iGEM 2021 — Team USTC-Software

[![](https://static.igem.org/mediawiki/2021/8/8b/HQ_page_logo.jpg)](https://2021.igem.org)

# Team:USTC-Software/Notebook

# Notebook

Document the dates you worked on your project. This should be a detailed account of the work done each day for your project.

### What should this page have?

* Chronological notes of what your team is doing.
* Brief descriptions of daily important events.
* Pictures of your progress.
* Mention who participated in what task.

### Inspiration

You can see what others teams have done to organize their notes:

* [2018 Munich](https://2018.igem.org/Team%3AMunich/Notebook)
* [2019 Georgia State](https://2019.igem.org/Team%3AGeorgia_State/Notebook)
* [2019 Newcastle](https://2019.igem.org/Team%3ANewcastle/Notebook)
* [2020 IISER Pune India](https://2020.igem.org/Team%3AIISER-Pune-India/Notebook)
* [2020 Lund](https://2020.igem.org/Team%3ALund/Notebook)
* [2020 NOVA LxPortugal](https://2020.igem.org/Team%3ANOVA_LxPortugal/Notebook)
* [2020 RDFZ China](https://2020.igem.org/Team%3ARDFZ-China/NoteBook)

[![](https://static.igem.org/mediawiki/2021/8/8b/HQ_page_logo.jpg)](https://2021.igem.org)

# Team:USTC-Software/Engineering

Document

USTC-SOFTWARE

ENGINEERING SUCCESS

[AWARDS](https://2021.igem.org/Team%3AUSTC-Software/Awards)

HUMAN PRACTICE

[Integrated Human Practices](https://2021.igem.org/Team%3AUSTC-Software/Human_Practices)

[Education](https://2021.igem.org/Team%3AUSTC-Software/Education)

[Communication](https://2021.igem.org/Team%3AUSTC-Software/Communication)

[Sustainable](https://2021.igem.org/Team%3AUSTC-Software/Sustainable)

[SAFETY](https://2021.igem.org/Team%3AUSTC-Software/Safety)

PROJECT

[Description](https://2021.igem.org/Team%3AUSTC-Software/Description)

[Model](https://2021.igem.org/Team%3AUSTC-Software/Model)

[Engineering](https://2021.igem.org/Team%3AUSTC-Software/Engineering)

[Implementation](https://2021.igem.org/Team%3AUSTC-Software/Implementation)

[Demonstrate](https://2021.igem.org/Team%3AUSTC-Software/Demonstrate)

[Features & Future](https://2021.igem.org/Team%3AUSTC-Software/Future)

[Contribution](https://2021.igem.org/Team%3AUSTC-Software/Contribution)

[Proof of Concept](https://2021.igem.org/Team%3AUSTC-Software/Proof_Of_Concept)

[Attributions](https://2021.igem.org/Team%3AUSTC-Software/Attributions)

TEAM

[Team Members](https://2021.igem.org/Team%3AUSTC-Software/Team)

[Collaborations](https://2021.igem.org/Team%3AUSTC-Software/Collaborations)

[Partnership](https://2021.igem.org/Team%3AUSTC-Software/Partnership)

![](https://static.igem.org/mediawiki/2021/8/8e/T--USTC-Software--slash.png)

![](https://static.igem.org/mediawiki/2021/3/31/T--USTC-Software--slash2.png)

![](https://static.igem.org/mediawiki/2021/8/8e/T--USTC-Software--slash.png)

![](https://static.igem.org/mediawiki/2021/3/31/T--USTC-Software--slash2.png)

# Engineering Success

### ![](https://static.igem.org/mediawiki/2021/9/9e/T--USTC-Software--circle.png) Overview

![](https://static.igem.org/mediawiki/2021/e/e7/T--USTC-Software--Engineering1.png)

With 13 talented students from different departments, our teams is full of variety of abilities, possibilities and sparks of thought. Given the size of our team, we draw on the overall development mindset of agile development. In software development, agile (sometimes written Agile) is a set of practices intended to improve the effectiveness of software development professionals, teams, and organizations. It involves discovering requirements and developing solutions through the collaborative effort of self-organizing and cross-functional teams and their customer(s)/end user(s). So we take iterative development.

### ![](https://static.igem.org/mediawiki/2021/9/9e/T--USTC-Software--circle.png) Investigation and Research

After reading a lot of papers related to synthetic biology, we found that traditional synthetic biology often relies on a large number of repetitive experiments to obtain results, and the failure of the experiments often means the passage of time and the stagnation of project progress. With the rapid development of data science, researchers can use machine learning or deep learning to find patterns or discover new phenomena in huge amounts of data. A presentation on the application of machine learning in materials science during the research gave us the idea of conducting a project about machine learning.

### ![](https://static.igem.org/mediawiki/2021/9/9e/T--USTC-Software--circle.png) Project Reorientation

As the project progressed, we found that there were many fields with similar requirements. We thought that if we developed a model with our own knowledge and technology, it might only help a small number of researchers and iGEMers, so we conducted another research effort and found that there are some mature machine learning models and results in certain biological fields. Thus, we talked with our teachers again and decided to build a tool that provides various biology-related machine learning models.

