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From 2013.igem.org

Contents 1 About Me 2 Week 1: May 28 - May 31 3 Week 2: June 3 - June 7 4 Week 3: June 10 - June 14 5 Week 4: June 17 - June 21

About Me

Hi! I'm Evan, and I'm very excited to be a part of the Wellesley iGEM team this year. I'm a Computer Science and Philosophy major at Wellesley College, but I didn't start out my college career with these majors. When I matriculated, I was deciding between a major in Philosophy, English, Psychology, or Visual Art. I sort of stumbled upon the wondrous world of Computer Science by accident; I took an intro class to fulfill one of my distribution requirements and absolutely fell in love. I applied to join the iGEM team (and Wellesley's Human-Computer Interaction lab) because user interface design is the perfect synthesis of visual art, psychology, philosophy, and computer science.

My main project on iGEM is Eugene DeSyne, a project that enables synthetic biologists to virtually generate a set of genetic devices with user-specified rules. This is the top-down extension of the MoClo Planner project, which lets users design devices from the bottom up: by first selecting parts, permuting them, and then selecting from the set of resulting devices. Other Wellesley iGEM projects include Tabula, an interface that enables users to surf through genomic sequences using Sifteo Cubes; ZMol/ZSeq, a 3D visualization of molecules and genomic sequences; and SifteoArt, an art installation that raises public awareness about synthetic biology.

Apart from academics, I play Ultimate Frisbee for the Wellesley Whiptails; I was B-team captain this past spring, and I'm going to be novice captain in the fall. In my limited free time, I occasionally dabble in portraiture using charcoal and oil paint. I'm also very passionate about queer rights, reproductive freedom, sexual assault awareness and prevention, and mental health awareness.

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Week 1: May 28 - May 31

Tue, May 28: Today was the first day of work and I'm already so overwhelmed (in a good way). First, we had a general summer research orientation, and then we all met in the Wellesley HCI lab. After a general human-computer interaction overview (what we do in the lab, the general process, personal introductions, etc), we were assigned to projects and then given a list of background research articles to read. We spent most of the day reading the articles. I only have a very vague/basic idea of what I'm supposed to be doing, but I drew up some preliminary designs for the user interface for Eugene DeSyne. That took about 3-4 hours; it's really difficult to try to consolidate and synthesize so much information into one coherent interface. I showed it to Consuelo at the end of the day and she...well, she pretty much destroyed it. It sounds a bit harsh, but I'm actually really happy she did; it felt like a baptism into the church of software development.

Thur, May 30: We're at the MIT wet labs today, taking a sort of crash course on synthetic biology. The car-less campus-dwellers (myself included) had to take a 7:30 train into Boston with the other commuters; I'm 19 but this was one of the first times I've felt like an adult. In the lab, we met Natalie, the lovely woman behind BioBuilder, and we learned about lab safety procedures, general lab protocols, and famous previous iGEM experiments, like E. coli that alternatively smell like bananas and wintergreen, and bacteria that float when exposed to two types of light. In the wet lab itself, we worked with E. coli to make them turn different colours under light and we also tested the strength/effectiveness of different plasmids. We finished up by creating a "genomic circuit" using a breadboard; I'd never used a breadboard before, and I had a lot of fun. It made me excited for the machine organization course that I'm taking in the fall at Wellesley. At the end of the day, the team went to a hole-in-the-wall cafe called Life Alive and got delicious smoothies to combat the 95-degree weather.

Fri, May 31: It was Wellesley's Commencement today, so most of us took the day off to see the class of 2013 graduate. Despite the scorching heat, the ceremony was beautiful; the commencement speaker was Valerie Jarrett, senior advisor to President Barack Obama and chair of the White House Council on Women and Girls. She reminded us to be flexible and resilient and to pace ourselves and feel free to ask for help. In addition, the HCI lab/our iGEM team's faculty advisor, Orit Shaer, received the Pinanski Prize for Teaching Excellence!! Commencement was a bit emotional for me, because so many of my friends from the Ultimate Frisbee team were seniors this year. I'll miss them (in fact, I already do), but I also can't wait to see the amazing things that they'll all undoubtedly go on to accomplish.

Week 2: June 3 - June 7

Mon, June 3: Today, our team again ventured out into the city to meet with our BU team counterparts at the BU Photonics building. After general introductions, they gave us a brief overview of synthetic biology as a discipline and some of their work in the lab. Afterwards, we learned Eugene, a programming language developed specifically for synthetic biologists. We were divided up into groups and given different circuits to model using Eugene. It was actually quite difficult; Eugene is an object-oriented language similar to Java, which I'm very familiar with thanks to Wellesley's CS department, but there was some Eugene-specific syntax that was a bit hard to grasp. Although the language does a good job of capturing many of the rules that need to be defined for genetic devices, there were still some things that were hard to define: things like "threshold". For example, for my group's circuit (shown on the right), the P-lambda promoter can either be repressed or induced, depending on the amount of cI present. This, in particular, was difficult to model.

Tue, June 4: We're back at BU today, and this time we're spending the day hearing presentations and giving presentations of our own. We got to learn about the BU team's iGEM projects, which were in their developmental stages, but still very interesting. Then, we presented our own projects and got some feedback from the BU team. This was our first presentation, and it was pretty clear that we need to work on some of our public speaking skills, but overall, I think it went pretty well. Afterwards, we got a tour of BU's wet lab--including getting to see their awesome flow cytometer--and went bowling as a whole BU-Wellesley team.

