Team:SYSU-Software/Attributions
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Team:SYSU-Software/Attributions
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Attributions
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 generous support and help.
In addition, our project is supported by School of Life Sciences, Sun Yat-Sen University, both financially and academically. Thus, we want to express our genuine 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. The following graphs are an overview of our attributions within the team.
Table | work description
Table | detailed attributions of each part of our project
Team Work
- biology group
Ruoheng Mo Responsible for the overall control of our team's operation, seriously considering every team member's viewpoints to decide what we do next, coordinating the progress of different group (bio group, programming group, math group, designers group) and also different parts of the project, delineating the deadlines and assigning tasks.
Weining Li Worked on providing the idea of our project, designed the experiments and designed the opto-controllable transcription factor part of Phoebus.
Shulin Jin In charge of the collecting and merging of opto-control protein data. Besides, I lead part of the HP works.
Binrun Liang Participated in the design of our project, data collection of the optical control database and wet experimental work, and completed some other basic works like HP and deliverables.
Junyi Dai Responsible for the docking task between the biology group and the digital module group in the team. I also did some basic work on searching and did part of HP work.
Wentao Deng Worked on the part of linker design, apart from this, I also took part in some other basic parts, like paper reading and HP works.
Tong Su Responsible for protein structure prediction, finding and interfacing with programmers for programs related to protein structure prediction and fusion protein activity prediction. I also participated in human practices, made a speech to senior high school students to promote Phoebus, and took part in experimental verification.
Bairu Liu My main job is to do some literature search and study related to the project, and participate in the discussion of the various sections of the project. I also write copy for videos.
Yuanjin Wang I helped the team narrow our focus to optogenetics in the early stage and participated in the readings, collecting domain information for example, and discussions along the process. Currently, I am working on HP program.
Jingyi Zhang At the beginning, I took part in collecting statistics of phytochromes and their mutations. I'm the narrator in our promotion video, and the writer of our presentation video. I'm also in charge of the "Phoebus community" functional design.
Yixian Guo I mainly worked in the aggregation of light-controlled proteins. I collect the required information and solve the problems by consulting the literature. I am also responsible for writing some materials.
Siduo Li Responsible for Linker Design project, developed the scheme of screening linker, realized the connection between photosensitive protein and target protein as well as maintained the activity of the fusion protein; Participated in the project of structure prediction and experimental design.
- modeling group
Hezhou Li I helped build the model of cascade reaction to predict the change of reaction rate brought by the change of light.
Yukang Zeng My major work was the design of back-end algorithms and plug-ins, and front-end and back-end integration. I participated in constructing the model that calculates the reaction rate of photocatalytic enzyme cascades, and the submodels that calculate parameters including the distance between active sites and their areas. I implemented the algorithms relevant to the aforementioned model and submodels, and designed the user interface of the plug-ins and the procedure of data transmission between the front-end and the back-end.
Haoran Lu Participated in the modeling of the two step enzymatic cascades reaction.
- programmers
Qianru Lao Make overall arrangements for the programming group, take responsibility for back-end server setup and maintenance, design and apply the trRosetta2 to structure prediction, develop and deploy the structure prediction, activity evaluation and sequence optimization modules of the software.
Siran Liu Responsible for the construction and maintenance of the back-end file server as well as the linker database, completing the efficient search and construction of the linker at the algorithm design level.
Li Liang Responsible for the construction of the database and website building.
Jingyun Ye Responsible for collecting the information of transcription factors, building a database for it and providing interfaces for our application to access.
Jingyun Huang Dedicated to the front-end web development; taking responsibility for the user interface, including Community and opto-controllable enzyme proximity. Additionally, implementing the connection with the related back-end server.
Qiyun Zhou Responsible for designing the overall architecture of the front-end app as well as how it can interact with the rest parts of the whole application.
Yue Qing Participated in web development on the pages of home and optical transcription.
Tian Wu Participated in the parts of the construction of front-end.
- designers
Yilin Zhong Responsible for art design, I mainly design and beautify our logo, poster and video.
Yuhou Chen Responsible for art design, I mainly design and beautify our logo, posters, video, and wiki pages.
Zeyu Huang Responsible for the design of our logo, poster, wiki, etc. In charge of wiki edition.
