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wet-lab training
brainstorming with BU
Bioethics and Biosafety Interview
Wellesley Faculty Interivews
brainstorming with BU
init student feedback
observing MIT&BU meetings
Next steps

Basic Wet-Lab Training with Natalie Kuldell at MIT

At the beginning of the summer, the entire computational team went to receive an introductory wet-lab training at MIT. We were given an extensive introduction into the human practice concerns of the iGEM competition, and also reminded of the nuances of working in an interdisciplinary research field such as synthetic biology, which stands at the crossroads between bioengineering, computer science, and cellular biology. We were able to participate first-hand on a project based on the Eau d’Coli lab (a previous iGEM project). Through this experience, our team realized that several factors could strongly affect the success or failure of a synthetic biology experiment: labeling equipment properly, meticulously following clearly written instructions, and communicating with other team members. We learned a lot about the technical difficulties of working in a laboratory environment, and realized that many safety concerns could potentially arise while working with biological organisms and chemicals, safety concerns that are not understood or known to the public because of synthetic biology’s recent emergence as a leading field. We realized the importance of educating the public, especially the next generation of synthetic biologists, on the safety concerns of working in a wet-lab environment, and started brainstorming on a project that eventually turned into SynFlo.

Brainstorming and Collaboration with BU

Brainstorming and Collaboration with BU: As our lab had also previously collaborated with the BU iGEM team, we decided to continue our collaboration this year by focusing on a project that helps visualize and simply a complex parts assembly method, the Golden Gate Modular Cloning method. We had three brainstorming sessions with BU, where we talked about semantic search, lab-organizing tools, potential outreach projects, and also collaboration-based software tools. A researcher in industry, Robert Kincaid from Agilent Technologies also came in and talked to us during the brainstorming process. Through out the summer, as we built SynFlo, MoClo Planner, and also SynBio Search, we kept constant communications with the BU team, and asked them for repeated feedback in the UCD process. We were able to test our software with the team, and their feedback made dramatic impact in the designs and implementations of our software projects.

Tamara Hendrickson Biosafety and Bioethics Interview

While we were in the initial stage of brainstorming, we had the privilege of sitting in on a bioethics lecture Professor Hendrickson, from Wayne State University, gave during the summer research program. From the talk the computational team learned that regulation, training, and organization are absolutely essential in working in a wet-lab environment. Also, in our follow-up interview with Professor Hendrickson, we able to ask her in detail about how collaborative research works in her laboratory, how trouble-shooting occurs among students and PIs, and how technology can be of assistance during a lab meeting. We also brainstormed lab organizational tools with Professor Hendrickson. As we realized that troubleshooting occurs not only between PIs and students, but also among students, we also interviewed a current Wellesley student Angela Lei, who used to research the Hendrickson lab. She gave us some insight to the lab structure from an undergraduate perspective, and spoke with us on how troubleshooting works in the wet-lab as well as the responsibility of students in peer-education.

Chris Arumainayagam Interview

As we started developing the MoClo Planner and also our outreach projects, we realized that the theme of creative troubleshooting occurs repeatedly in research laboratories, and that a variety of organizing tools were used by different professors in related fields. Professor Aruimainayagam from the Wellesley chemistry department suggested to us to look at Quartzy as a potential inspiration for lab organization tools. In addition, in our interview he spoke extensively on visualizing troubleshooting trees, software that can be used to record citations and track related works, managerial tools his lab uses on different mediums, and also how organization and student-leadership works in his laboratory. Professor Aruimainayagam reminded that while it is important to design application using cutting-edge technology, there must exist a balance between innovation and user comfort. If a synthetic biologist is not comfortable with the design product, regardless of how advanced in technology our tools are, it is of no use in increasing understand of synthetic biology research, research efficiency, and advancements in the field. Thus, we needed to think about current technology prevalent today, and how people’s interactions with tools such as iPads, smartphones, tablets, and other devices could shape what users think should be intuitive in our software designs.

Interview with professor Sequeira

Professor Sequeira from the Wellesley biology department also sat down with us, and gave further suggestions on how to visualize a troubleshooting tree and how graphics can enhance scientific research. This interview was especially interesting because Professor Sequeira had just finished a long-term biology project taking several years, and was able to speak about trouble-shooting with long-term goals in mind. While we originally thought troubleshooting in a lab mainly involved supervising day-to-day tasks, Professor Sequeira reminded us to think in larger scopes. Would the visualization techniques we had in mind work for keeping track of project statuses over the span of not just days, but months, and years? How can technology help us find results and data we’ve had from the past, say, in puling graphs from a notebook entry recorded several months ago? Can the projects we build be easily accessed and understood by people who are not domain-experts in computer scientists, namely synthetic biologists? Those are just several of many interesting questions that were brought up in our interview.

