Team:Wellesley Desyne/Notebook/TiffanyNotebook

Contents 1 Week 1: May 28 - May 31 2 Week 2: June 3 - June 7 3 Week 3: June 10 - June 14 4 Week 4: June 17 - June 21 5 Week 5: June 24 - June 28 6 Week 6: July 1 - July 5 7 Week 7: July 8 - July 12 8 Week 7: July 15 - July 19 9 Week 8: July 22 - July 26 10 Week 9: July 29 - August 2

Week 1: May 28 - May 31

Tuesday: First day of the iGem summer program in the HCI lab at Wellesley College! I've worked through the majority of the assigned readings. I was assigned to work on the Eugene DeSyne team along with Catherine, Evan, and Sravanti.

Thursday: The team went to MIT for a BioBuilder workshop with Natalie Kuldell, but as a graduating senior, I had previous obligations and did not attend. According to the rest of the team, it was an interesting day.

Friday: Graduation Day! I received my BA in Biological Sciences.

Week 2: June 3 - June 7

Monday: The whole Wellesley iGem team went to Boston University to meet with the BU iGem team and learn more about the biology behind synthetic biology. As a biological sciences major, it was a bit of a relief to listen to some biology concepts that were easy to understand compared to the computer science ones that I was learning very slowly as I went along. We learned about Eugene, the coding language that the BU iGem team currently uses to find the possible permutations for their synthetic biology circuits. The Wellesley and BU iGem teams split up into mixed teams to try and code some example circuits into Eugene ourselves.

Tuesday: Day two of BU iGem, we presented our projects to the BU team. We asked them to give us their comments and suggestions about how we could more tailor our projects our audience. Some aspects of our projects were met with a little bit of skepticism and criticism, but the Wellesley team took it in stride because we were still in the design process and things were still in the process of changing.

Wednesday: Today, Sravanti joined the Eugene Desyne team! The team began to work on paper prototypes for the user interface we wanted for the project. I did not spend too long working on this as I needed to help conduct gesture studies for another project, Tabula. For the gesture studies, we asked participants to pretend to conduct certain tasks using either an upright or a horizontal touch interface along with Sifteo cubes, and recorded their thought processes and gestures. I was mainly responsible for recording the gestures and created a form to record everything in as uniform a manner as possible. As we went through the three user studies for the day, I noticed how I changed in how I chose to record gestures in order to record more quickly and accurately.

Thursday: More user-studies for Tabula. While there are a set of very common gestures that people generally use, there are certain individuals that approach the tasks that they are set to in a very interesting manner that we do not see from any of the other participants thus far. Also, as a lab at a women's college, we have certain difficulties in recruiting enough cis-gender males to participate in our studies so we have been using our personal connections to try and rustle some up.

Friday: Yet more user-studies for tabula.

Week 3: June 10 - June 14

Monday: We successfully finished the Tabula user-studies! I went through all the gestures I recorded for all participants and made sure things were recorded as uniformly as possible for the sake of easing the way during data analysis. I was not responsible for analyzing the data. That honor fell to Diana and Consuelo. The Eugene Desyne team continued to refine their UI design and came up with a new one, influenced by UML, that utilizes tree visualization in showing the build of the parts.

Tuesday: Together, the Eugene Desyne team refined the tree visualization method for rule creation in creating devices. We worked through how we would represent some example circuits provided by Swapnil. Even now, we can see that we are going to need some more examples of more complicated circuits to work through.

Wednesday: Our PI, Orit, really liked our proposed design. From my perspective, as a biology major, there was some good stuff already where the our design would be more convenient to use than being forced to code it in Eugene. Catherine came up with the name for our UI, Eugenie! The logo includes a genie lamp and a little bacteria genie coming out of it. It's very cute!

Thursday: We continued to work to brainstorm and refine our designs for our joint brainstorming session on Friday with the BU iGem team. We met with Orit to go over everything. One of the things were struggled with was how to represent our data once it was created. We decided we could either go with a list, or display data visually. Displaying the data visually presented a problem because with all the permutations that are supposed to be generated in using Eugenie will result in an unmanageably large amount of data to represent. As a preliminary design, we came up with either a tree representation or a pile representation.

Friday: Joint brainstorming session with BU today. People really liked our idea for the Eugenie logo. People seemed to prefer the tree visualization method. The unanimous opinion was that data should just be displayed in a huge list that one could browse through and filter for certain results if desired. It was good to get feedback from everyone. I think some members of the BU team were forgetting that I focused mostly on molecular biology in my undergraduate coursework and research. They repetitively explained the same things in great detail to me. I appreciate their attention to detail, but it was a little baffling because they did not seem to believe that I really understood what they were saying.

