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. Development of 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.

Having little experience with programming, the possibility of applying my knowledge in Biochemistry to help create an application was very appealing. The chance to improve in programming and possibly learn different coding languages definitely was the icing on the cake.
Biochemistry is something I have always been fond of, but having a chance to translate that knowledge into something that people could use and benefit from was extremely exciting. iGEM was a chance to make that happen.

During my time as a member of the UCSD Software iGEM team, I learned many different coding languages including html, JavaScript, Python, and Java. Throughout the entire development process I got a chance to work with the front-end and the back-end parts of the application development, with my primary focus being web development, as well as the user interface portion of the application. This was an enriching experience as I learned many different techniques as time went on, and now feel more comfortable as ever with the ability to design web applications in the future. The project taught me many skills and bonded me with all my teammates, and as a result we were able to develop an application that we believe could possibly change data mining.

When I applied to become part of the UCSD iGEM team, I understood that it would be a substantial challenge given my lack of knowledge about synthetic biology. As the Spring quarter progressed and we were introduced to a plethora of programming concepts, what was being asked of us as members of the iGEM team became clear. Instead of shirking at the responsibility that lay before us, everyone started the project with the enthusiasm about the task we had been given.

As we moved into summer, I had the opportunity to work on code for the search algorithm, JSON file creation, and generation of the Pigeon images as well as work on the complexity analysis. Each project has enabled me to build a strong background in programming and synthetic biology, and I hope to continue to pursue both in the future.

We have had a great opportunity to build a complex, novel application that has the ability to change the landscape of synthetic biology by allowing community collaboration. We have enabled the community to stand upon the shoulders of a SBiDer-sized giant.

I started aboard the UCSD Software iGEM team after hearing about a project for undergraduates centering around the relatively new field of synthetic biology. The subject was one I had no practical experience with but was one that I had been avidly following since I had first heard of the term "synthetic" being applied to a field of biology. With no knowledge of how to program in any language and with only an introductory knowledge into genetic circuitry, I decided to apply for a chance to help in the endeavor. At first, I was both intimidated by the scope of the project planned and the skills set of my future team members and mentors, but I grew more excited and impressed the more skill I had begun to learn and concepts I started to understand. My skill set expanded rapidly in the oncoming months to include ways of analyzing problems algorithmically and constructing methods to approach a solution above the various programming languages I learned.

These skills were implemented with equal rapidity as I worked to create a user interface for the manually-curated network of synthetic genetic devices. The weeks passed before I had realized, and I felt overwhelmed at times by the material I needed to not only learn but master in order to create a viable component to the SBiDer project. However, with guidance from the graduate students and practice, I was able to implement the front-end application that was capable of rendering a visual network of the database information that could dynamically be altered and manipulated to allow users to explore connections of the database through a graphic interface. I additionally spent time learning from other team members about the nature of the genetic circuits to improve my biological foundation as well as how to manipulate and represent data in order to begin constructing a way to aid in creating models of the circuit behavior.

Like all goals worth pursuing, working with the UCSD iGEM team required many hours of difficult work and challenges to be solved. The result , however, improved my own personal ability and produced a project with a growing potential to aid a large audience of people. After the conclusion of this year's jamboree, I hope to have the pleasure to continue working with my team to create a lasting impact upon our campus by educating other undergraduates and providing them the skills to tackle an opportunity like this both in an academic setting and in other aspects of their life. I am proud of my team and our work and grateful for the many outstanding people that allowed this event to unfold.

This is my first year taking part in iGEM, and also my first research project as an undergraduate student. When I read about UCSD building a team to take part in iGEM, I knew wanted to be a part of the team but was apprehensive at first as I wasn’t sure if, as a Computer Science major, I’d fit into a team participating in a Synthetic ‘Biology’ competition. After meeting Jenhan for the first time, though, a lot of my fears had subsided. He eased me into the team and let me know that I didn’t require a lot of background or experience in biology as this project was meant to be a learning experience for everybody.

He couldn’t have been more right about that; we learned a ton of skills this summer, ranging from reading scientific papers, mining data, building a database based on that data to figuring out how a real world software project works. We learned about little details such as setting realistic expectations and deadlines for tasks. I personally learned a lot about what entails the field of Synthetic Biology (reading nature journals on the topic definitely helps ;). Having worked on the website and the application that we built, I also picked up several web development skills.

Overall, it was a fun & highly enriching learning process. Over the course of the summer, we put together an awesome app with the help of our advisors. I feel proud to have been part of the team that build one of the most breathtaking Syn Bio apps this year – SbiDer. Special shout-out to all our advisors –Jenhan, Justin, Ben & Ryan for guiding us and inspiring us throughout summer. Stay awesome people.

An interest in artificial intelligence coupled with a philosophical inclination developed an affinity for the notion of consciousness, which, in turn, entertained the idea of "biological programming." With this newfound interest in research, I sought to find a lab position in biotechnology at UCSD; however, research in a DNA biotechnology lab did not suffice. Prior to iGEM, I never considered Synthetic Biology as a potential avenue in biotechnology research. However, after Jenhan, our team coordinator, provided me with a brief description of Synthetic Biology, I was undoubtedly convinced that I had found my niche in research.

As our software project unfolded during the summer, I became responsible for the design, visualization, and analysis of our complex genetic network. Following the formation of our modeling framework, a Petri-Boolean model, and the integration of different genetic circuits from multiple sources, I proceed to generate a graphical representation of our database, which conveyed the connectivity between the different genetic circuits. In addition, I performed a structural and connectivity analysis, to demonstrate the increase in potential genetic circuits that our network can provide.