Wed, June 5: Sravanti joined the Eugene DeSyne subteam, and I'm really glad she did! We got a lot done today. After listening to some user-input recordings for the paper prototype of Eugene DeSyne that the HCI lab had previously worked on in the spring, we came up with a list of likes and dislikes for the user interface design. In particular, my group decided that we didn't want to have to use very many light-boxes that can clutter the screen, and we liked the idea of being able to switch between or hide different working spaces, similar to the Mac OSX multiple desktop feature. We spent most of today working on two different preliminary ideas for the interface, which we'll present to the rest of the lab tomorrow, during our first SCRUM meeting of the summer.

Thur, June 6: Today, we had our first SCRUM and received a lot of valuable feedback from the lab, and especially Orit. Thus far, one of the biggest challenges for Eugene DeSyne has been trying to design a rule-creating system that has both a low threshold (i.e. it is easy to use/understand) and a high ceiling (i.e. it is powerful). We've been looking to technologies like Tern, which is a tangible wooden-blocks based language and Tinkerblocks, a visual block-based language that one of our very own Wellesley professors is designing. Orit pointed us in the direction of Scratch, which is easier to use than Tinkerblocks (which assumes basic Java programming skills) and is more powerful than Tern (which can only give a robot a limited set of instructions, like turning, making sounds, or spinning). She also told us to come up with a list of first-order logic symbols needed for genomic sequencing, and then use the list as a starting point for our interface design. It's really nice feeling like we actually have a direction toward which to progress, now.

Fri, June 7: We continued to work on interface designs with our mentor, Casey, today. We tried to distance ourselves from our previous designs and from block-based programming; in particular, we've started looking at game interfaces like Little Alchemy and Little Inferno (we also took frequent breaks to play these games :D). We're drawing inspiration from Little Alchemy's icon-stacking mechanism for recursively creating new icons and Little Inferno's general interface. The latter interface's "table" option--a permanent space on the bottom of each screen in which to put items for easy access--is especially relevant to Eugene DeSyne; being able to quickly access genomic parts and previously defined rules is definitely a key goal for our design. We spent the day drawing up new prototypes influenced by these games and preparing for our next presentation on Tuesday.

Week 3: June 10 - June 14

Mon, June 10: Today we met with Orit to discuss the interface design that Sravanti and I came up with last Friday. It seemed like she really liked it, but she encouraged us to come up with two more ideas by looking into UML and MoClo Planner's bio-visualization. She mentioned that, although our game-ified design was simple and effective, a lot of synthetic biologists might want a more "serious" interface (in my mind, unfortunately, serious = boring). Sravanti and I spent most of the day reading up on UML and trying to come up with inspired ideas; I guess the lesson for the day is that coming up with a great idea in the beginning stages (and becoming very attached to it) makes it difficult to come up with others. But the week is young, and I have faith that we'll be able to conjure up some ideas before we meet with the BU team on Friday. On a less academic note, the lab had our first potluck today, for which my S.O. and I made chocolate chip cookies, and it was great! Consuelo's chili was particularly delicious.

Wed, June 12: Sravanti and I came up with a new design, influenced by UML, that utilizes a tree visualization of rule creation, and Orit absolutely loves it. I think this design is more of what the biologists are looking for, but I'm still pretty attached to our game-ified icon design. We spent today simulating Eugene's built-in rules and Swapnil's rule examples with both of our implementations to make sure that our visual languages were expressive enough to cover everything that's needed. Now that we've come up with two solid rule creation models, our next problem to tackle is how to visualize query results; there can be anywhere from one to thousands of search results, so we need to figure out how to show this without overwhelming the user. It sounds relatively simple, but it's actually a formidable problem.

Thur, June 13: There isn't much to report on for today; every team spent all day today preparing for tomorrow's brainstorming session with the BU team. The Eugene DeSyne team worked on making handouts and poster prototypes of our preliminary designs, which meant I got to bust out my old Intuos 3 tablet to draw up some examples for our icon design.

Fri, Jun 14: We had our brainstorming session with BU today, and it was extremely helpful. Among other things, we got to practice our public speaking skills (which still need work, but were vastly improved compared to our last presentations) and received some valuable feedback from our BU counterparts. They all seemed to like the idea of integrating both the tree and the icon designs to create some kind of hybrid design that utilized both visualizations; in addition, it became clear that we have to restructure our designs to work at a higher level. Basically, we've been designing our visualization assuming that synthetic biologists will be working on what we call "Level 0" (working with specific promoters, genes, RBS's to make transcriptional units), when in fact they want to work on the "Level 2" domain (working with series of transcriptional units to form devices). I anticipate making some major changes to our work when we come back in on Monday.

Week 4: June 17 - June 21

Mon, June 17: WE GOT TO START CODING TODAY!! Hooray! As somebody who briefly but seriously considered art school and/or a studio art major, I thought I'd enjoy the design process a lot more, but to be honest, it's beginning to get draining. There's a huge gap between "traditional" art (painting, charcoal, the stuff I like to do for fun) and interface/web design, which is a lot more...impersonal.