iGEM 2019 — Team UESTC-Software

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# Team:UESTC-Software/Notebook

Description

![](https://static.igem.org/mediawiki/2019/b/ba/T--UESTC-Software--logo.png)

* [Home (current)](https://2019.igem.org/Team%3AUESTC-Software)
* Project

  [Description](https://2019.igem.org/Team%3AUESTC-Software/Description)
  [Design](https://2019.igem.org/Team%3AUESTC-Software/Design)
  [Advantages](https://2019.igem.org/Team%3AUESTC-Software/Advantages)
  [Attributions](https://2019.igem.org/Team%3AUESTC-Software/Attributions)
  [Contribution](https://2019.igem.org/Team%3AUESTC-Software/Contribution)
  [Notebook](https://2019.igem.org/Team%3AUESTC-Software/Notebook)
* [Model](https://2019.igem.org/Team%3AUESTC-Software/Model)
* [Human Practices](https://2019.igem.org/Team%3AUESTC-Software/Human_Practices)

  [Integrated HP](https://2019.igem.org/Team%3AUESTC-Software/Human_Practices)
  [Public Engagement](https://2019.igem.org/Team%3AUESTC-Software/Public_Engagement)
  [Collaborations](https://2019.igem.org/Team%3AUESTC-Software/Collaborations)
* [Demonstrate](https://2019.igem.org/Team%3AUESTC-Software/Demonstrate)
* [Team](https://2019.igem.org/Team%3AUESTC-Software/Team)
* [Awards](https://2019.igem.org/Team%3AUESTC-Software/Awards)
* [Safety](https://2019.igem.org/Team%3AUESTC-Software/Safety)

[4.1] Create teams: We have created a team with 15 people from biotechnology, biomedical engineering,
software and
other majors
[4.6 & 4.13] Team meeting: We held preliminary discussions for brainstorming to gather inspiration, and
ultimately determined the theme of continually improving BioMaster.
[4.15] Exchange for proposals on project with Senior Student Zhang Kaiyue, leader of UESTC-China in 2015 iGEM.
[4.25] According to the questionnaire, we decided to add some new databases. We went to Shangsheng Law Firm in
Sichuan to consult lawyer Liang about the copyright of database usage.

More

[5.3-5.4] 2019 Southwestern iGEM Exchange Conference of China was co-hosted by us and UESTC-China in Qingshuihe
campus of UESTC. From this meeting, we got some
suggestions on optimizing search and improving database mapping relationship.
[Week 2&3&4] We set up five groups: database, art design, Human Practices, new function and web
authoring. The project was officially launched.
[6.1] We held a large-scale publicity science activity in Sichuan Science and Technology Museum.
Students from the University of Hong Kong were invited to organize activities to exchange database technology
with students from computer majors. Patrick suggested on adding docker to
increase the portability of the project and prolong the project generation cycle.
[Week1&2] Front-end and back-end groups began to learn knowledge about programming; database group searched
for
suitable databases; design group designed web logic; function group and Human Practices group explored the
needs and
collected ideas.
[6.16] We interviewed Professor Zheng Xuelian, a senior teacher of UESTC-China, and discussed the development
of synthetic biology. Under her suggestion, we added an education module to our project.
[week 3] We utilized web crawler to get a small amount of database data, which validated our ideas and
technologies.
[Week 4] A new sequence alignment model was eatablished to improve integration accuracy. We learned about
Amazon's S3 cloud database service and decided to use local MySQL + cloud database to store data. The new
project was named “BioMaster 2.0”.

More

[week 1] We got the required data through download or API access, including 11 databases: UniProt, BRENDA,
BioGRID, etc. Simultaneously, we collated the copyright agreements of various databases to ensure the
legitimacy and rationality of our project.
[week 2] We updated the team wiki information for 2018 . Besides, the
database of BioMaster 1.0 was integrated, and useful information was migrated to BioMaster 2.0. Considering the
performance and function, we decided to abandon think PHP and used Laravel to develop our project instead.
[week 3] We constructed and configured the server to run demo. Besides, we compiled the prototype web page of
Wiki, started to build the front-end web page prototype of BioMaster 2.0, and gradually completed the docking
with the back-end. All pages for BioMaster 2.0 was designed. During this week, we started designing synthetic
biology
brochures and table games BioME.
[7.20] We interviewed Professor Zeng Dong of our school about search optimizing. He recommended Elasticsearch
as a search plug-in for us.
[week 4] To solve the problem that some sequences in the old screening model were ignored, we decided to use
"full sequence + feature annotated short sequence" as the BLAST object in the new model. In the pre-processing
of iGEM part source data, we BLAST the corresponding short sequence according to the information given by
feature, and screened the result of blast preliminarily. Finally, we got 3 groups of different tables for
source data by 3 different sorting methods.

