Team:Tongji Software/Human Practices
HUMAN PRACTICE
NEW YORK UNIVERSITY SHANGHAI
This is the first time that we have attended the meeting since we formed the team. At this Shanghai regional meeting, each team showed their project ideas, which made us realize that iGEM is a big family full of ideas and creativity. Of course, our team also showed the initial concept of the software. Exposed to the opinions of all teams including the experimental team and the software team, we further clarifying the in-depth direction of our project.
Fig1. Presentation in New York University Shanghai
INTEGRATED:
Before attending the meeting, we have determined that the theme of the project is the metabolic pathway. After communicating with other teams at this conference, we learned more about the experimenters, the target users of our software, and their needs for information on enzymes and parts. So, we added the functions about enzyme and parts to our software.
CHINA PHARMACEUTICAL UNIVERSITY
This meeting is the Nanjing Regional Meetup. After a period of work, we had completed the idea of our software workflow and presented it to more teams at this conference. Here, we accepted the comments of teachers and entrepreneurs. The most impressive one is that focus on just one thing. Because of the limitation of time, we may be not able to make every part to be perfect, but we can lay emphasis on a certain aspect and make this aspect to be as good as possible. With this suggestion, we adjusted our plan about the software.
Fig2. Team member in Nanjing regional meetup
INTEGRATED:
After the Shanghai regional meeting in NYUSH, we originally intended to implement path search, enzyme selection, and parts design in our software. After learning more about current tools on parts, in light of the recommendations made by the judges at this meeting, we decided to focus the software on pathways and enzymes, especially enzyme selection, which led us to teachers and labs, seeking theoretical support.
GENSCRIPT
GenScript is a very strong biological company, involving a number of research directions. When we learned that GenScript was providing the enzyme combination screening experiment, we contacted GenScript. For some reason, we could not have face-to-face communication with GenScript, but we got in touch with their technicians by phone. Over the phone, we introduced our project idea which is a pathway construction platform with functions like pathway search, enzyme selection, parts browser, so as to provide users with a relatively integrated pathway construction platform. Because GenScript didn't involve in software development field, they showed some interest in our software. In further communication, we learned about GenScript's work on enzyme combination screening. According to the requirements of users, after obtaining a pathway, a certain enzyme was selected for each step of the reaction, and then the enzymes in each step were randomly combined to test which group of enzymes was more suitable through experiments.
GenScript's work in this field is basically consistent with our ideas and results in enzyme screening. Our software can do a preliminary screening, equivalent to pre-test, which can reduce a lot of work and improve efficiency.
Then we discussed the customer requirements and found that the target users of the enzyme combination screening experiment had requirements for enzyme selection. In order to select a suitable enzyme combination, a large number of experiments were needed for verification. Due to the limited conditions, this part of the work can only be assigned to the company to do batch experiments. Through discussion, we found that our software can meet the needs of these target users, which means that our software is of practical significance. And we are looking forward to have a further discussion with GenScript after the completion of the software.
EAST CHINA UNIVERSITY OF SCIENCE AND TECHNOLOGY
In order to further investigate the project, with the help of our PI Fei Jian, we contacted the teacher of microbiology in East China University of Science and Technology, professor XuZhang. We introduced our project to the teacher, who was also interested in iGEM and our project content, so we had a very deep communication with professor zhang. The suggestions from him are as followed.
Firstly, compared with making all enzymes into one single bacterium, making a flora seems to be more practical and feasible. We can put each step of the reaction in a pathway into a single flora, instead of just putting them into a bacterium to complete the whole pathway, which made us reconsider the synthesis environment of a pathway.
Secondly, we should consider the influence of the external environment, because the expression of some enzymes is relatively dependent on the condition of the external environment. Therefore, cofactors of enzyme were added to the selection of enzymes as an influencing factor.
Thirdly, enzyme kinetics was also considered as the screening method for enzyme selection.
Fig3. Communication with professors in ECUST
INTEGRATED:
Based on last year's project, we are prepared to focus on adding the function of enzyme selection, which is approved by the teachers. Because of this human practice, we opened up our horizons in this regard. After reading the literature, we gave up the teacher's advice on the flora, but we still listened to some of their suggestions and started to integrate the physical and chemical properties of the enzyme from the public database. So far, we have completed the idea of the function of the software. Next, we need to work on the practicality of the software functions.
GENEWIZ
In order to verify whether our software is useful, we paid a visit to GENEWIZ and wanted to get some useful suggestions from company. GENEWIZ is a company that involved in many biology fields like gene synthesis, protein optimization and synthetic biology, besides, some of our team members are users of GENEWIZ. So, we chose it as the first company to visit and we thought we may get some answers we want.