![]()

### ![](https://static.igem.org/mediawiki/2021/9/9e/T--USTC-Software--circle.png) Birth of Educational Version

After our platform was built to provide some tools to predict four properties of proteins, we introduced out platform to teachers and students in related labs at school, in addition to some iGEMers. During this period, we tried to do some science popularization, and at the same time we found that education has an extremely important role in synthetic biology development, so we had the idea to make an educational version. The purpose of the educational version is to introduce the basics of synthetic biology to students who do not know about synthetic biology, and to introduce the basics of machine learning to some biology researchers who want to combine machine learning with synthetic biology.

![]()

### ![](https://static.igem.org/mediawiki/2021/9/9e/T--USTC-Software--circle.png) Hot-plug Extensible Module

During CCiC, the Conference of China iGEMer Community, we start a collaboration with team SJTU-Software from Shanghai Jiao Tong University. We needed to introduce their model of predicting RNA secondary structure in our project. To facilitate the addition of models, we designed the hot extension model, which is for more modules to be directly inserted into our service. Our background structure was born with hot-plug features. To be specific, each of scripts from contributors are packed into different python modules. And each module should export a class with the same name of module. This makes it possible to conveniently add more models to the platform.

### ![](https://static.igem.org/mediawiki/2021/9/9e/T--USTC-Software--circle.png) Improvement

After CAT was basically completed, we printed brochures about our project and related knowledge. The main content is as follows:

![](https://static.igem.org/mediawiki/2021/b/b1/T--USTC-Software--Engineering3.png)

### ![](https://static.igem.org/mediawiki/2021/9/9e/T--USTC-Software--circle.png) Project Effectiveness

We introduced the platform after the iterations to teachers and students in school labs and got a lot of positive feedback. We used the educational version to popularize science to students of all ages, and they were almost interested about this, which made us have a great day. We are very glad that we chose the iterative mode for development. We also got a lot of valuable suggestions during the Human Practices process, and we will make this project better in the future.

Sponsors

### [School of Life Science, USTC](https://biox.ustc.edu.cn/)

### [Initiative Foundation](https://www.ustcif.org.cn/default.php)

Links

### [Homepage](https://2021.igem.org/Team%3AUSTC-Software)

### [Projects](https://github.com/igemsoftware2021/Team_USTC_Software/releases/tag/V1.0.0)

Contact Us

### Mail: USTC\_Software2021@163.com

### University of Science and Technology of China, No.96, JinZhai Road Baohe District, Hefei, Anhui, 230026, P.R.China

![](https://static.igem.org/mediawiki/2021/8/82/T--USTC-Software--toback.png)

[![](https://static.igem.org/mediawiki/2021/8/8b/HQ_page_logo.jpg)](https://2021.igem.org)

# Team:USTC-Software/Experiments

# Experiments

Describe the research, experiments, and protocols you used in your iGEM project. These should be detailed enough for another team to repeat your experiments.

If you made Parts this year, please remember to put all information, characterization, and measurement data on the Part's Main Page on the [Registry](http://parts.igem.org/Main_Page).

### What should this page contain?

* Protocols
* Experiments

### Inspiration

* [2019 Nantes](https://2019.igem.org/Team%3ANantes/Experiments)
* [2019 TU Eindhoven](https://2019.igem.org/Team%3ATU_Eindhoven/Experiments)
* [2019 Mingdao](https://2019.igem.org/Team%3AMingdao/Demonstrate)
* [2020 Amsterdam](https://2020.igem.org/Team%3AAmsterdam/Experiments)
* [2020 NCTU Formosa](https://2020.igem.org/Team%3ANCTU_Formosa/Experiments)
* [2020 USAFA](https://2020.igem.org/Team%3AUSAFA/Experiments)

[![](https://static.igem.org/mediawiki/2021/8/8b/HQ_page_logo.jpg)](https://2021.igem.org)

# Team:USTC-Software/Results

# Results

You can describe the results of your project and your future plans here.

### What should this page contain?

* Clearly and objectively describe the results of your work.
* Future plans for the project.
* Considerations for replicating the experiments.

### Describe what your results mean

* Interpretation of the results obtained during your project. Don't just show a plot/figure/graph/other, tell us what you think the data means. This is an important part of your project that the judges will look for.
* Show data, but remember **all measurement and characterization data must also be on the Part's Main Page on the [Registry](http://parts.igem.org/Main_Page).** Otherwise these data will not be in consideration for any medals or part awards!
* Consider including an analysis summary section to discuss what your results mean. Judges like to read what you think your data means, beyond all the data you have acquired during your project.

### Project Achievements

You can also include a list of bullet points (and links) of the successes and failures you have had over your summer. It is a quick reference page for the judges to see what you achieved during your summer.

* A list of linked bullet points of the successful results during your project
* A list of linked bullet points of the unsuccessful results during your project. This is about being scientifically honest. If you worked on an area for a long time with no success, tell us so we know where you put your effort.

### Inspiration

See how other teams presented their results.

* [2019 Newcastle](https://2019.igem.org/Team%3ANewcastle/Results)
* [2019 Munich](https://2019.igem.org/Team%3AMunich/Results)
* [2019 Tec Chihuahua](https://2019.igem.org/Team%3ATec-Chihuahua/Results)
* [2020 Aalto Helsinki](https://2020.igem.org/Team%3AAalto-Helsinki/Results)
* [2020 GreatBay SCIE](https://2020.igem.org/Team%3AGreatBay_SCIE/Results)
* [2020 Queens Canada](https://2020.igem.org/Team%3AQueens_Canada/Results)