Week 4: June 17 - June 21

Monday: Using HTML and CSS, I worked on creating a log-in page for Eugenie. This was my first time working with HTML or CSS so it was somewhat slow-going. As a Biology major who has only taken one CS course, I know I'm the weakest in terms of programming, but most people have never used HTML or CSS either so at least we were all starting at the same place. As a team, we also chose a tentative color scheme for Eugenie.

Tuesday: Evan and I went to BU to ask the BU iGem team about Eugene and about some design things. We also wanted to get some more complicated examples of circuits that they had designed or seen in the literature. We were also there to observe how the BU iGem team did their work using Eugene during the design process. The meeting did not wind up being super useful as they didn't have many examples, and Traci was not there. The meeting was not also design heavy, so was not very useful for observation.

Wednesday: Willy Lensch from the Harvard Stem Cell Institute, and director of the HSCI summer internship that I participated in last summer, came to speak about stem cells and the ethical questions that arise from developing experimental therapies. These questions have never had to be asked before the development in scientific technology has given us the opportunity to do things that we have never been able to do before.

Thursday: The Eugenie team continued to work on drag-and-drop using JQuery and made some progress with getting objects to drag to multiple panes using pictures of cute animals.

Friday: We continued to work on drag-and-drop in Eugenie through the day. We have also been thinking about the backend programming that needs to go into Eugenie. As a lab bonding event, we went out to dinner at TGIF's, and then watched Monster's University.

Week 5: June 24 - June 28

Monday: We continued to work on Eugenie.

Tuesday: We have until Monday to complete a working copy of the web application of Eugenie before we move the project to a Microsoft Surface. Pressures has begun to mount because we all don't want to see our hard work and struggles in HTML/CSS/JQuery/AngularJS go to waste because we still can't get drag-and-drop to function properly. Unfortunately, the project did not move forward very much today despite our best efforts.

Wednesday: We continued to work on fixing drag-and-drop in Eugenie. I have been trying to contribute as best I can. Barton Fiske (http://zspace.com/barton-fiske/) came to talk to us about zSpace. It was interesting to learn in greater detail about the technology that our zSpace team is working with.

Thursday: We continued to struggle through working on the drag-and-drop in Eugenie. Michelle Borkin (http://people.seas.harvard.edu/~borkin/) came to speak at Wellesley and gave a really great talk. Her multi-disciplinary approach to problems has served her well in creating a unique program for use in analyzing deposits of fat in heart arteries that has actually improved the rate at which doctors correctly identify these problem areas.

Friday: Fun day with the BU iGem team. We went to the MFA for some out of lab culture absorption. While we did wander through a good portion of the museum, most notably, we went to see the Michelangelo exhibit and Samurai armor exhibit. It was really amazing. The BU iGem team then returned back to their lab as they still had work to do, but the majority of the Wellesley team then went to the Isabella Stewart Gardner Museum, which was beautiful.

Week 6: July 1 - July 5

Monday: We have decided to make Eugenie into a surface application rather than a web application based on the limitations we have discovered while attempting to develop Eugenie as a web-application. It's time to dust off the C# hats. Together, the Eugenie team discussed the backend coding that would be required for creating the surface application.

Tuesday: We created a paper prototype for the surface application version of Eugenie, and created a video to show to the BU iGem team. Then we began trying to fix the drag-and-drop in the surface application in the afternoon.

Wednesday: We continued to work on drag-and-drop for Eugenie now on the surface. It is giving some trouble, and our deadline for getting it to work is Monday. The stress is mounting, but we will overcome it together. We went to a talk given by Dr. Jagan Srinivasan, who works with C. elegans and how they communicate using scent. He has done some great work, and was a great speaker.

Thursday: Happy 4th of July!

Saturday: Worked on drag and drop. Touching the items causes them to disappear, but we are unable to drag the items. The item

Sunday: Success with drag and drop! We finally managed to get the items to drag and drop, though they were appearing at a random half of the screen. It took us the longest time to finally find where the drag target was, but once that happened, progress was made!

Week 7: July 8 - July 12

Monday: With the help of Casey, we fixed the drop target so it takes up the entire section of tree view. The Eugenie team split up so Sravanti and I are working on syncing the tree and behavior panels, while Catherine works on the shuttering of our UI panels, the icons, and the general look and feel of our UI. Sravanti and I did not make much headway, but we know that the pressure is on now because our deadline is to have a solid working prototype by Wednesday.

Tuesday: Sravanti and I successfully linked the tree panel and behavior panel! We databound the objects that we were dropping into the tree panel so that there was a response in the behavior panel. It wasn't initially working, and it took us an hour to realize that it was because we had a textbox hardcoded. Life lesson learned: hardcoding is a bad idea sometimes!