In this human practices, we first gave a brief introduction about the functions that the software had already done and what we wanted to do, therefore, we pointed out that enzyme selection and optimization are the key points of our project, and we would like to know how to make our results more reliable and more practical.
On enzyme selection, firstly, they suggested that we could widely read articles about protocols to realize certain pathway, and conclude their methods to select enzymes. Secondly, they told us that the selected enzyme's physical and chemical character must be very stable, which means it can work as widely as possible. Thirdly, we should take the whole process and the final result into consideration, because enzyme selection is not a separated job and every best step does not have lead to an overall best.
On enzyme optimization, they honestly told us that each enzyme optimization was able to be a project, so it was hard to find a general method for all enzymes, but we caould consult some teachers major in biochemistry, maybe they had some ideas about it. Although we didn’t get a specific method from GENEWIZ, they gave us some suggestions about scoring those enzymes. From gene synthesizing, their production department gave us some deduction items, the most typical of which was some sequences in certain species like E. coli were difficult to synthesize in the productive process.
Fig4. Communication with GENEWIZ
INTEGRATED:
Going to a synthetic biology company for communication is the best way to test the usefulness of software. During the conversations with the staff, we thought that if the functionality of our software is perfectly implemented, the results it gives will be very informative. So we referred to the experience and information provided by the company's staff and began to establish the ranking criteria of our own in terms of enzyme selection. In this way, the prototype of our software is formed, which means we can show it to more people for suggestions.
CCiC
CCiC, which full name is Conference of China iGEMer Community, is a very important and helpful platform for iGEMers in China. There are experienced judges from iGEM to give us advice from a professional and competition point of view, and we also have the opportunity to learn about other teams' projects, and we will also provide advice and help to each other.
In the CCiC presentation, we already had a demo of the software. In this way, we made the iGEM teams from China have a specific understanding of our software, so that we can seek cooperation to verify that the results given by our software are credible. At the same time, we also had technical exchanges with other software teams.
For the overall design, we received suggestions of the web page design. For example, we should know more about what users want so that we can design corresponding functions. What’s more, the design on the web page should be more user-friendly, which means we should point out what steps should users do.
Fig5. Post session in CCiC
INTEGRATED:
After the practicality, we need to consider the credibility. In terms of results verification, we found the China Agricultural University, using their pathways to verify our software results in a collaborative manner, and got good results. At the same time, we also provided them with relevant information. This proves the credibility of our software. In addition, for the function about parts which we do not intend to focus on, we used the existing database of the University of Electronic Science and Technology to expand our software and as a collaboration. After the software's functionality was successfully implemented, we decided to start a user survey of the software interface design under the advice of CCiC's judges.
Questionnaire
Fig6. Partial result of questionnaire
We set a questionnaire to confirm the design of our software web page about which kind of web page users want, including color, hint style, result form, file options and record saving. This is the final step in completing our software.
SUMMARY
1. OVERALL DESIGN
When our team was founded, we reached a consensus and decided to start this year's work based on last year's project and identified the theme as metabolic pathways. In NYUSH conference, we decided that the core function of our software is pathway design, which involves pathway search, enzyme select and parts design. We contacted GenScript and they told us that a platform of pathway design was useful and it would reduce the amount of work to both researchers and the companies. We found that databases about parts contain small amount of data, and it was a lot of work to clean up the data, so we changed parts design into parts browser, and we focused on the iGEM parts database.
2. PATHWAY SEARCH
In Genewiz, they asked us about the reactions in the database, and they told us that we could find some prediction data which could provide a direction for researchers whose material was rare or new. We accepted their suggestion and we found a database called ATLAS, which contains novel reactions for us to use. We cleared up their data and integrated it into our data.
3. ENZYME SELECTION
The biggest obstacle in the selection of enzyme is the selection of parameters. For this reason, we visited ECUST and sought the help of Professor Zhang Xu of microbiology. The professor said that the physical and chemical properties of the enzyme itself are very important, and that the stability of the enzyme can be influenced by external conditions. So we took KKM, KM, pH and temperature into account when we ranked the enzyme.
4. PARTS BROWSER
All the academic institutions we consulted agreed that the parts design of regulatory type is of great practical significance. Due to the limitation of database, we can’t make the part design, but we made a browser to make it easy to find parts with certain function or character.
5. VISUALIZATION of SOFTWARE WEBSITE
Through CCiC, we met many experienced iGEMers. They suggested us to know more requirements of users and based on this to do visualization. So we set a questionnaire and the interface design of our software was determined in the form of user research.
All in all, through the integrated human practices among teachers, companies, and iGEM teams, we have finally realized a powerful, practical, credible, beautiful, and user-friendly software.