Database
- TF Database
Footprint DB
Sebastian A, Contreras-Moreira B. footprintDB: a database of transcription factors with annotated cis elements and binding interfaces. Bioinformatics. 2014 Jan 15;30(2):258-65. doi: 10.1093/bioinformatics/btt663. Epub 2013 Nov 14. PMID: 24234003.
cristrome DB
Shenglin Mei, Qian Qin, Qiu Wu, Hanfei Sun, Rongbin Zheng, Chongzhi Zang, Muyuan Zhu, Jiaxin Wu, Xiaohui Shi, Len Taing, Tao Liu, Myles Brown, Clifford A. Meyer, X. Shirley Liu, Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse, Nucleic Acids Research, Volume 45, Issue D1, January 2017, Pages D658–D662, https://doi.org/10.1093/nar/gkw983
TB database
Reddy TB, Riley R, Wymore F, Montgomery P, DeCaprio D, Engels R, Gellesch M, Hubble J, Jen D, Jin H, Koehrsen M, Larson L, Mao M, Nitzberg M, Sisk P, Stolte C, Weiner B, White J, Zachariah ZK, Sherlock G, Galagan JE, Ball CA, Schoolnik GK. TB database: an integrated platform for tuberculosis research. Nucleic Acids Res. 2009 Jan;37(Database issue):D499-508. doi: 10.1093/nar/gkn652. Epub 2008 Oct 3. PMID: 18835847; PMCID: PMC2686437.
hTFtarget
Zhang Q, Liu W, Zhang HM, Xie GY, Miao YR, Xia M, Guo AY. hTFtarget: A Comprehensive Database for Regulations of Human Transcription Factors and Their Targets. Genomics Proteomics Bioinformatics. 2020 Apr;18(2):120-128. doi: 10.1016/j.gpb.2019.09.006. Epub 2020 Aug 26. PMID: 32858223; PMCID: PMC7647694.
TRANSFAC
Wingender E, Chen X, Hehl R, Karas H, Liebich I, Matys V, Meinhardt T, Prüss M, Reuter I, Schacherer F. TRANSFAC: an integrated system for gene expression regulation. Nucleic Acids Res. 2000 Jan 1;28(1):316-9. doi: 10.1093/nar/28.1.316. PMID: 10592259; PMCID: PMC102445.
- Conserved Domain Database
Marchler-Bauer A, Anderson JB, Cherukuri PF, DeWeese-Scott C, Geer LY, Gwadz M, He S, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Liebert CA, Liu C, Lu F, Marchler GH, Mullokandov M, Shoemaker BA, Simonyan V, Song JS, Thiessen PA, Yamashita RA, Yin JJ, Zhang D, Bryant SH. CDD: a Conserved Domain Database for protein classification. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D192-6. doi: 10.1093/nar/gki069. PMID: 15608175; PMCID: PMC540023.
Project Adviser Support
Prof. Jianhua Yang Offered timely advice and instructions throughout the process. He gave us advice on how to plan our schedule, arranging the progress.
Guanzheng Luo Prof.Luo allowed us to do experiments in his lab, and ask some of his postgraduate students to answer our questions and gave us assistance.
Zhumei He Prof.He gave us suggestions on biosafety regulations and safety problems of our software.
Tianqin Li Gave advice on software design, presentation, Human Practices and Collaborations.
Tianlun Lei Gave advice on software design and helped us conduct the wet-lab work.
Yanrong Lv Majored in marine biology, former 2017 iGEM SYSU-Software team member, participating in interviews; providing the idea of the project, experimental and bioinformatics guidance.
Project Support and Advice
Mr. Jianfei Xi gave us some information on how researches design or choose linker; Dr. Chuanfei Liu gave us instructions on user intellectual protection; Dr. Biao Lv and Dr. Huang discussed with us the needs of bio-technology companies, and told us what kinds of software are helpful.
Fundraising Help and Advice
School of Life Sciences, Sun Yat-Sen University covered Team Registration Fee and experimental Fee, which greatly reduced our burden. Prof. Cui Jun, Ms. He Sumin helped us a lot on registering for the 2021 iGEM Giant Jamboree and paying the fees.
Lab Support
Prof. Guanzheng Luo kindly provided us with the lab and experiment materials and related equipments, which guaranteed our success of the experiments. Ms. Chen Hongxuan kindly gave us directions and advice in the wet-lab.
Human Practices and Science Communication Support
The Student Union of School of Life Sciences gave us support on the mini class and the speech to freshmen and sophomores.
Wiki Support and Presentation Coaching
School of Communication and Design, Sun Yat-Sen University provides us with wiki design support. Prof. Yang Jianhua trained us on how to organize the presentation clearly and logically.
Technique Support
Team SYSU-CHINA helped us develop experimental plans and guided us how to do experiments. Ms. Senxuan Han guided us how to do experiments. Former members Mr. Junli Du, Ms. Yue Zeng, Mr. Enze He and Mr. Yuze Fu gave us instruments and advice.
Collaboration Support
We sincerely thank the 8th iGEM CCiC for inviting us to the conference. We sincerely thank SYSU-CHINA for providing us with wet-lab support, co-holding some HP activities, trying our software and giving back precious feedback.
Acknowledges for General Support
