Human Practices
Synbio is just a S-Din away!
SYSU-Software 2017
Overview
During our project “S-Din”, we brainstormed many aspects concerning our project and took them into practices to confirm or to overturn our hypothesis. Then we tried to integrate them into our final project in order to improve the project functions and user experience.
At the beginning of our project, in order to get answers to questions about user needs, safety, software regulations and legal issues, we conducted numerous interviews with professionals working in related fields. They gave us useful and significant suggestions (Silver page). We have considered all comments from professionals and integrated them into our design of S-Din (Gold Integrated page). We conducted further user interviews and user needs analysis, promoted S-Din and synthetic biology to the public (Public Engagement page).
Please see our human practices highlights during the entire product development on our Gold and Integrated Human Practices page.
When designing the project we have come up with many fine details for the software. Some came from our original ideas, others came from professionals in different fields. (See Silver)
We tried hard to put these inspirational details into the application of our software "S-Din". We tried to make more positive contributions to scientific and societal practices, and reduce and even eliminate the potential negative impacts.
Integrated database
Inspirations we have learned
By communicating with other iGEM teams, and chatting with different bio-lovers, we realized that fragmented data costs a lot of time and energy. We hope to establish such a database in S-Din, in a standard and easy-to-understand format. It will save one's time, which enables one to focus on his project ideas.
Integrated into the project
In S-Din's database, we standardize a new data format for different types of data: parts, projects, keywords, and papers. Based on this format, our database is integrated into a unity, and accessible to set up interaction network and analysis. The S-Din search engine and S-Din Design are both working under this standard.
Figure 8: 20 standard parts in S-Din.
Figure 9: Each genetic design uses standard parts and interaction lines.
Figure 10: According to the standard data format, users can add their new parts to S-Din's database.
The Tree of Words & Network Analysis
Inspirations we have learned:
We interviewed several lab researchers and found that how to trigger one’s inspiration is a challenge for us, but several related previous works may create a new idea. To find out related projects and to guide users to a clearer direction, are what we consider to achieve in our software.
Integrated into the project:
In order to stimulate one's inspiration in synbio work design, we tried the following explorations: The tree of words, and network analysis.
The tree of words: When you first enter the search engine of S-Din, you could search any word you like, or try selecting a word to explore more! When clicking, You will see the subordinated words. After few repeats, you will finally get the projects that you want. This function is designed to help specify your need, and help you understand your idea better.
Figure 11: The tree of words.
Network analysis: This function is designed to help you find out potential relationships between two parts, projects or keywords. Sometimes the recommendation may be hard to understand, but perhaps it would open a new direction and lots of inspiration for you.
Figure 12: Our analyses show keyword relationship and year relations when searching "UV light" in S-Din.
S-Din Statements
Inspirations we have learned
According to Mr. Li Yuzheng's advice, it is necessary to write a software statement, and show the statement to users when they first use our software. Only when users agree to provide their private information can our software collect and use it. What's more, Prof. He Zhumei reminded us of adding biosafety statements and interactive interface with users.
Integrated into the project
We combined the software statement with biosafety statement, then wrote the integrated S-Din statements. See statements, which consists of Terms of use, Bio-safety Alerts, Privacy Policy and Cookie Policy.
Integrated Human Practice
S-Din is a product born for solving synthetic biological problems and serving the biologists and ordinary people who are interested in synthetic biology. In our "Integrated Human Practices" page, we'll show essential human practices work we have done around S-Din, including user needs analysis, function improvement for user feedback, product assessment, and public promotion.
User needs analysis
Study the needs of other iGEM teams & ordinary bio-lovers
In the discussion with SYSU-CHINA iGEM team and SCAU-China iGEM team, we reached an agreement that fragmented data makes it time-consuming and laborious to collect and reuse data. (Silver page)
Nowadays data or information online is abundant but scattered. Many people spend much time on integrating them by themselves. instead of spending more time on their ideas for their core work.
Figure 13: How a man may assign his time in a project when getting integrated data by himself
In fact, this trouble is possible to be solved ---- by a dedicated software. If we could establish an integrated database, consisting of a unified standard of data composition and data format, we should find out the relationships among the data more easily. Besides, a data format standard makes it more convenient and engineering to store, reuse and combine the data. And engineering work is what computers are good at.
So our team desired to change the workflow into the figure below:
Figure 14: How a man may assign his time in a project when getting integrated data with a dedicated software.
Study the needs of ordinary bio-lovers
At the same time, we chatted with some students who are interested in biology work. They told us:
"We'll like the software if it shows details of each bio-project, in a way easy to understand."
"It would be better if the software can provide a basic analysis of the work."
"Could you develop a software which can recommend interesting projects of my own?"
...
We found that the needs above are the most popular. To achieve these goals, an enough huge and integrated database is critical. Of course, mathematical algorithms should be equipped with our software.
