Difference between revisions of "Team:UESTC-software/Collaborations"

Line 15: Line 15:
 
}
 
}
 
p.title {
 
p.title {
font-size:40px !important;
+
font-size:45px !important;
 
  text-align: center !important;
 
  text-align: center !important;
 
}
 
}

Revision as of 17:12, 11 October 2016

三级页面

Collaborations

Collaborations and sharing, the key to step forward

As iGEMers, we all know sharing and collaborations are core values of iGEM. If a team seal themselves off, not only will be trapped in projects, but also cannot stand in a higher position to grasp the overall situation. Instead of cooping ourselves up, we actively cooperate together for the betterment of synthetic biology as a whole. UESTC-Software has collaborated with other 4 teams in 3 different ways:

  • (1) Solving problems for UESTC-China, our brother team.
  • (2) Mentoring and supporting TMMU-China, which is a new team.
  • (3) Having meetup with SCU-China,TMMU-China,UESTC-China and SICAU.
  • (4) Participating meetup with NJY-China organized by TMMU_China.

Development of Data-Processing Tool for UESTC-China

Background

This team’s goal is to degrade plastic and produce isobutanol. In view of increasingly serious issues on plastic pollution, greenhouse effect and energy shortage, UESTC-China comes up with an idea to try solving these three problems. That’s to use genetically modified bacteria to achieve their goal. With their work going on, there was a stumbling block related to data processing simulation.


Fig.1. the experiment of UESTC-China

Needs

In the course of experiment, there was a stage where team members should complete the drawing of the enzyme activity curve, through which to compare the work effect of each plasmid vector, so as to select the best one. A sea of data made it difficult to finish the data processing by manual method. Owing to the lack of programming ability, they had to use procedural means to solve the problem which took up lots of their time and energy.

So they seek for our support of programming. We carried forward the spirit of collaboration to solve their problems relying on our skills.

Solutions

In the communication process, our team members entered the lab to have an idea of what we could help. Through the analysis of the process and the dynamic combination of the varied data number, we decided to design an algorithm for the fast simulation and solve the complex work with MATLAB.

  • 1. We batched import data collected in the experiment to MATLAB to generate a matrix, which can give the results they need quickly and accurately. Besides, it can generate EXCEL files automatically to help them do further analysis.
  • 2. Another function is that the system can find out large data errors and remove these bad data. In this way, they don’t have to manually check, greatly improving the efficiency any more.
  • 3. On this basis, we also provided a further function of curve fitting. With smooth curve instead of scattered data points, it makes the results more intuitive, easier to understand and analyze.

Some results are shown in Fig.2 and Fig.3:


Fig.2. Enzyme activity data simulation


Fig.3. Enzyme activity data analysis

The program we designed helped UESTC-China reduce the data processing time most definitely, made them come to conclusions and start next step as soon as possible.

Support for TMMU_China

Background

Our team built a friendly connection with other iGEM team like TMMU, and we provided some useful supports for them in order to contribute to iGEM the competition itself, even to synthetic biology.

During our iGEM trip, we helped TMMU_China to build Protein Calculator, a web app to predict experiment result based on their modeling.

These programming work is time-consuming but helpful, we believe our effort can cut enormous workload and free their time so that they can focus on their experiments and research.

Main work

After communication and discussion about the workflow and details, our engineer group began to build and test the web app since our Chongqing Trip. We use Django to manage the web and put all necessary contents into HTML files, with related models and views in Python files.

The main work

1. Setup the Web;

2. Fullfill all need in front end;

3. Implement file upload and download function;

4. Turn TMMU’s Matlab software into C to handle input;

5. Implement the parameter passing and result display.

The web app

This web app, Protein Calculator, needs three inputs: experiment parameters, cnism value and time. The first one is passed by fulfilling our standard file to upload the experiment parameters, then TMMU’s algorithm can plot a result curve to simulate the growing situation. Then, users type the specific cnism value and demand time, they can get a specific function curve at this point.

The whole workflow is the combination of 3 modeling:

1. Gene expression model;

2. Colony growth model;

3. Protein diffuse model;

The details of their modeling can see in TMMU_China wiki. You can also see this web app in their modeling part as a symbol of our cooperation.

The web app

Cooperation is always the main topic of iGEM. The interface and logrolling can really make a difference in our work progress and the friendship between different teams.