Interview wth Christine Loh

After we interviewed Professor Hendrickson we realized that issues of biosafety and bioethics would be handled slightly different in industrial research settings than in academia. Thus, towards the end of the summer session we sought out Christine Loh, who is currently working at Sirtris Technologies in Cambridge, and interviewed her on development of a lab-organizing software tool, and also about biosecurity and bioethics concerns that may occur in doing proprietary research. Ms. Loh gave us feedback that information security was a strong concern in industry, and data sharing should be able to be limited. Thus, if we were to design collaboration research tools, data sharing options must be considered before we designed the program. Also, personal data organization was very important in during industrial research, because for later drug trials or for biological patent obtainment meticulous records of procedures and processes must be kept. Usually all this information is kept personal, and on paper, but issues come up if paper copies are taken home or lost. Sensitive research information is often shared among collaborators, but should information be shared and accessed via a cloud? Would the cloud be secure? Our search engine SynBio Search and our designing tool MoClo Planner are designed for academia, but if they were designed for industry, would the layout and security measures change? Sources and research we deem to be reliable- would they remain so if the stakes were higher, and research we do eventually lead to human medical testing? Ms. Loh gave us a preview of the potential questions that synthetic biology would face in the coming decade, as more biological constructs move from academic research settings into application in current biotech industries.

Interview with other Wellesley students and getting some initial feedback

Before we tested our iGEM software with BU and MIT iGEM teams, we were able to test them out with other Wellesley biology and biochemistry students, who gave us important feedback on the design and usability of our software. The usability testings we did were all recorded with consent, and from observing our users we were able to refine our software more and go through several iterations of the MoClo Planner design. Also, after each round of testing, students would provide us with written and verbal feedback on features they thought were strong and features that needed improvement in the next iteration of the MoClo planner. Thus, while the MoClo Planner was designed specifically with synthetic biologists in mind, general biologists and undergraduate students also gave us constant feedback in improving the efficiency and clarity of our designs.

Sitting in on MIT& BU Lab Meetings

While initial testing of the MoClo Planner was occurring, we focused on peer-education and student collaboration techniques, and also on how troubleshooting works in a team environment. One of our team members went to MIT iGEM team’s meetings weekly, and took notes on presentation styles, technologies used, data sharing methods, and potentially software tools we would built to improve the efficiency of the wet-lab meetings. We also sat down and observe BU iGEM team’s lab meetings, and realized that the dynamics between the teams were very different in terms of collaborative troubleshooting, data sharing, and organization. How can we design tools that can assist all kinds of different iGEM teams? How can we design tools that not only can be used in individual PI and student meetings, but also roundtables among several PIs and more than a dozen undergraduate and graduate researchers? How would data sharing and file sharing work in an organized manner? How to the students keep track of the troubleshooting suggestions they receive from their advisers at these meetings for future references? These are just some of many questions that were brought up in our observations and in our interviews with both teams.

Next Steps to Take in the UCD Process

While we talked to a variety of users this summer, there is still much work to be done in terms of user-centered design. In our next step, to improve the MoClo Planner we are hoping to also redesign it to allow for top-down design process; from our interviews with the BU team we realized that both bottom-up and top-down assembly methods would be useful for synthetic biologists, whether it be for characterizing a specific part, or for constructing a working, complex biological module. In terms of our SynFlo project, because we understand and appreciate the importance of biosafety and synthetic biology education, we will push for broader familiarity of the field and safe lab techniques through the usage of our project, a MS Surface and tangible Sifteo Cube game for high school students. For SynBio Search, further user studies will be conducted with iGEM teams, both domestic and international, as we refine the design and test the robustness of our search engine with synthetic biologists and continue to ask for their feedback. We are hoping to design a collaborative surface tool to facilitate lab meetings, and hoping to address many questions arose in terms of data sharing, biosecurity, and collaborative research methods. This is only a brief summary of what we have accomplished this summer in terms of feedback from potential users, but we are sure that many more innovative insights and comments from our users are to come as well.