Team:SYSU-Software/Scientific
Scientific and Societal Thinking
During the project, we brainstormed many aspects concerning our project. These aspects can be roughly divided into two problems: What impact will our project have on societal questions, and will our project promote or offer convenience to scientific and engineering practices?
Through the discussion and inspection, survey and practice, we had a better awareness of our project in the context of society and environment, scientific and engineering. These inspirations help us improve our project a lot.
(1) Practices in Science and Engineering
1. Studying the needs of wet-lab teams and open communication in iGEM
Motivation
Synbio needs software. As a software team we need to contact with wet-lab teams, to listen to their needs, and to put our efforts to where they are most in need. It is also very interesting and exciting to meet people who will be most likely to be affected by our project, and whose opinions will be most beneficial for us to develop the project.
Practices
A survey during the NCTU_Formosa meetup
Xiao Feng, Jinjin Lin, Liang Tang, Xiaoran Yang, Yi Shi and Xiangyue Hu
In late July, we attended the meetup held by 2015 NCTU_Formosa. We shared our idea and listened to suggestions from other teams.
Photo of team members in NCTU_Formosa meetups.
In the poster session, instructor of 2015 iGEM team NYMU-Taipei, Prof. Chang, Chuan-Hsiung, asked us a question.
“Whether synthetic biologists or iGEMers would think of your project as what they exactly need? Or whether they could find other software for a substitute?”
(During the project we always thought of Prof. Chang's question, and his words always motivate us to make our project meet the need of wet-lab synthetic biologists. He also gave us precious advice on how to find out the needs of iGEMers. For example, he advised us to do survey and find the needs of iGEMers, and to make software to satisfy these needs.)
Photo of Prof. Chang (left) and Xiao Feng (right).
Following his advice, we made a survey among the iGEM teams participating in the NCTU_Formosa meetup. We asked them questions about what they expect if they need software. Here are some of their answers:
“We’d like a tool to predict the performance of our design…And after obtaining experiment results, we need a tool to model our system. However, matlab is hard to use.” by BIT-China
“There’re so many tools with the same or similar functions. It’s hard to choose from…usually, we’ll ask team members of previous years for recommendations.” by Fudan
Obviously, for wet-lab teams a software that can predict the performance of, or model, their systems is needed. Usually they prefer ONE software with integrated functions, not several tools with separate functions.
A newsletter by 2014 iGEM team Amoy, Paris Bettencourt and Pasteur
We also learned about the needs of iGEM wet-lab teams in the newsletter by Amoy, Paris Bettencourt and Pasteur. In the 6th issue on software, they devised an open questionnaire about software：
What software are you using in iGEM this year?
What software have you used in previous competitions?
What kind of software do you need most?
Which features are you looking forward to?
Newsletter by Amoy, Paris Bettencourt and Pasteur.
We made a statistical investigation form this questionnaire and here are some representative answers:
For the first question, we know the most popular software used by wet-lab teams are the Microsoft Office and MATLAB (represented by WLCMilwaukee and UPV Valencia team). In addition, software that assist wet-lab is also popular, such as BitBucket, snapgene and primer premier (represented by NJU_CHINA and SYSU_China team).
For the second question, we know in previous competitions the most commonly used software are adobe and matlab (by Bettencourt Paris and WLCMilwaukee team).
For the third question, a software for wet-lab teams should be user-friendly. This is because wet-lab teams lack experience in working on source code, and they have little time to “discover” the function of a software (represented by Colombia team). Other features for a good software should contain basic functions like mathematical modeling, design of construct, and analysis of DNA sequence (rpresented by Colombia, Bettencourt Paris and WLCMilwaukee team)
Obviously, we know that software in synthetic biology should contain the basic functions like design and modeling, while it should guarantee the user experience as much as possible. In the wet lab we need powerful analysis software. Software to deal with the text and graphic is also necessary. But no team has mentioned that they have used any communicating software. There being no such kind of software makes it hard to exchange ideas between the teams. Further, if we cannot easily find out the information on the work done by previous iGEM teams, it will increase a lot of unnecessary labor. What’s more, it does no good to the reuse and redesign of previous design.
The Peking CCiC meetup and inspiration of building an interactive platform
Xiao Feng, Weilin Xu, Shengkun Dai, Qianhui Wan and Zhengyang Wen
In the mid-August we attended CCIC (Central China iGEM Consortium) held by 2015 iGEM team Peking. Taking advantage of this opportunity, we introduced our project to other teams and exchanged ideas with each other
Photo of team members participating in the Peking 2015 meetup.
“Redesign is an excellent idea. It could help a lot in reusing the former iGEM works. You know, they are difficult to be reused now.”— By LZU-China
“We have some common ideas in the computer-aided circuits design. But is aiding in design the only way that software helps synthetic biology?”— By HFUT-China
“Even software track should pay attention to biosafety problems.”— By NUDT_CHINA
“We still believe the communication between iGEM teams is not enough, especially the transparency in the experimental material, which affects the repeatability of the projects.”— By Nankai
We learn that wet-lab teams value communication between teams too. Most of them think that communication should not be limited to meetups; instead, communication should be held online, real-time and professional.
