iGEM 2020 — Team Tsinghua-A

[![](https://static.igem.org/mediawiki/2020/8/8b/HQ_page_logo.jpg)](https://2020.igem.org)

# Team:Tsinghua-A/Notebook

* [Home](https://2020.igem.org/Team%3ATsinghua-A)
* Team

  [Team](https://2020.igem.org/Team%3ATsinghua-A/Team)
   [Attributions](https://2020.igem.org/Team%3ATsinghua-A/Attributions)
* Project

  [Description](https://2020.igem.org/Team%3ATsinghua-A/Description)
   [Background](https://2020.igem.org/Team%3ATsinghua-A/Background)
   [Design](https://2020.igem.org/Team%3ATsinghua-A/Design)
   [Contribution](https://2020.igem.org/Team%3ATsinghua-A/Contribution)
* Engineering

  [Engineering](https://2020.igem.org/Team%3ATsinghua-A/Engineering)
   [Implementation](https://2020.igem.org/Team%3ATsinghua-A/Implementation)
* Human Practices

  [Human Practices](https://2020.igem.org/Team%3ATsinghua-A/Human_Practices)
  [Collaborations](https://2020.igem.org/Team%3ATsinghua-A/Collaborations)

# 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)
* [2014 ATOMS-Turkiye](https://2014.igem.org/Team%3AATOMS-Turkiye/Notebook)
* [2014 Tec Monterrey](https://2014.igem.org/Team%3ATec-Monterrey/ITESM14_project.html#tab_notebook)
* [2014 Kyoto](https://2014.igem.org/Team%3AKyoto/Notebook/Magnetosome_Formation#title)
* [2014 Cornell](https://2014.igem.org/Team%3ACornell/notebook)

[![](https://static.igem.org/mediawiki/2020/8/8b/HQ_page_logo.jpg)](https://2020.igem.org)

# Team:Tsinghua-A/Engineering

* [Home](https://2020.igem.org/Team%3ATsinghua-A)
* Team

  [Team](https://2020.igem.org/Team%3ATsinghua-A/Team)
   [Attributions](https://2020.igem.org/Team%3ATsinghua-A/Attributions)
* Project

  [Description](https://2020.igem.org/Team%3ATsinghua-A/Description)
   [Background](https://2020.igem.org/Team%3ATsinghua-A/Background)
   [Design](https://2020.igem.org/Team%3ATsinghua-A/Design)
   [Contribution](https://2020.igem.org/Team%3ATsinghua-A/Contribution)
* Engineering

  [Engineering](https://2020.igem.org/Team%3ATsinghua-A/Engineering)
   [Implementation](https://2020.igem.org/Team%3ATsinghua-A/Implementation)
* Human Practices

  [Human Practices](https://2020.igem.org/Team%3ATsinghua-A/Human_Practices)
  [Collaborations](https://2020.igem.org/Team%3ATsinghua-A/Collaborations)

# Engineering Success

For all the algorithms we intorduced in *Design*, we have coded demos and achieved our design **GOAL**!

[Our Ultimate Goal Here!](https://2020.igem.org/Team%3ATsinghua-A/Implementation)

## Feature Extracting VAE

In order to show our idea in a more vivid way, we design a website to better illustrate the whole pipeline through an interesting game. For every user, he/she can upload a photo that contains a human face. Once uploaded, the photo will go through the pre-trained model, it will first go through a VAE network, the feature obtained then will be passed through the encoder network to generate the respective DNA sequence. We have used celebA database (a large-scale face attributes dataset with more than 200K celebrity images) to generate a large DNA database. So once the DNA sequence of that photo is generated, it will match the most similar celebrity in the database!

![](https://static.igem.org/mediawiki/2020/1/15/T--Tsinghua-A--Vae_eng1.png)

**Click Start Now!**

![](https://static.igem.org/mediawiki/2020/9/9b/T--Tsinghua-A--Vae_eng2.png)

**Choose a picture and upload!**

![](https://static.igem.org/mediawiki/2020/4/48/T--Tsinghua-A--Vae_eng3.png)

**Get magic!**

![](https://static.igem.org/mediawiki/2020/7/72/T--Tsinghua-A--Vae_eng4.png)
![](https://static.igem.org/mediawiki/2020/3/3e/T--Tsinghua-A--Vae_eng5.png)

## Data Encoding Algorithms

#### Image

##### Compressing

![](https://static.igem.org/mediawiki/2020/9/9b/T--Tsinghua-A--image_eng.png)

As for medical images, a 3 step-formed image out of 16 steps will be able to satisfy the need of diagnostic in most occasions. And a 3 step-formed image would only take 10% storage place compared to raw image, which saves a lot of storage space.

