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Team:Wellesley Desyne/Notebook/SravantiNotebook
From 2013.igem.org
Sravanti's Notebook
Contents |
Week 1: May 28 - 31
This week, I began my research at the Human Computer Interaction lab. It was a great introduction to synthetic biology, and I enjoyed getting to know my labmates.
Tuesday:
Today, we received an introduction to the lab and the projects we are working on this summer. I was assigned to Tabula, which is based off of a previous project in the lab, G-nome Surfer. There’s a user testing for Tabula next week, so I got caught up on what has been done so far and what my tasks were for the near future. I dived into the code for G-nome Surfer to get familiar with it and to formulate the code for Tabula. It was my first experience coding with C# and XAML, so it was tricky, but I anticipate the coding becoming easier.
Wednesday:
Today, I continued coding for the Tabula project. We’re redefining G-nome Surfer, so what I’m doing is using elements of that project to make a similar project for Tabula. In particular, I worked on making the chromosome bar for a specific mouse genome visible, which was much harder than I thought it would be. Much of the code is intertwined with other code, so it’s not as simple and just copying and pasting code. I got the bar to be visible at the end of the day, which was nice, but I still have a lot of work to do. First, I have to get a specific gene to show up in the chromosome bar, and then I have to create a second chromosome bar. Tomorrow, we head to MIT, so that’ll be good to have a more formal introduction to synthetic biology.
Thursday:
Today, we headed to MIT for the Bio Builder workshop with Natalie Kuldell. We learned about the basics of synthetic biology as well as the motivation to study it. The last time I took biology was a couple semesters ago, so it was nice to try wetlab work again and get a feel for how synthetic biologists do their work. It was particularly helpful to note the parallels between computer science, or engineering in general, with synthetic biology. It was also nice to see what other iGEM teams have done in the wetware track in the past to understand the needs of synthetic biologists for our research. One thing I thought was interesting was that during our experiments in the wetlab, what frustrated me a little was the fact that I was simply running through the procedure without some visual reference as to what was actually going on in the cell. I understood at a high level that we were trying to turn cells different colors, but I think it would be nice to actually visualize the process rather than simply mixing together different solutions with cells. In the afternoon, we made a synthetic cell using “parts” from the MIT parts registry with the help of a computer program. It was nice to create a cell, but again, I felt as if I was simply running through the procedure without any deeper understanding of what was going wrong. I think it could also be interesting to build upon this computer program to show different combinations of parts that could work and provide an explanation as to why it works, which I believe would be more meaningful than trial and error, which is what I would have reverted to had I been working through the program; however, we are already implementing a similar design idea with Eugene DeSyne. Overall, I thought it was a good crash course to synthetic biology and I learned a lot.
Friday:
Today, I continued my work on the chromosome bar. Bringing in the information for the genes is very complicated, as I have to bring in lots of extra code. However, I think after I fix all of the errors and import the other files from G-nome surfer, it should go more smoothly.
Week 2: June 3-7
Monday:
Today, we traveled as a team to Boston University to meet with their iGEM team and to learn more about synthetic biology. We built upon our knowledge from Friday’s BioBuilder workshop at MIT and learned specifics about how plasmids are created and details about the transcription and translation processes. It was nice to learn from other students, and to see how they view synthetic biology and the iGEM competition from a wetlab standpoint. In the afternoon, we worked on coding in Eugene, which is a computer language built specifically for designing synthetic biology devices. As a programmer, I appreciated the close correlation between Eugene and Java, but I also see the challenges for synthetic biologists who may not be familiar with programming in C or Java. It was also valuable to work through specific Eugene circuits with BU team members - seeing how they use parts, properties, and rules provided good insight for our team to start brainstorming for the Eugene DeSyne project.
Tuesday:
We also spent today at Boston University collaborating with their iGEM team. Today, we learned about ideas for their iGEM projects and presented our ideas as well. The nature of their projects was very different from ours; even so, their work related to ours in several ways. They are looking to expand and characterize the MoClo library as well as identifying different optimizations of genetic circuits, and we are trying to provide a search engine tool for synthetic biologists to find the optimal genetic circuit with given constraints. Through the past couple days, I’ve seen that we could have the same goal, but approach that goal in two very different ways based on either wetlab or computational techniques. It was also helpful to gain feedback from the BU team with our project ideas so far. Learning about what they value in synthetic biology tools and what they find most useful will be invaluable when coming up with prototypes for our projects in the coming days.
Wednesday:
Today was my first day on the Eugene DeSyne team, as I moved from the Tabula project. Using the feedback from BU as well as a few ideas that the lab came up with previously, we came up with a couple of prototype designs for Eugene DeSyne, which will act as a search tool for synthetic biologists to search for genetic devices and refine their searches based on specified parameters, such as rules that include/exclude genes, specify the order of parts, etc. The first design we came up with used multiple panels that mimicked the workflow of Eugene but without actually writing code. We liked the visual of splitting results into different “piles” based on categorization and incorporated this idea into both of our design prototypes. Our second design emphasized the focus the rule parameters biologists will be looking for by dedicating half the screen to selecting rules, creating them, and turning them “on and off”, although the latter feature is not supported by Eugene. These are very preliminary ideas, and I think having more input from the BU team will help narrow down which features we would like to include in Eugene DeSyne and which direction to take our future prototypes.
Thursday:
Today, we continued to brainstorm ideas to further develop our ideas. We delved into greater detail with both of our designs, and ran through example queries. With some direction from Orit, we decided to focus our efforts on visualizing first-order logic in different ways. We came up with a refined user interface, but we'll probably refine our ideas tomorrow.
Friday:
Today, we let go of our limitations when designing. Casey came to talk to us about our designs, and afterwards, we were inspired to not let something like a web interface limit our design. In a sense, we started from scratch, and came up with a completely new design. We have an icon based idea now, which uses elements from games such as Little Alchemy to overlay icons on top of one another to create new icons. We created sample icons for each property to overlay on icons for each part, which we felt was more intuitive for a novice user and was much easier than actually coding. We broke away from the conventions of visual programming language, and although our project is heading in a different direction, I'm really happy with it because it's more creative and exciting than our previous designs, which I think will be great when it comes time to actually code our design.
Week 3: June 10-14
Monday:
Today, after coming up with our icon idea on Friday, we came up with an alternative idea. After some direction from Orit, we decided to investigate two projects: the MoClo design from last year's iGEM project, and UML, or Unified Modeling Language. We drew more inspiration from UML and its organized design. We liked the way it compartmentalized the properties and methods that applied to an object. While we were inspired by such a design, we decided to create a tree, which was very different from our icon idea. The tree creates a hierarchy of devices, part types, and specific parts, and the rule creation is implicit within the tree - we'll develop it more tomorrow!
Tuesday:
Today, we iterated on yesterday's design and developed it further. We thought up