Inspirations on project
At the beginning of our project, we aim to develop a computer-aided circuit design software. The bi-directional dialogue between us and wet-lab teams reminded us of what kind of software is really needed.
“Communication should never be limited to meetups; for synthetic biology community there should be an open platform for collaboration and co-development. “
That is where the idea of “open platform for synbio community” comes from. For iGEM, it should be a platform to promote communication and more importantly, collaborations between the teams. And it also helps in the reuse and redesign of the previous works, and in preventing “re-inventing the wheels”.
2. Transparency and Reproducibility in iGEM
Motivation
Transparency and Reproducibility are at the heart of scientific practices. iGEM is a competition standing at the front of synthetic biology, so transparency and reproducibility of the work done by iGEM teams are particularly important. However, information of all these wonderful works done by previous iGEM teams are scattered around in the wikis.
Practices
A survey on information completeness in previous iGEM wikis
Liang Tang, Xiao Feng
Before picking a project, in early May we did a survey of how information of projects was stored and represented in the Wiki of previous teams. We aimed at finding out how well their designs were documented in the Wiki.
Numbers of biological parts used by previous teams in genetic design with or without BBa number documented in their wiki.
These included:
1. Whether they used the standard parts in Registry when they were constructing their circuits?
2. If so, whether they documented the information of all the parts they used (the bottom line is, whether they well-documented the parts they used in their constructs.)
We can see that in the wiki of previous teams, there is not enough information for others to reconstruct their circuits. Only about 3/4 of the promoters that previous teams used were well-documented in the wiki. As for protein coding sequences that previous teams were using in their projects, only about 70% of the CDSs were well-documented in their wiki.
It is obvious that in the wiki, information about designs and constructs done by previous iGEM teams is by no means enough. Without enough information about the parts they used as well as the experimental protocols they obeyed, reproducibility in iGEM is hardly ensured.
Attended a lecture given by Prof. Rong, Yikang
Shengkun Dai, Weilin Xu
In early September, Prof. Rong, Yikang gave a lecture talking about his research interests, and at the beginning of his lectures he spent an hour talking about the importance of transparency and reproducibility in scientific research. He gave many ideas on how to improve transparency and reproducibility in designing experiment. His lectures helped us identify the important aspects when we considered how to promote reproducibility in iGEM: a well-documented experiment design, well-designed biological as well as technical replicates, as well as caution about statistics.
Inspirations on project
The fact that information only stored in wiki of previous teams brings about two problems disturbing the reproducibility as well as the transparency in iGEM:
1. All the information concerning the projects of previous iGEM teams is scattered about in the wiki. Finding out information about previous projects is like “looking for a needle in a haystack”
2. Representation of their designs did not conform to a well-established standard; these may lead to confusion and misunderstanding of the work they did.
So we aimed at designing a standard platform for information parsing and sharing. This platform should standardize the way every team store the information of their projects, and also should allow other iGEMers and scientists to give feedbacks.
3. Safety and Security
Motivation
Development of Genetic Design Automation poses great challenges to biosafety in synthetic biology. Genetic design is made easier with the help of software, but software itself does not think for itself the consequence of users’ genetic circuits. Some designs might be quite dangerous if misused. We looked for ways to utilize computational effort to tackle problems in safety and security.
Practices
Weekly meetings discussing how computational effort can protect wet-lab practices
Weilin Xu and other team members
In late June Weilin Xu gave us a talk on how to be safe in iGEM. We were alerted the safe practices in wet-lab team. We also learned the Risk Group of microbes.
In the discussion, we discussed about the safety problems in project design. Team leader Xiao Feng talked about aspects in biosafety in project design, say:
Weilin introduced biosafety in iGEM to us
1. How can we use algorithms to determine the danger of a circuit?
2. If the genetic circuit contains any unknown parts, what should we do?
We reached an agreement that it is the responsible conduct in synthetic biology that matters. Software can help in some way, but it can do little when it comes to parts with unknown origins or unknown functions.
Also, to determine whether the genetic design is danger, one should not depend entirely on the origins of biological parts; we should focus on not only the origins but also the functions of the parts.
Consulted experts on biosafety in the campus
Weilin Xu, Xiao Feng and Zhengyang Wen
In mid-September we visited and consulted Ms. Jie Zhang, specialist on biosafety in the school, about questions of how to be safe in a project.
Office of Laboratory Biosafety in our school.
Ms. Jie Zhang talked with us about safety in our school
We talked about biosafety in genetic engineering, a topic most relevant to us. Although she was not familiar with software engineering, nor did she know thoroughly what we did in the project, she gave us many constructive suggestions, say:
1. There must be rules for users to obey. Users should obey these rules in order not to make mistakes.
2. Rules are not enough; there should be warnings, tips, etc., for users to clearly remind themselves of their responsibilities in biosafety and biosecurity.
