Document

Overview

For the human practices, we have two main goals. One is to improve our own project. Another is to promote us, iGEM and synthetic biology to the public. Our integrated Human Practices will mainly talk about how HP affects the project. And in our Education& Public Engagement, you will find more about how we let people engage synthetic biology.

Integrated HP

At the beginning of the competition, we decided to construct the integrated biobrick database. Because of the specialty of the project, our main users will be iGEMers and synthetic biologists. Then we thought carefully about how to make sure our project would work well and meet the needs of those who conduct synthetic biological experiments. So, we created a complete ‘investigation-improve-test-feedback’ framework with 7 steps and 2 rounds of tests and feedback to improve our project. Then we did our human practices in correspondence to every step of this circle.

Here’s the 7-step circle. You can click the fellow bottons to straightly see any step you want to know or you can read it step by step.

Problems and Idea

First, we encountered the problems when using iGEM Registry to conduct experiments and we came up with the idea of constructing this BioMaster database to solve the problem.

Preliminary Investigation

Then, preliminary investigation is essential which will be our directions for the first construction. We did some surveys and questionnaires for nearly 100 participated iGEMers or professors about the problems they met when doing synthetic biological experiments. Of course, we analyzed what we investigated. What’s more, not only online research but we communicated with different teams face to face for their opinions and their needs for a new biobrick database. Also, we consulted a lawyer for the rights of using other databases in case we violated some regulations.

Questionnaires and Analysis

Before the start of our project, we need to know clearly what problems we are facing and what our users’ needs are. Only in this way will we make sure that our project is adaptable and user-friendly. We designed an online questionnaire ‘Investigation of situation about the use of iGEM parts’ and spread it to over 16 districts and nearly 100 iGEMers and synthetic biologists.

Of course, questionnaire cannot live without analysis. We spent some time analyzing the results and used the method of binary-crossover analysis. Surprised results were found and it inspired us for the next step.

Our analysis results

We used binary-crossover analysis to the question ‘How do you feel about searching information in iGEM Registry? ’ and ‘What difficulties or problems you would encounter when constructing a gene circuit? ’. The former is the independent variable X and the latter is the dependent variable Y. Through this method, we were surprised to get a message that was easily ignored before. From the initial statistical results, the ratio of option A ‘I don't know which part to use’ is the smallest. However, after analysis, we could see that most dissatisfied people chose ’I don’t know which part to use’. In other words, in our project we should focuses more on this issue. According to this, we are more determined to added more accurate information to the database as much as possible.

Fig.1.Satisfaction

Fig.2.Cross analysis table

Fig.3.Cross analysis chart

A visit with iGEM team

We went to UESTC-China and communicated with them about their opinions. First, we asked the problems they may want to avoid and what they think is a user-friendly database. Their opinions are important for us to design the database.

“If we can search for biobricks by keywords and functions will be more than goodness. Also, if a database can provide information such as judging form would be better.” — Leader of UESTC-China Changyu Li

Consulting the lawyer and Our statement

Considered that BioMaster may involve with intellectual property issues and issues for users, we deliberately visited Mr. Zheng Yonggang, Senior Partner and Director of Sichuan Shangsheng Law Firm who has handled many related events and has rich experience in this field. He indicated that since these databases are open resources and there’s no confirmation on these databases that we are able to use it. No intellectual property issues are involved. We checked carefully on every database we integrated to avoid any missing possible regulation on the property of database. At the same time, we made a statement mentioned clearly what we integrated and we have no commercial intentions.

Details of Consult and Our Statement

Conversation with lawyer

Question1: Does BioMaster cause any infringement when using data and providing links to related documents from other databases?

Answer: If related resources are open to everyone and there’s no statement, using related data will be fully reasonable and legal. What’s more, BioMaster only provides references and the original links which is open on the related websites. So there will be no infringement.

Question 2: If users cause some influences on the project or others via using data in BioMaster, is BioMaster responsible for it?

Answer: Since the software is free and there is no interest dispute between the two parties. Users should use the voluntary principle when using it. Therefore, even if there are adverse consequences, the software provider is not responsible.

Statement

0 Version Start!

With the investigation and analysis, we merged it with our idea and we started our 0 version so that what we constructed would better fit user’s needs.

Professional Advice

When the 0 version was done, what we need was more professional and authoritative suggestions. To make sure the comprehension of the suggestions, not only universities but institutes and bio-technology company were visited. They gave us very specific suggestions and what we should improve. At the same time, we gained experience on establishing the database.