More

[week1] Inspired by SynBioHub and SBOL designer, we planed to devise visualization functions to display the
auxiliary design functions in our own database. In the next month, we designed and compiled a web version of
SBOL aided design tool according to the official standard of SBOL, which was used to realize sequence
visualization.
[9.7] We went to Shishi High School for iGEM propaganda and published our brochure.
[week2] We finished the EC Number Prediction. The prediction tool used machine learning and constructed
multiple binary classifiers. It combined three independent predictors based on subsequences, sequence
similarities, and amino acid physicochemical features. It provided probabilistic enzymatic function by
predicting the EC number.
[week3] The display form of the information in the database was determined. We finished all database pages
codes and added special effects by using bootstrap response
framework and other plug-ins when designing the response of web pages. In addition, we realized the adaptive
function of different screen sizes of web pages. We started to integrate all the new functions into the program
code and did some UI beautification as well.
[week4] We kept on writing drafts and adjusted web page layout. We started to write drafts for our presentation
and design our PPT. The PC version of Bio-ME is finished, which enabled users to learn the basic knowledge of
synthetic biology.

More

[week1] We continued to process the data of the screening model, merging and labeling 3 sets of tables.
By compressing the range of independent variables, we set 36 groups of different parameters, draw the frequency
distribution histogram and Poisson distribution fitting curve, and marked the reasonable threshold.
[8.7] We went to Chengdu Junyu Biotechnology Co., Ltd. to visit the researcher, Mr. Zhang Yunfei, and consulted
about the database function. He mentioned the importance of prediction in biology. Therefore, we decided to add
EC number prediction function as a supplement to BioMaster 2.0 database on the basis of promoter prediction
last year.
[week 2] We further analyzed the screening results and fitted the tail thresholds of 36 groups of curves with
normal distribution to obtain the median values, so as to determine the threshold of the formula. We used
triple intersection as a criterion to evaluate the accuracy of the results, and drew the proportion of triple
intersection under different parameters in the whole data set. Thus, the screening formula was successfully
deduced when finding out a set of parameters with the best performance under reasonable thresholds.
[week 3] We optimized the demonstration of interaction networks and used open source software platform
Cytoscape to visualize interaction networks. According to Zeng Dong's suggestion, we adopted Elasticsearch to
achieve full-text keyword search. Although we encountered many problems when trying to integrate Elasticsearch
into BioMaster 2.0 framework, we never gave up. This work continued until week4, and we finally solved all
these problems.
[8.20-23] We went to Shenzhen to participate in the 6th CCiC and exchanged with the various Chinese iGEM teams.
Taking the opinions of other teams into account, we decided to add some practical features to BioMaster, such
as ID conversion and BLAST API.
[week 4] After debugging for a long term, we successfully constructed the scoring equation of screening model.
We obtained the best screening settings: 0.65 for threshold, 1-5-4 for coefficients. We also made a large
number of random sampling tests on the obtained data from the new model, and especially enumerated the special
cases such as data contamination. All the test results showed that the new model had a better screening
performance.

More

[week1] We started to write drafts for our
presentation and designed our PPT. We completed the development of docker in BioMaster 2.0. Users were able to
download the blog from GitHub and ran it in docker by themselves. Without the support of remote server, they
could also experience the data search function of BioMaster.
[10.8-10.12] We invited CAU-China, Tongji-Software, SJTU-Software and other teams to try out the software and
collected their feedback.
[10.11] We went to Sichuan University and invited Professor Liang to use our software. She provided some
suggestions on the timeliness of data.
[week2] We added the update function to ensure data timeliness, and also simplified the maintenance of the
database. Besides, we finished our wiki and started to upload our web pages. We recorded our demonstration
video for BioMaster 2.0, finished our judging form and applied for four best awards.
[10.15] We held the Second iGEM Festival in UESTC.
[week3] Web debugging, database testing and rehearsal. We added some annotation for our codes and submitted
them to GitHub. The final version of our poster came out and we prepared for our trip to Boston.
[10.21] Wiki freeze
[10.31] Our journey began!

More

### Contact Us

uestcsoftware@vip.qq.com

NO.2006.XiYuan Avenue,UESTC,Chengdu,China

![](https://static.igem.org/mediawiki/2019/b/b2/T--UESTC-software--xiaohui.png
						)

![](https://static.igem.org/mediawiki/2018/f/f8/T--UESTC-Software--uestc_jwc.png
						)

![](https://static.igem.org/mediawiki/2018/7/7d/T--UESTC-Software--life_s.png
						)


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# Team:UESTC-Software/Experiments

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[HOME](https://2019.igem.org/Team%3AUESTC-Software)

TEAM

[Team Members](https://2019.igem.org/Team%3AUESTC-Software/Team)
[Collaborations](https://2019.igem.org/Team%3AUESTC-Software/Collaborations)

PROJECT

[Description](https://2019.igem.org/Team%3AUESTC-Software/Description)
[Design](https://2019.igem.org/Team%3AUESTC-Software/Design)
[Experiments](https://2019.igem.org/Team%3AUESTC-Software/Experiments)
[Notebook](https://2019.igem.org/Team%3AUESTC-Software/Notebook)
[Contribution](https://2019.igem.org/Team%3AUESTC-Software/Contribution)
[Results](https://2019.igem.org/Team%3AUESTC-Software/Results)
[Demonstrate](https://2019.igem.org/Team%3AUESTC-Software/Demonstrate)
[Improve](https://2019.igem.org/Team%3AUESTC-Software/Improve)
[Attributions](https://2019.igem.org/Team%3AUESTC-Software/Attributions)

