Team:Wellesley HCI/Notebook/VeronicaNotebook

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Veronica's Notebook

May 29: First day of the summer session!

Today, we attended the Summer Research Program Orientation - we got to meet our fellow researchers and faculty. Orit presented an introduction about human-computer interaction and the design process we will be following. We received our mentors and were also split into subgroups to start our research. My group - Casey, me and Nicole - is researching semantic search and the importance of it in a synthetic biology setting.

Jun 6: A day in the wet lab

We spent the entire day at MIT with Professor Natalie Kuldell. In the morning, she presented several lectures. She introduced the field of synthetic biology and explained the typical process of synthesis, abstraction, and standardization. We learned about the more technical side of synthetic biology - how researchers find the section of the gene they want, how the cell duplicates genes, etc. Professor Kuldell then discussed "Eau d'coli," an iGEM submission from MIT in 2006. It was very interesting to learn about their project, as it is a real application of synthetic biology that our software project aims to improve. MIT's goal was to genetically engineer E.coli cells to smell like banana and wintergreen. We covered their entire process, as well as that of the cells and cell parts. In addition, we watched a video of MIT's presentation at iGEM to fully understand the challenges they came across. As I learned, I connected their process with our semantic search project, and wondered a couple things - how did they search the smells and narrow them down to only banana and wintergreen? How did they know what promoter to use? Was it written somewhere that indole was what produced the natural smell of E.coli? After Professor Kuldell's lectures, we went through a lab safety lecture and then headed to the lab to conduct some experiments of our own. The first lab, titled "What a Color World," was related to the MIT iGEM's "Eau d'coli" project. We prepared 2 different E.coli strains for transformation and then transformed them with purple-color generator and green-color generator. In the second lab, titled "iTunes device," we examined promoter and RBS (ribosome-binding site) combinations to optimize beta-galactosidase output. We used test tubes, pipets, petri dishes, and a spectrophotometer to determine which combination was the best. I was shocked by how precise the measurements had to be, the length of time it took to see any results in experiments, and how much work had to be done to prove one small thing. Our day ended with an overview of the day and our impressions of synthetic biology.

Jun 12: A day in the wet lab

We spent the entire day at Boston University's Photonics Building with their iGEM wet lab team. We began the morning with an introduction to synthetic biology and biology basics: we learned the definition of synthetic biology - as quoted from Ahmad Khalil and James Collins, two well-known researchers in the field, "Synthetic biology is bringing together engineers and biologists to design and build novel bimolecular components, networks and pathways, and to use these constructs to rewire and reprogram organisms." We then went on to cover the parts of a transcriptional unit, including the definitions of a promoter, a ribosome binding site, a gene and a terminator. In addition, we reviewed plasmids and bacterial transformation. Finally, we learned about the methods that the BU wet lab team is using; knowledge of their experimental process enables us to better understand the needs of our potential users. We also shared our researched features and potential projects. Overall, it was a valuable experience to learn about a real wet lab team's process and to share our ideas.

Jun 13 & 14: Brainstorming!!

As a continuation of yesterday's brainstorming, the Boston University iGEM team came to Wellesley today. Before they arrived, we gave a demo of our Beast surface and its applications to a representative from Agilent. He gave us some thoughtful feedback. In the afternoon, we all gathered in a room and covered the walls with ideas. We had four different categories - the Lab Organization Tool (originally the eLab Notebook), the Beast (both micro and macro features), Semantic Search, and Art. For the first hour, everyone wandered around the room, exploring the ideas and notes already written and then adding their own. Then, we sat together as a group and discussed each topic. We came up with several great ideas for each topic, and we have our work clearly cut out for us.