This project not only introduced me to the potential of Synthetic Biology, but also fostered an interest in the application of engineering principles to elucidate the fundamental mechanism by which signal transmission occurs in complex biological systems.

I initially heard about iGEM through an email from the Undergraduate Bioinformatics Club (UBIC) at UCSD, of which I am currently serving as the Internal Officer. I was looking for a research opportunity over the summer to further gain exposure to computational biology before my final year of college. When I first met Jenhan, I was a little taken aback to discover that most of the team had already been involved with the competition for a few weeks, but when I heard the scope of the project, my interest immediately grew and I was excited to be a part of UCSD's first ever iGEM team.

At first, familiarizing myself with iGEM proved to be a greater challenge than I had expected. I had no previous exposure to the field of synthetic biology, and because I had joined at a later date than most of the team, I started the summer already behind everyone else's knowledge and frequently felt lost during meetings. In addition, difficulties in finding housing in San Diego over the summer meant that I was making an hour­long commute to meetings twice a week and working remotely for the rest. Despite this, iGEM has been a great experience. Through this project, I learned the Python programming language, refined gaps in my programming knowledge base, and learned a great deal about synthetic biology theory. In particular, I focused on network analysis and network motifs. For my part of the project, I read through literature detailing various network motif finding algorithms and implemented one of them on our network in order to conduct analysis and demonstrate an increase in functional genetic circuits in our network.

I definitely feel that I chose the right way to spend my summer by joining the iGEM team. Not only have I learned a great deal about synthetic biology, a field which I previously knew nothing about, but I have learned how to work in a large group environment, how to collaborate on a brand new project, and how to meet tight deadlines. IGEM has provided me with a valuable skill set which I plan to use in a hopefully long and successful career in the bioinformatics industry.

This is my third year being involved with iGEM - previously I've been an undergraduate iGEM team member 2011 as well as a mentor in 2013 - and so I thought I was ready for anything and everything. However, iGEM at UC San Diego this year caught me by surprise. Before I get into the summer's surprises, I'd like to thank our sponsors. Without generous support from Synthetic Genomics and the San Diego Center for Systems Biology, none of this would have been possible - their support gave UCSD students a chance to experience a genuine research experience in an interdisciplinary and collaborative setting. I had an excellent summer designing the project with the undergraduates, teaching them, and working with them. I think UCSD's first iGEM team has managed to impart useful lessons to all those involved, and I'm highly hopeful a second team will follow next year.

Even as an iGEM veteran, the amount of work involved in coordinating this project and mentoring each of the students was quite unanticipated. Fortunately, I had quite a bit of help. I'd also like to thank my fellow mentors, Ben, Justin, Ryan, and Andreas, for helping out and stepping up as needed. Each one of them selflessly gave their time to give patient guidance for the undergraduates. Barry Demchak, Kei Ono, and the rest of the Cytoscape group gave us some great technical advice that really helped to make sure that the team took the most effective software development strategy. Other individuals that gave us some great advice include Jason Kreisberg and Prof. Todd Coleman. Risa Shibata and Anna Lu also deserve a lot of thanks for their invaluable help with logistics and making sure that we could fly to Boston and be at the Jamboree. So I'd guess the amount of work involved in iGEM was ultimately balanced by the amount of support we received.

As the project is finally wrapping up, I'm amazed at how much the students were able to accomplish in the past few months. Many of our students had little exposure to coding, and I'm glad that iGEM at UCSD was able to help them grow into proficient and innovative programmers. On the other side of the coin, we had a few computationally oriented students who managed to leverage synthetic biology concepts to help build a project that everyone on the team can take pride in. I think the project was very ambitious in its design, and I was definitely surprised when all the pieces finally clicked together. I think this was due in no small part to the leaders that emerged from amongst the undergraduates. Without the motivated students involved in this project, we would not have even gotten halfway through the project. Each of the students who worked hard on this project should be proud of themselves.

Overall, I'm very glad to have had an opportunity to be involved in UCSD's first ever iGEM team. iGEM is a great program, and my experience with iGEM in the past is one of the main reasons why I decided to pursue graduate studies. And I hope that I've done my small part to show students that research can be exciting, meaningful, and enjoyable.

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.

Advising for iGEM has been a fascinating engagement and a positive force towards my personal and professional development this summer. I enjoyed discussing and formulating our project with the undergraduates. The novelty of their insight was exciting and fun. Their perspectives are untainted by the priors of the field and often stemmed new and exciting conversations. Educating new students was also a great way to consolidate and confirm my understandings and preconceptions. Revisiting details assumed in professional conversation is hard but ultimately beneficial. I was delighted to discover several shortcomings in my current understanding of Synthetic Biology over the course of teaching this project.

I also had the opportunity to learn new skills such as database construction, normalization, maintenance and accession. I had never managed a database before. This posed a special challenge to advising its construction. Learning enough to advise is certainly more difficult but ultimately very rewarding. I had the immediate enjoyment of learning something new followed promptly by the joy of sharing my understanding with an eager audience.

It was also interesting to managing a team of this size for the first time. There were some pitfalls and lost time in the beginning but eventually my co-advisors and I learned enough about distributed management and collaborative infrastructure--mostly google docs--to effectively manage a team of 10 undergraduates.

I realize that I saw many professional benefits in my ongoing experience with iGEM, but all professionalism aside, I really enjoyed my time teaching, learning and leading this iGEM project.

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.