Difference between revisions of "Team:SJTU-software/Human Practices"

We discussed with different disciplines and fields scholars, their views inspired us a lot. Interviewing experts greatly advanced our project.

Our interview concentrated on the topic “Application of metabolic network alignment tool in the laboratory”. Dr. Tao told us design of metabolic networks in synthetic biology focus on these aspects: 1.Yield; 2. Efficiency(in A -> B, concentration of B/A); 3. Period. Then we briefly introduced the idea of our software (a metabolic network alignment tool). Dr. Tao was greatly interest in the tool. He also analyzed a number of factors that lead to the difficulty of metabolic network alignment. How to evaluate similarity of two metabolic networks? How to grade the result of alignment? How to evaluate similarity of different compound…… His opinion made us have a deeper understanding of how make our software more practical and functional in the laboratory.

In Prof. Daniel Figeys’s Lab, they have developed a advanced bioinformatics software “iMetaLab”. Their project is originally designed for human/mouse gut metaproteomics protein identification and quantification, rooted from the MetaProIQ workflow. Upon the rising request, they wrap up the workflow into a desktop standalone version, with taxon analysis module built in. In the meantime, they have been working on some meta-function annotation and enrichment analysis, as well as some data visualization modules. Then they realize that it would be good to wrap up all related functions and share them to the community. They aim to make iMetaLab a free and one-stop toolset for gut metaproteomics, with increasing amount of tools under development. This interview inspired us how to make our software “Metlab: a metabolic network alignment tool” more user-friendly and complete. The process of their software development enlightened us to make “Metlab” a functional toolset with many tools related metabolic network.

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Participants: Sun Yet Sun University, Shanghai Jiao Tong University, Fudan University, Nanjing University, Central South University.

From May 18th 2018 to May 20th 2018, our team members attended Biology Undergraduates Development Symposium（BUDS）,which was held by School of Life Science, Sun Yet Sun University.

During poster presentation, we present a poster on our work to foster communication and possible future collaboration between different iGEM teams. In the communication conference, we introduced the idea of our projects, gave our suggestions and shared fresh ideas. Through the communication we learned from each other, which was a great help to our 2018 iGEM projects.

From July 7th 2018 to July 13th 2018, our team member took part in Science Summer Boot Camp on “Microbes and Biotechnology” at the University of Ottawa. The charming of the summer boot camp lies in its interdisciplinary integration, we learned many bioinformatics analysis methods which promoted our projects “Metlab: a metabolic network alignment tool” implementation.

The one-week summer boot camp closes with a scientific symposium with invited speakers, student presentations and posters. We presented our project and got a lot of advice from professors and students. The interesting and pleasant summer boot camp served as valuable inspiration to advance our project of 2018 iGEM with fresh motivation.

This year, we continued to be an active participant in the iGEM Asia Pacific Conference, since we consider this conference as a great platform for us to report our interim achievements. In the poster session, our project intrigued many teams, especially those that also focus their projects on synthetic metabolic pathways. They believed that our comparison between the designed metabolic pathway and the natural biochemical network would help them accomplish their project better.

During the presentation, we demonstrated the background and design thought to the conventioneers and the professors, and they gave us some sincerer and professional suggestions. We also discovered our own shortcomings through this conference. We couldn’t present our algorism lucidly to our audience, so that we will pay special attention to this problem for the Grant Jamboree presentation.