synthetic biology principles when designing our software.
Shengkun Dai gave us advice on solutions when we faced convoluted problems, and guided us how to construct our project with scattered ideas.
Peng Nie, team member of 2014 SYSU-Software, gave us advice on software designing, including the principles in software engineering to judge a software.
Weilin Xu gave us suggestions on the competition rules, correcting our mistakes during whole project.
Wiki support:
Xiao Feng gave us suggestions on how to plan the layout of our wiki and reminded us to construct necessary pages in our wiki.
Weilin Xu gave us suggestions on our wiki contents that we should demonstrate our work in a simple way.
Presentation Coaching:
Prof. Jianhua Yang gave us advice on how to clearly express our project in the presentation and provided an example flow.
Xiao Feng gave us advice on which parts in our project should be emphasized and how to integrate our presentation into an intact story.
Human Practice and Collaboration Support:
School of Life Sciences have provided a lot for our activity of Biology Festival and our presentation for High School Summer Camp. We acknowledge them for their kind help.
Many thanks to the South China University of Technology, where the Bio-5-Talk held and arranged. Their activity provided a platform for us to spread synthetic biology with material objects.
We collaborated with NJU-China 2016 iGEM team and developed a tool for generating siRNAs based on given mRNAs, and NJU-China tried and helped us identify the bugs in the tool.
