Team:Tongji-Software/Attributions
Attribution
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.
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
FBA
Wei Cao and Haiyan He learned COBRA toolbox and built FBA model.
Microorganism recommendation
Zhichao Ma and Xiangzhen Li built and optimized microorganism recommendation model.
SMILES Comparison
Xiaotian Yu learned RDkit toolbox and added SMILES Comparison to our project.
Design
Yuchen Xing, Yuejia Li were responsible for wiki design.
Yuchen Xing, Wei Cao and Zhichao Ma designed software interface.
YueJia Li also carried poster design work.
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
FBA
Wei Cao and Haiyan He learned COBRA toolbox and built FBA model.
Microorganism recommendation
Zhichao Ma and Xiangzhen Li built and optimized microorganism recommendation model.
SMILES Comparison
Xiaotian Yu learned RDkit toolbox and added SMILES Comparison to our project.
Design
Yuchen Xing, Yuejia Li were responsible for wiki design.
Yuchen Xing, Wei Cao and Zhichao Ma designed software interface.
YueJia Li also carried poster design work.