Collaboration was the theme of this past spring, summer, and this fall.

We have created a computational synthetic biology tool, SBiDer, that fosters collaboration among the global synthetic biology community. SBiDer also has a potential to bridge between other fields of biology and the field of synthetic biology by enabling ontological interpretations of biochemical reactions as well as genetic interactions. Furthermore, SBiDer database can become the first universal database for the field of synthetic biology. Lastly, we have minimized the barriers for collaborative development of SBiDer by modularly engineering SBiDer on an open source platform. We encourage the global community to extend, develop, and optimize SBiDer - together.

Our team has developed SBiDer from the ground up, and my primary tasks have been the engineering of the database and the search algorithm. Engineering the database and the search algorithm were daunting tasks that challenged me in many ways. Yet, I embraced the challenge. The more arduous the project became, the harder I worked. As a result, this assiduous process has provided me with a fantastic opportunity to improve my skills in computer programming, bioinformatics, and mathematical modeling. Now, I truly appreciate the value of the challenges that I faced and the priceless opportunity of this education.

Developing SBiDer codes was hard, and effectively leading a groups of people was even harder. Technical challenges not only made me a critical thinker, but also harnessed my skills as leader that ultimately made me a better scientist. In the process of interacting with my teammates, I felt a maturation of myself. I have learned to be more conscious about others’ struggles. I learned to sacrifice for others in developing the project, which is key in teamwork. I learned a lot about proper teamwork ethics. Looking back, I am surprised how much I have learned about communication, effective leadership, project development, and more. I believe these skills have made me a better scientist. Without working together, we would not have been able to develop SBiDer. SBiDer is a result of our communal effort.

I believe that science and collaboration are closely intertwined, for collaboration fundamentally advances science. I am grateful for the opportunity in developing SBiDer and working with my team: Joaquin, Jenhan, Justin, Ben, Ryan, Andreas, KP, Lauren, Valeriy, Gary, Fernando, Luyao, and Rohit. I learned tremendously from the collaboration that was coalesced with the science. And finally, we made SBiDer. The past seven months have been filled with learning opportunities, arising in unexpected manners that have led a an enjoyable and fruitful journey.

I hope the community enjoys SBiDer and can contribute to its further development.
All in all, collaboration was not only the theme of this past spring, summer, and this fall, but it will be the theme of my life.

I was excited for the start of summer 2014 for the experiences and work that would be done by our UCSD iGEM team. The focus of my work was the database creation. The initial progress of the SBiDer database included lots of learning SQL and Python for the usage in the SBiDer database creation. Although I had some programming experience in Python which helped populate the database, the creation of the database itself was not an easy task. To create just any database is easy, but what I found to be really difficult was creating a database schema that planned ahead for the SBiDer network. I had great team members and together we managed to both create a reliable schema and populated a database that helped move our project forward.

I came into iGEM expecting to learn a lot of about programming, but iGEM was also a great experience to learn teamwork. Communicating seems like a given in a team project, but that doesn’t mean that ideas are put into clear words. I learned to talk clearly with my teammates to establish tasks we had to do and how we could work together. As the project was coming to a close we really depended on one another and I learned to sit down and work out problems with people. For the future I expect UCSD iGEM teams to be able to build upon our successes and failures. Being part of iGEM this summer has encouraged me to begin a club on campus that focuses on synthetic biology, stressing programming and teamworking skills that would make future UCSD iGEM teams successful and competitive.

When Jenhan first approached me about mentoring undergraduate students for a summer software project in synthetic biology, I was initially very excited at the opportunity, but at the same time I was nervous. Many of the students we recruited had very little experience programming, and our project was very ambitious. We spent the better part of the Spring quarter teaching skills to the undergraduates ranging from synthetic biology concepts, to algorithm development, to learning how to read scientific papers. I was pleased and impressed at how quickly the undergraduate students were able to pick up these new skills, and when summer arrived, we were ready to hit the ground running.

My undergraduate background was in biology and mathematics, but all of my research experience had been in bioinformatics up to this point. I had never worked on a synthetic biology project either, but after attending IWBDA 2014, I was able to learn more about the field, giving me the confidence to move forward in mentoring this group of undergraduates. Software development was also a new project style for me, so the process has also been a great learning experience for me as well. Much of my summer was spent helping the students develop and analyze algorithms to perform searches and queries across our manually-curated networks. I was also involved with the database schema development to better represent the network we were trying to present. As a member of the Trey Ideker lab at UCSD, I have spent the past year working closely with network biology and tools used in network biology, which has been important to the development of both the back-end database and the front-end application.

Additionally, as a new graduate student, I felt it was an excellent opportunity to begin sharpening my skills as a teacher and mentor to students not only on their projects but also their academic careers. I have found that I myself have a great love for teaching and lecturing, and it has truly been rewarding to see how far many of these students have come this year. This year, we have also been part of UCSD's very first iGEM team ever, which in itself, comes with a unique set of challenges. Our team did all of its own fundraising to pay for the registration costs of iGEM as well as the travel costs to Boston. Along the way, we have also pitched our team in addition to the project itself to several labs at UCSD in hopes of creating a sustainable team for years to come. However, even with these limited resources and barriers to our project's development, particularly in terms of our wet lab validation for this project, I am extremely pleased with what we've been able to accomplish this summer and I am proud to have been a part of UCSD's first iGEM team.

After my first discussion with the graduate students, who were just about to launch an iGEM project at UCSD, my impression was that the aims of this project were extremely ambitious. This made me very curious and I was excited to be on board. It soon fleshed out what would be the precise goal of the project and which tasks should be done. The great organization and strict planing, the regular meetings and terrific support of the undergraduate students by their mentors finally made this project an ongoing success.

During the project, everybody could learn and experience a lot of new aspects of research in diverse fields, reaching from project planing, organization, and conduction on the one side through scientific disciplines bioinformatics, database management systems, software design, interactive graph drawing, data exchange formats and standardization, and synthetic biology to communication, writing, and presentation skills on the other side. It can be assumed that this large interdisciplinary and highly collaborative team work was the first experience of this kind for the majority of students and therefore a great experience for all participants. It is remarkable that the project was always focused on the overall goal to obtain a useful product at the end rather than endlessly discussing tiny details of each aspect.

As assumed at the very beginning, this was an enormously challenging effort, but all participants made this project a success. To me, it is still amazing how all this could be achieved in this short time and while in parallel educating the undergraduate students in so many disciplines.

In this summer, I donated my efforts on helping UCSD iGEM team to set up a new modeling format which modularized devices as individual function and standardized the function’s structure. Based on the concept of iGEM, we started from building up dozens of sub-functions that represents a set of simple devices which were the fundamental bio-brick in synthetic biology. Then we searched some literatures and picked up a system for testing our novel modeling method. Two arrays of ODEs were defined for representation of the circuits we chose. A python script was written to integrate these ODEs.

As result, the plot from wet-lab experimental data was reproduced by our differential equations. The simulative output approximately matches the curve plotted in citation which shows the idea that modeling single devices and linking them as connecting bio-brick works like we expected. In next step, we tried to plugin this function into our web app but we didn’t finish because time was over. It is hopefully to be done in future.