She was also interested in the poker we designed on the topic of biosafety. She advised us that more innovative methods are needed in order to improve the awareness of people in the lab and people outside the lab alike.
Photo with Ms. Jie Zhang.
Inspiration on project
As a platform open to public in our project, CORE has the responsibility to properly deal with the problem of safety and biosecurity. We should classify the standard parts according to their origins (risk group) as well as their functions. Users of CORE should confirm that the benefits of this design for public outweigh its risks. Also, in the process of genetic design, we should remind the users of their conducts to the synthetic biology, to the human beings, and the world.
(2) Social Impact: Reflection and Practices
Our team has been working on the software aiding circuit design for years. We want our software could be not only competitive in Software Track but also be applied to actual scientific research and industrial product design. We think a lot about how our software influence the society if released and accordingly, how should we optimization our project.
1. Intellectual property
Motivation
We hope our software, CORE, can be open to the synthetic biology community. And one important thought is to protect the intellectual property, to respect the hard work done by others. Sharing should be based on the respect of others.
Considerations
There might roughly two methods to help protect intellectual property rights
1. When we re-design the work done by others, we should appropriately cite the work and take note of what changes have been done to the genetic design.
2. We can deploy the CORE on a semi-public server, so that their data and genetic design can be saved in a local database.
Inspirations
Intellectual property is to protect the intellectual achievement of the authors. As a software for genetic design and idea communication, it's necessary for us to do something about it. We stand on the author's point of view and set some corresponding rules. For example, all ideas rose by other users will be site with the names of the author. In addition, users can deploy CORE in their laboratory privately, and construct genetic circuits together with the help of CORE, online (though it is highly recommended to deploy CORE on a public server like world-wide-web).
2. Laws and regulations
Motivation
In scientific research or industrial production, we all require to obey the laws and regulations. Synthetic biology is a field booming in the 21st century, so inevitably, there might not be enough laws and regulations on synthetic biology to regulate the practices in synbio. In China, synthetic biology is new and full of challenges; whether scientists get prepared for it?
Practices
A talk with student from humanity
Xiao Feng, Weilin Xu, Shengkun Dai and Jiaming Hui.
Team members of SYSU-Software come from mostly sciences and engineering, so a talk with students of humanity background is interesting and exciting.
In early September, we were pleased to have a talk with a student of humanity, Jiaming Hui, on the topic of how genetic engineering and synbio have an impact on Chinese, and what do China do to regulate the practices in genetic engineering and synbio.
We were pleased to know that in China, there are already laws that regulate many aspects of the scientific research and production of products of genetic engineering. After we introduced to Jiaming about what is synthetic biology, Jiaming told us that in China there are laws relevant to synbio; however, because synbio is a discipline with rapid development and a wide field of research interest, more regulations on synbio are needed.
We learned from Humanistic thought.
We also discussed with Jiaming about the video made by Yongyuan Cui, a celebrity who does not support genetic engineering. Jiaming had no remark on this video, believing that every one should have the right to express their opinion. He further added that as celebrities, they should be cautious about their words and comments in the public.
Inspirations on project
The talk with Jiaming involved no sciences or technologies; we were concerned about the social impact of the technology itself. With his help, we realized the importance of regulations. Maybe in the project, we should consider reminding users of their social responsibility and all these regulations? An user agreement may help.
3.Ethics
Motivation
Ethical issues are important in the study of synthetic biology. Synthetic biology has enable scientists to change the genetic makeup of an existing living things, so it might raise controversy. CORE is designed to help re-engineered the genetic makeups of bacteria, so it is necessary to consider the ethic issues in the project.
Practices
Consulting Prof. He on bioethics considerations when designing a project.
We consulted Professor Zhumei He, experts on bioethics and biosafety in the campus. He gave us a small lecture about biological ethics, including the widespread controversy caused by transgenic technology, genetic therapy and human cloning. He also gave some advice in biological ethics to our software.
we have a discussion with prof. He.
1. Users must be prohibited from re-engineering the genetic makeup of embryo.
2. Users should be reminded of their potential responsibility in ethics and safety.
3. Users, no matter who they are and where they come from, should be equal with respect to the right to know what synbio brings to them, and what might be the good and the bad of synbio.
We also invited Prof. He to do some assessment on the software. For more details, please navigate to “Human Practice/Risk Assessment”.
Inspirations on project
Software in synbio should help the progress of synbio but should NEVER violate the public consensus on ethics and safety. In general, users cannot directly operate on embryos using CORE, and a user agreement embedded in CORE should tell users what can be done and what should not be done. So we should focus on the second and third notations by Prof. He. The equality in the right to know should be ensured by open communication; a bi-directional dialogue between scientists and ordinary people