Team:NMU China/Software
Combatting COVID-19
Naval Medical University CHINA
Software description
Professional parts figures, generally displayed in literatures, is the basis for visualizing various functional elements in protein or nucleotide sequences. However, how to draw it has always been a big headache to most researchers.
Usually, Professional parts figures are drawn by mapping software such as photoshop. However, it’s difficult to precisely determine the position and the size of the bio-parts. What’s worse, if there’s anything wrong with the bio-part in between, the domino effect will be extended to its downstream ones, which is quite annoying.
In order to address the problem, we designed a software based on PyCharm as an extensive part of our project, in which users would be provided with multiple choices to help simplify and customize the process of drawing. Our goal is to create professional parts figures within minutes.
Example
Here are some parts figures drawn by this software. It’s noted that these circuits do not really exist, we demonstrate them to help you better understand what results our software will present when it works in relative environment.
Example 1
Example 2
Example 3
Preparation:
- Find the sequence structure of related genes or proteins you want to draw from websites like GeneCards.
- Download and open the software, you will see the interface as shown below.
- Set the sequence’s length by typing in the Start Number and End Number.
Explanations about some of the buttons:
- X position: where to place the part on the track
- Y position: how far the part will be off the track
- Repeat: how many times Poly A would be repeated, used for drawing Poly A tail only
- Name: to name the part you are drawing
- Fontsize: in which size the name will be demonstrated
Add parts to the figure:
- Choose the type of bio-parts you are going to draw.
- Customize the parameters of the bio-part.
- Press the button “Add” to place the part on the genetic circuit
Remove parts from the figure:
- Select the part you are about to remove from the list demonstrated in the right side of the interface.
- Press the “Remove” button.
- If you want to create a new biological sequence diagram, just click “Remove all”.
Alter part’s parameters:
- Select the part you are about to modify from the list demonstrated in the right side of the interface.
- Alter the part’s parameters customized before.
- Press the “Replace” button and form new parameters.
Easy to draw：
Each time you choose a kind of part in the category list, there will be some suggested defaults to help beautify the appearance of it. What’s more, we have made the icon automatically adapt to different pages with its own ratio of length to width unchanged.Easy to modify：
The “Preview” button makes it possible to check the already-done parts figure in real time and correct the errors timely. Even if you have saved the figure as a file, you can also open it again and make modifications based on its original structure.
Easy to obtain：
As we mentioned above, we designed this software with the aim of offering time-efficient ways to draw professional parts figures, which means the quicker we could obtain a figure, the closer we are to our final goal. Therefore, for instant application of parts figure in academic literatures, you can choose to save it as a file or directly take a screenshot from the previewed image.strength
Design visualization:
We couldn’t help emphasizing it again that the advantage of this software is design visualization—what you see is what you have drawn.User-friendly:
Just by several clicks of buttons and setting the relative paremeters of the part, you will get a part figure within minutes with little knowledge in fields like computer or art.Output sharing:
Online sharing could be realized if one upload his parts figure in a certain database. And others could download it and make quick modifications based on its original structure.weakness and corresponding improvement
| Weakness | Improvement |
|---|---|
| Limited scope of customization. | Expand the scope of customization with more precise and detailed choices and better improve user experience. |
| Can be used only when downloading its installation package. | Develop web-based tool so that more people could create parts figures online. |
Obviously, we have successfully created parts figures in a more convenient way by referring to the modular concept in IGEM. Similarly, we could simplify some of the most complicated processes by setting up a standard and creating a template. In our next step, we are planning to establishing a database of these genetic parts. With key information of the part, you could easily invoke its standard image to construct a part figure without tying in its parameters one by one, which would be a small progress compared with our original design. Sincerely hope that our software could make you more effective in making professional parts figures.