Studying the needs of biology labs
During the summer, we visited several biology laboratories of Sun Yat-sen University. Researchers warmly greeted us. Thanks to Prof. Lu Yongjun's help, we finished our interlab task and wet-lab validation in his laboratory. Meanwhile, we chatted with the researchers and conducted a small survey of their project idea.
By talking with researchers working in the lab, we were surprised that lack of ideas is one of the common problems when they work on a synthetic biology project.
“A good beginning is half done. That is to say, a good idea of a genetic circuit design is half done of the whole project.” A researcher named Dong told us.
Since ideas are so significant to a project, where do researchers' ideas usually come from? We did a small survey of researchers in several labs.
Figure 15: The sources distribution of researchers' project idea.
From the figures above, we learned that the majority of researchers’ idea source is professional research articles and journals ---- they work before, but a novel idea may arouse from them if the researcher reuses their essence and aims to an accessible direction. However, each paper usually describes its design in the author’s own style and standard, which is usually hard to understand and absorb its design ideas for one’s own creative work.
“We all hope to stand on shoulders of the giant, but it's hard at this stage to combine or transfer the senior's ideas in order to form my own ideas.” Researcher Dong said.
How to trigger one's inspiration? What if our software could help people with inspiration? This "Inspiration" inspires all of us. However, it is a challenge for us, because “inspiration” is such an abstract concept, and is hard to measure and specify. But hope is still alive: several related previous works may create a new idea. To find out related projects and to guide users to a clearer direction, are what we consider to achieve in our software.
Thanks to the inspiration flashed across our mind, we decided to create an onomatopoeia "S-Din" as the name of our project and software, as it sounds like turning on a bulb.
Needs & Functions Integration
Here are S-Din's core functions we developed for users' needs.
Integrated database
In S-Din's database, we standardize a new data format for different types of data: parts, projects, keywords and papers. Based on this format, our database is integrated into a unity, and accessible to set up interaction network and analysis. The S-Din search engine and S-Din Design are both working under this standard.
Keyword Tree & Network Analysis
In order to stimulate one's inspiration in synbio work design, we tried the following explorations: The tree of words, and network analysis.
The tree of words: When you first enter the search engine of S-Din, you could search any word you like, or try selecting a word to explore more! When clicking, You will see the subordinated words. After few repeats, you will finally get the projects that you want. This function is designed to help specify your need, and help you understand your idea better.
Network analysis: This function is designed to help you find out potential relationships between two parts, projects or keywords. Sometimes the recommendation may be hard to understand, but perhaps it would open a new direction and lots of inspiration for you.
To learn more about these functions, check Gold Integrated page for details.
Project Assessment
Safety assessment
We examined all parts in our database, and no part is from chassis of Risk Group 3/4. The "Unknown" parts are examined again with DSMZ Database. They are safe enough.
Figure 16: Risk group distribution of parts in S-Din's database.
We checked the parts again to judge if it has "Red Flag" tag. Only 26 parts are tagged. Since we are dedicated to providing an open platform for synthetic biology, the users won’t be limited if they search for ‘Red Flag’ parts; However, users will be warned and advised not to do so once they attempt to design new circuits with ‘Red Flag’ parts.
Figure 17: Red Flag part distribution in S-Din's database.
More safety details on Safty page.
Societal effect assessment
Once we had ideas of S-Din, we interviewed professionals or scholars in different fields and searched related policies. We had a better awareness of our project in the context of scientific inspiration, societal attention, safety and security, and legal considerations.(Silver page)
When S-Din was finished, we introduced it to the professionals. With their advice and help, we wrote a product statement combined with four parts: Terms of use, Bio-safety Alerts, Privacy Policy and Cookie Policy.
See statements page for more details.
Public promotion
When S-Din started to take shape, we promoted it to several iGEM teams and biology laboratories. They were interested in our software and tried out, then we were glad to receive their encouraging user feedback:
"Your database is wonderful! Our project may be more smoothly if cooperated with S-Din!" by Hong_Kong_HKUST
"An integrated software for synbio community." by SCAU-CHINA
"An inspiring try, I like it very much. Hope it will be more perfect in the future, and our lab could really use it." by Researcher Shen from Prof. Lu Yongjun's laboratory
"More professional articles in database might be better?" by researcher Lin from Prof. Yang Jianhua's Laboratory
Figure 18: We recommend S-Din to researchers of LU laboratory.
Ordinary bio-lovers are also interested in S-Din, especially its name.
"The name 'S-Din' is cool! I like it!" by Lin
"The software is smart! How does it know what I really want to search?" by Zheng
"What if S-Din can recommend some daily headlines, like newspapers, Synthetic Biology Daily?" by Li
Figure 19: We introduce our product S-Din to ordinary students of SCAU.
We are very excited to witness a hit in public when S-Din first met with the public. From the original inspiration to the real software product, our software can't be born without continuous communication and timely feedback with public and all related fields. We are deeply impressed by the power of human practices. Although this version of S-Din is not perfect, we'll continue to create a better product.
Synbio is just a S-din away.