Communication with Dr. Dai

On 31st Jul, we attended the scholars' forum on synthetic biology, led by Dr. Dai Junbiao from the Shenzhen Institute of Advanced Technology of the Chinese Academy of Sciences. After the forum, we communicated with Dr. Dai. We simply introduced what BioMaster is and what we want to achieve. He gave us his opinions and what he think about our projects. Also, he provided something that we should improve such as experimented data.

Full conversation

Question 1: When the experimenter conducts synthetic biology research and gene circuit construction, what aspects of the biological bricks should our database focus on and provide information to facilitate its work?

Answer: First, the sequence information of the components is very important. Second, the description of the function of biological components is also critical. At the same time, if you can provide data of some experiments carried out on some fragments or sites, it would be better. The experimenter will make good use of this information.

Question 2: What ideas or suggestions do you have for our project?

Answer: The starting point of your project is very good. According to my understanding, the registry on iGEM online does have a lot of deficiencies, and some information even has errors. So, this is indeed a problem which is both distressing and worth solving. As for the suggestion, after the user finishes searching for the information of the biobrick, you can also provide some other biological components related to the biobrick. In addition, when searching for biobricks in the database, I hope that you can provide more ways and means to make it more convenient for users.

Talking with Gene Technology company and Professor in NUDT

On 3rd Aug, our members went to Chengdu life baseline technology co. LTD and interviewed engineers who is working on a database. They gave us useful suggestions on the optimizing of details. One of the engineers shared his experiences on the construction of database.

At CCiC, we had honor to get acquaintance to Professor Zhu in NUDT. He encouraged us to keep working on our database and he suggested that we should classify the biobricks by species.

“You can build the prediction results into a database. So, when users can't find what they need, they can use this as a reference.” —Engineer Xu of Chengdu Life-Baseline Technology Company

“In my opinion, you better assort the data by organism, which makes your database more convenient.” —Professor Zhu in NUDT

5th CCiC and Southwestern Union

We took part in 2 big conferences in China held for iGEMers to share experiences and communicated with each other. In the meantime, it’s a good chance to be acquainted with iGEM teams and collaborated with them.

The 5th CCiC was held in ShanghaiTech University with over 500 people participated. On this conference, we gained valuable advice and we first brought our project and many teams gave us their suggestions.

Southwestern Union was established for many universities in southwestern of China. Not only universities, but high school teams joined in it.

For more pictures

Improve

After second round collection of suggestions, we improved our project and our interval test version was finished.

Internal test & Feedbacks

We sent our internal test version to many iGEM teams and doctors and they gave us their feedback of using it. These feedbacks will be the supportive advice for further improvement. Meanwhile, we noted that some teams encountered some difficulties in finding the data they need. Therefore, our database helped them find it more easily. Via emails, questionnaires or WeChat, we received several feedbacks from iGEM teams or experts.

“The database is detailed and comprehensive, with relatively high practicability. However, it needs to be more aesthetically pleasing.
The search results page can add a description of the search terms. And the search results can be sorted in chronological order.
Database compatibility with browsers needs to be improved and some pages have Chinese words.” —NKU_CHINA

“The UI surface is very user-friendly. However, there’s some details you should be more careful. I suggest that you should provide what medal the team won on the searching of Team Wiki. ” — Pro. Zhu Lvyun in NUTD

“BioMaster is of great excellence. It indeed provides us many useful statistics for us so that we can refer to it. BioMaster brings conveniences to our experiments. If some relevant references are provided and display biobrick information in a visualized way, it would be more user-friendly.” —UESTC-China

“Your information is comprehensive and the UI surface is user-friendly. However, the ranking of search results is to be optimized when searching with iGEM_ID, such as searching for BBa_K104000, the first display of BBa_K1040001, and BBa_K104000 in the back position. You’d better give out a guidance to each information, for example, new user may not know what EPD& RegulonDB contains of.” ” —USTC-Software

Final Release

With all the the feedbacks and adjustment, our final 1.0 version of BioMaster was borned. To promote it, we held a little release in our university with over 80 undergraduates attended. Simultaneously, we did a live show on the hottest live platform “Douyu” with more than 1600 people watching and comments.

Silver

We chose questionnaires and analysis to get to know users’ needs for a new biobrick database. And we communicated with experts and professors for the professional suggestions on our projects. Also, to make sure that we will not violate any regulations related intellectual property issues.