Team:Tongji-Software/Attributions

ATTRIBUTIONS
What makes Alpha Ant meaningful and wonderful is those
people’s great work.
 Since we are from different majors, all things can be covered by everyone of us. More information about team members could be found in Team.Generally, we have three main sessions: biology logic thinking and investigation, programming and modeling, design.
It’s more like a workflow. At first, everyone is engaged in previous biology research and decide to do a topic about pathway design. Secondly, biology group try to get access to different database and deliver data to programming group. Then data processing and main part programming are followed. At last, design group can figure out how to show our software reasonably and wiki design.
Overview
Previous Research
  • Haiyan He, Xiaotian Yu, Zhichao Ma and Wei Cao are responsible for learning synthetic biology and mining proper topic.
  • Wei Cao investigated the barriers that experimenters could occur in metabolic engineering and interviewed Professor Ping Li for Tongji University for general workflow of metabolic pathway research.
  • Zhichao Ma communicated with postgraduate students major in bioinformatics.
  • Xiangzhen Li did some research on graph theoretic algorithm.

Database
  • Xiaotian Yu, Xiangzhen Li and Zhichao Ma were responsible for getting data from KEGG Database and data processing.
  • Haiyan He and Xiaotian Yu were responsible for calculating thermodynamic data by using equilibrator.
  • Zhichao Ma and Wei Cao was responsible for getting data from Brenda, ChEBI, DrugBank and KnowledgeBase.

Search algorithm & Ranking criteria
  • Xiangzhen Li did a lot of research on Graph Theoretic Algorithm and wrote code of DFS.
  • Xiaotian Yu and Wei Cao read some paper about atom conservation. Then they worked together on coding and model building.
  • Xiaotian Yu and Zhichao Ma worked on toxicity of compound and added it to ranking criteria.

Additional Functions
 1.Organism recommendation
Zhichao Ma and Xiangzhen Li built and optimized microorganism recommendation model.
2.Flux Balance Analysis
Wei Cao and Haiyan He learned COBRA toolbox and built FBA model.
3.Atom conservation
Wei Cao and Haiyan He learned COBRA toolbox and built FBA model.
4.SMILES Comparison
Xiaotian Yu learned RDkit toolbox and added SMILES Comparison to our project.

Design
  • Yuchen Xing, Yuejia Li,Wei Cao were responsible for wiki design.
  • Yuchen Xing, Wei Cao and Zhichao Ma designed software interface.
  • YueJia Li also carried poster design work.

Human Practices and Collaborations
 1.Visiting WuXi AppTec
Wei Cao communicated with WuXi AppTec and made an interview on experts in WuXi AppTec. Haiyan He, Xiaotian Yu, Zhichao Ma and Xiangzhen Li participated this interview and proposed many great ideas. Haiyan He give an excellent speech on this meeting.
 2.Communicate with programmers
Zhichao Ma made a speech on a forum in school of life science and technology, Tongji University. There, we got a lot of suggestions on modeling.
 3.Contact with experimenters
Wei Cao made a speech on professor Ping Li’s class and then investigate need of experimenters.
4.EuroAsia Meetup
All members attended EuroAsia Meetup in Shenzhen, China. Wei Cao and Xiaotian Yu did presentation in this Meetup. All the member answered questions during the speech.
 5.CCiC
  • Xiaotian Yu contacted with Shanghai-tech, who held CCiC in Shanghai.
  • Xiangzhen Li , Xiaotian Yu and Wei Cao gave the committee a great presentation.
  • Haiyan He was responsible for poster exhibition part.
  • Yuejia Li designed the poster.

6.Meeting with SJTU & Fudan_China
Wei Cao contacted with SJTU-software and helped arrange meeting with SJTU-software. Haiyan He contacted with Fudan_China and helped arrange meeting with them. And rest of the team attended this meeting.
 7.Game : “Go Ant!”
Xiaotian Yu developed the whole game. Of course, the rest of teammates gave him some advice. Yuejia Li designed the magnificent background, which made the game even more fun!
 8.Visiting Meihua Group
Haiyan He, Xiaotian Yu, Zhichao Ma and Wei Cao participated this visit and proposed many great ideas. Xiaotian Yu gave an excellent speech on this meeting
 9.Visiting Cathay Industrial Biotech
Haiyan He, Xiaotian Yu, Zhichao Ma and Wei Cao participated this visit and proposed many great ideas. Xiaotian Yu gave an excellent speech on this meeting
 10.Visiting Key Synthetic Biology Laboratory of CAS
Xiaotian Yu, Zhichao Ma and Wei Cao participated this visit and proposed many great ideas. Weicao gave an excellent speech on this meeting
 11.Mini Lectures for High School Students & Freshmen
Xiangzhen Li and Wei Cao gave these lectures for high school student and freshmen.
 Financing
  • Xiaotian Yu is in charge of Financial management.
  • Wei Cao is responsible for flight tickets booking and hotel reservation. The rest of team members help plan the whole trip.

Advice and human practice support
  • Professor Qi Liu gave us advice on search algorithm and help us contact with WuXi AppTec.
  • Professor Ping Li taught us basic knowledge of synthetic biology and introduced MEIHUA GROUP to us. Then we visited the company and got a lot of useful comments on our software.
  • Associate professor Ye Leng helped us make a speech in The first affiliated middle school of Tongji University.

We are sincerely grateful to everyone who help us in many ways.