PARTS

[Parts Overview](https://2019.igem.org/Team%3AUESTC-Software/Parts)
[Basic Parts](https://2019.igem.org/Team%3AUESTC-Software/Basic_Part)
[Composite Parts](https://2019.igem.org/Team%3AUESTC-Software/Composite_Part)
[Part Collection](https://2019.igem.org/Team%3AUESTC-Software/Part_Collection)

[SAFETY](https://2019.igem.org/Team%3AUESTC-Software/Safety)

HUMAN PRACTICES

[Human Practices](https://2019.igem.org/Team%3AUESTC-Software/Human_Practices)
[Education & Engagement](https://2019.igem.org/Team%3AUESTC-Software/Public_Engagement)

AWARDS

[Entrepreneurship](https://2019.igem.org/Team%3AUESTC-Software/Entrepreneurship)
[Hardware](https://2019.igem.org/Team%3AUESTC-Software/Hardware)
[Measurement](https://2019.igem.org/Team%3AUESTC-Software/Measurement)
[Model](https://2019.igem.org/Team%3AUESTC-Software/Model)
[Plant](https://2019.igem.org/Team%3AUESTC-Software/Plant)
[Software](https://2019.igem.org/Team%3AUESTC-Software/Software)

[JUDGING FORM ⇗](https://igem.org/2019_Judging_Form?team=UESTC-Software)

# 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.

Please remember to put all characterization and measurement data for your parts on the corresponding Registry part pages.

### What should this page contain?

* Protocols
* Experiments
* Documentation of the development of your project

### Inspiration

* [2014 Colombia](https://2014.igem.org/Team%3AColombia/Protocols)
* [2014 Imperial](https://2014.igem.org/Team%3AImperial/Protocols)
* [2014 Caltech](https://2014.igem.org/Team%3ACaltech/Project/Experiments)

Loading menubar.....

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# Team:UESTC-Software/Results

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[HOME](https://2019.igem.org/Team%3AUESTC-Software)

TEAM

[Team Members](https://2019.igem.org/Team%3AUESTC-Software/Team)
[Collaborations](https://2019.igem.org/Team%3AUESTC-Software/Collaborations)

PROJECT

[Description](https://2019.igem.org/Team%3AUESTC-Software/Description)
[Design](https://2019.igem.org/Team%3AUESTC-Software/Design)
[Experiments](https://2019.igem.org/Team%3AUESTC-Software/Experiments)
[Notebook](https://2019.igem.org/Team%3AUESTC-Software/Notebook)
[Contribution](https://2019.igem.org/Team%3AUESTC-Software/Contribution)
[Results](https://2019.igem.org/Team%3AUESTC-Software/Results)
[Demonstrate](https://2019.igem.org/Team%3AUESTC-Software/Demonstrate)
[Improve](https://2019.igem.org/Team%3AUESTC-Software/Improve)
[Attributions](https://2019.igem.org/Team%3AUESTC-Software/Attributions)

PARTS

[Parts Overview](https://2019.igem.org/Team%3AUESTC-Software/Parts)
[Basic Parts](https://2019.igem.org/Team%3AUESTC-Software/Basic_Part)
[Composite Parts](https://2019.igem.org/Team%3AUESTC-Software/Composite_Part)
[Part Collection](https://2019.igem.org/Team%3AUESTC-Software/Part_Collection)

[SAFETY](https://2019.igem.org/Team%3AUESTC-Software/Safety)

HUMAN PRACTICES

[Human Practices](https://2019.igem.org/Team%3AUESTC-Software/Human_Practices)
[Education & Engagement](https://2019.igem.org/Team%3AUESTC-Software/Public_Engagement)

AWARDS

[Entrepreneurship](https://2019.igem.org/Team%3AUESTC-Software/Entrepreneurship)
[Hardware](https://2019.igem.org/Team%3AUESTC-Software/Hardware)
[Measurement](https://2019.igem.org/Team%3AUESTC-Software/Measurement)
[Model](https://2019.igem.org/Team%3AUESTC-Software/Model)
[Plant](https://2019.igem.org/Team%3AUESTC-Software/Plant)
[Software](https://2019.igem.org/Team%3AUESTC-Software/Software)

[JUDGING FORM ⇗](https://igem.org/2019_Judging_Form?team=UESTC-Software)

# Results

Here you can describe the results of your project and your future plans.

### 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.** 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.

* [2014 TU Darmstadt](http://2014.igem.org/Team%3ATU_Darmstadt/Results/Pathway)
* [2014 Imperial](http://2014.igem.org/Team%3AImperial/Results)
* [2014 Paris Bettencourt](http://2014.igem.org/Team%3AParis_Bettencourt/Results)