We hope this friendship can live from iGEM2016 to a far future, and hope the web app stemming from this friendship can really help researchers to achieve their destination easily.

iGEM Southwest China Union Meetup

We are developing and growing

Last year, UESTC iGEMers led the establishment of iGEM SouthWest Union of China (iSWU), which is a sustained platform for all the iGEMers in the southwest region of China. Nowadays, iSWU has a markedly increase in the number as well as the kind of teams.

This year, there were four universities and one organization interested in synthetic biology participating in the iSWU communication held in Sichuan University. The meetup focused on the theme, “To promote the communication and cooperation among iGEM teams in the southwest region of China” and the main activity forms were to discuss teams’ projects and to share experience. It gave all teams an opportunity to achieve understanding and exchanging deeply.


Fig.7. A group photo of iSWU

We are recognized and encouraged

In communication meeting, professors impressed the innovation awareness and excellent iGEM quality on us. Yun Zhao, the vice-president of SCU college oflife sciences, stressed that there is no need to mention first time in science, all science to do is the first time. Nianhui Zhang, the coach of SCU, shared the experience of his iGEM team leading trip and affirmed we were valued. His word encouraged young scholars to research on innovation and fight for great achievements.


Fig.8. Our team’s presentation

We are exchanging and improving

With excellent and lively presentation, all the teams aroused passionate discussions and get numerous responses from others, including suggestions on the thoughts of project, detailed Q&A on integrated design and reflection on application. As the unique software team, we described the contents we had completed and plans to do concisely. Many members showed their interests to our project. For Bio101, some asked the DNA storage capacity and the superiority of the algorithm we used. One of the professor suggested us to take subsection coding strategy. Others played the game, Bio2048, and hoped us to help them complete the extra work such as biological game. These precious feedbacks we got from the meetup led us to what we should focused on.


Fig.9. We shared with other teams

Modern technology makes information transmission more convenient, but there is no other way better than face-to-face communication. iSWU meetup helped the teams acquire reflections, inspiration and enhance efficiency to perfect the projects. Thus it can be seen, the communication will make a significant improvement for all attendees in the Giant Jamboree.

Meetup with TMMU_China and NJY-China

This year, TMMU-China as a young team needs a lot of support from other experienced teams. iGEM encourages helps and collaborations among teams, especially with the new teams. Just a month away from the Giant Jamboree, TMMU-China invited UESTC-Software, UESTC-China and NJY-China to gather in Chongqing. They arranged a meetup and aimed to prepare for the final presentation in Boston.


Fig.10. The group photo in TMMU-China

The same experience, the same mood

As an excellent team, we are full of enthusiasm to share our rich experience of competition and provide guidance for them. TMMU-China is in unclear condition for iGEM as we once were. We can deeply feel the mood of them. Therefore, we hoped to collaborate with them to give them courage.


Fig.11. The presentation of TMMU-China

The different styles, the different feels

This meetup was completely consistent to the final competition process, with 15-20 minutes for presentation, question time and poster introduction. Although the scale was not better than the final event, it was really a good opportunity to feel different styles of presentation. We exchanged the final preparation for the competition, discussed the summary of the achievement, and found the problems existing in many aspects.


Fig.12. We communicated with the teachers from TMMU-China and NJY-China

The new collaboration, the new harvest

Significantly, it was our first time to contact with NJY-China. We learned from their indefatigable efforts. They were willing to cooperate with other teams and visit different universities to make improvement. They focused on public awareness about the spread of synthetic biology knowledge. Our Human Practice is doing the same effort.


Fig.13. The introduction from NJY-China

The meetup was hold on the basis of project’s completion, so we inspired each other in all aspects. With such a good platform for collaboration, we can help others and recognize ourselves at the same time, become less blind and less helpless. We got the inspiration from sharing, we found the courage from communicating.

What we harvest from the collaboration

Through all the collaborations we took part in, we learned a lot and shared happiness. We knew collaboration, competition and communication deeper and better. What we acquired is not only about the iGEM competition itself, we made friends and expanded our eyesight. We communicated face to face to understand what they did and make them know what we were doing , through which we improved our own abilities. And we encouraged and competed each other to hold on the scientific trip, which made us know about the importance of the competitors and collaborators to scientific workers. All these memories will be a unique part of the iGEM experience as well as our scientific life experience.

CATALOGUE
CATALOGUE