##### Encoding

By combining compressing algorthim and fountain code, we established an image file system with 2 dimensions. One dimension gives different images, the other gives different qualities.
For different images, different version of the image is selected and encoded for the DNA database, which can largely reduce the length of sequence needed.

![](https://static.igem.org/mediawiki/2020/b/b3/T--Tsinghua-A--img_eng_res.png)

#### Text

##### Randomly generate medical records

Because the medical records database is private and difficult to obtain, and considering the BP limitation of wet experiments, a simple database is randomly generated for demo writing. After investigation, we believe that the current use of medical records have written rules and language norms. Therefore, we can simplify the medical record into the collection of personal information of the patient and the factors of symptoms and corresponding time. (Name + time + symptoms)

##### Greedy algorithm

The core is for name coding and disease coding. Referring to "A Method for coding Symptoms and Signs applied to computer case management System" and "Diagnostics", the corresponding number of common symptoms is converted to fixed-length quaternary code.

##### Huffman algorithm

Considering the situation of a larger medical record database and referring to "the Study on Chinese Character Coding with Low Redundancy TWO-DIMENSIONAL Code", we counted word frequency and adopted Huffman algorithm for symptom coding. Frequency statistics of letters and symptom vocabulary were performed in a small database and coded. At the same time, the special coding sequence is used as the segmentation of three important information, which also makes it possible to use PCR for keyword retrieval later.

![](https://static.igem.org/mediawiki/2020/3/37/T--Tsinghua-A--designrecord.png)

#### Waveform

It can be seen that the ECG data is relatively stable in a certain stage, and only changes dramatically in the part of R wave. According to the characteristics of ECG signals, storing the difference can save storage space effectively. So we use first-order difference method to the ECG data sequence.

![](https://static.igem.org/mediawiki/2020/c/c5/T--Tsinghua-A--ECG1.png)

As illustrated in the table, most of the results are between -8 and 7. There are very few values outside the -127 to 128 range. Hence, variant-length coding algorithm of 2-4-8-16 bits, a method similar to Huffman algorithm, is taken to compress the length of data. Then the data is written to a binary file and converted into fountain code.

![](https://static.igem.org/mediawiki/2020/2/24/T--Tsinghua-A--ECG2.png)

Our experimental data comes from MIT-BIH Arrhythmia Database. At present, we have coded demo in MATLAB. The results showed that our method can compress the raw data to about 20% of the original size. The compression ratio is smaller than ZIP and RAR

[Back](https://2020.igem.org/Team%3ATsinghua-A/Description)

[![](https://static.igem.org/mediawiki/2020/8/8b/HQ_page_logo.jpg)](https://2020.igem.org)

# Team:Tsinghua-A/Experiments

* [Home](https://2020.igem.org/Team%3ATsinghua-A)
* Team

  [Team](https://2020.igem.org/Team%3ATsinghua-A/Team)
   [Attributions](https://2020.igem.org/Team%3ATsinghua-A/Attributions)
* Project

  [Description](https://2020.igem.org/Team%3ATsinghua-A/Description)
   [Background](https://2020.igem.org/Team%3ATsinghua-A/Background)
   [Design](https://2020.igem.org/Team%3ATsinghua-A/Design)
   [Contribution](https://2020.igem.org/Team%3ATsinghua-A/Contribution)
* Engineering

  [Engineering](https://2020.igem.org/Team%3ATsinghua-A/Engineering)
   [Implementation](https://2020.igem.org/Team%3ATsinghua-A/Implementation)
* Human Practices

  [Human Practices](https://2020.igem.org/Team%3ATsinghua-A/Human_Practices)
  [Collaborations](https://2020.igem.org/Team%3ATsinghua-A/Collaborations)

# 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

* [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)

[![](https://static.igem.org/mediawiki/2020/8/8b/HQ_page_logo.jpg)](https://2020.igem.org)

# Team:Tsinghua-A/Results

* [Home](https://2020.igem.org/Team%3ATsinghua-A)
* Team

  [Team](https://2020.igem.org/Team%3ATsinghua-A/Team)
   [Attributions](https://2020.igem.org/Team%3ATsinghua-A/Attributions)
* Project

  [Description](https://2020.igem.org/Team%3ATsinghua-A/Description)
   [Background](https://2020.igem.org/Team%3ATsinghua-A/Background)
   [Design](https://2020.igem.org/Team%3ATsinghua-A/Design)
   [Contribution](https://2020.igem.org/Team%3ATsinghua-A/Contribution)
* Engineering

  [Engineering](https://2020.igem.org/Team%3ATsinghua-A/Engineering)
   [Implementation](https://2020.igem.org/Team%3ATsinghua-A/Implementation)
* Human Practices

  [Human Practices](https://2020.igem.org/Team%3ATsinghua-A/Human_Practices)
  [Collaborations](https://2020.igem.org/Team%3ATsinghua-A/Collaborations)

# 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.

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