Wednesday: I went to BU with Casey to present our current iteration of the Eugenie UI with the sliding bars. They were alright with our new design. The BU team is working on synthetic biology circuits that they are coding in Eugene. Orit wants us to make sure that we can use Eugenie to generate the same results as they are generating with Eugene code for all their circuits. The only problem with this is that they are not going to run the code and get the results until the end of July, since apparently it will take about a week and a half in order to return all the results. So, we're not going to be able to check our program results with theirs until then. We are also at the disadvantage of working with CLOTHO 2 since we cannot have access to CLOTHO3.

We also reiterated our goals for iGem: 1. Give Eugenie the ability to browse the database and clotho for information to populate the objects. 2. Implement the rules of NOT, CONTAINS, and BEFORE 3. Making sure the drag and drop behavior works well 4. Make sure the visualization of results is exportable in the desired format, and perhaps is displayed visually in Pigeon

Thursday: Catherine and Evan have finished creating the sliding panels. They have also successfully created snapping tiles in the tree view. Sravanti and I are working connecting the objects to a database, with moderate success.

Friday: Sravanti and I successfully got the search function to work for Eugenie! For the moment, it is case sensitive, but when you search for "promoter," "terminator" etc., the parts will show up! Right now, any new search results will just append to the end, but it's something that we will fix on Monday! Overall, a good day in the lab.

Week 7: July 15 - July 19

Monday: Sravanti and I have made it so that search is no longer case sensitive, and new search results do not append to the end of the previously generated search results. We have created a popup to show the properties of a part when you click on the part. However, every time you click on the part, it generates a new pop-up window. We will be sure to fix it later. We also started to tentatively work on the styling on the popup box.

I have started making the poster for the end of Wellesley Summer Science internship program conference style poster session. It's been slow going at the beginning, as always when making a poster, but at least I will not have to spend hours making figures this year like I have in the past!

Tuesday: We fixed the binding for the name information for each part in the pop up box. We have managed to get direction to show up as well, but for the moment, it relies on that information being in the correct spot in the data file. We will not worry about that too much specifically right now because we need to databind information from the database for the popup box anyway. I continued to work on the poster.

Wednesday: Continued to work on databinding and the poster. The writing is coming along. I started to think about how I was going to set up the poster. I'm not super creative when it comes to displaying information, I tend to go the route of "simple is best," but that might be too boring for the tastes of this lab. I've been told that my design could be more fun, which is a valid criticism. I am also struggling to come up with a color scheme for the poster. It was suggested that we go with the common lab color scheme of blue and orange. I wanted to go with something a little different, but I'm pretty sure my efforts would come out looking like one of those terrible Geocities websites despite using the aid of a colorwheel.

Thursday: It was hard to be productive today because overall we struggled to get a connection to the internet. And since everything is either saved on GoogleDrive or Dropbox, we were stuck. Before things went down around mid-afternoon, Sravanti connected the popup box to the iGem database, but it stopped working when the connection to the internet started to fail.

I started writing both the public and technical abstracts. Having stared at the same information for so long, and trying to reword it in many different ways is starting to make my head spin. Thankfully, Evan stepped in and helped write a version because I just didn't know how to reword it any longer.

At the end of the day, we headed out to Bikram Yoga as a lab. It was fun, and hot! I don't know if I have the strength of will to do it again, because it was really painful to be in such great heat and moving around. I have never sweat so much in my life.

Friday: We were still struggling with the internet connection. Logging in as a guest gave some of us access to our emails, but GoogleDrive access was still spotty. We got as much done as we could. We also sent our summer interns off. Those kids were great, and I hope they had a great time this summer. The team then took the afternoon and went out to smoothies at Life Alive with the BU iGem team!

Week 8: July 22 - July 26

Monday: Editing of the poster has continued. Orit has given me her feedback for the abstracts, so I spent my time before lunch heavily editing both the public and technical versions. I learned today that the abstracts are actually due next week, and not today at 4 pm, so I am greatly relieved. I have continued to edit what writing is to go on the poster. Catherine helped out greatly by writing the explanations for why tree view and behavior view are important, and helping me edit the writing of the poster. Consuelo has helped the Eugenie team out a lot by helping us edit the styling of the poster and by reading over and editing both abstracts. They still need some work, but we're getting there steadily! Evan is working on the logo for Eugenie, and they say they are almost done! I am very excited to see it.

Sravanti is continuing to work through getting the popup box to be populated with the information from the database. She has made great progress today. Eugenie is really starting to come together!

Our official, very last minute deadline for all the heavy development is next Thursday. It's crunchtime!

Tuesday: Today, I really finished up the writing for the poster. It's in a place where I would be comfortable to print the poster and print the abstract, but I know there is most likely things that Orit would like to change, but at least it won't be stressful editing by the time we have to print on Tuesday next week.

Wednesday: Catherine and I worked on the poster and the protocol for our preliminary user testing where our lab mates and the BU iGem team will act as our guinea pigs. It was an extremely long day. We got both of the things done.

Thursday: Catherine and I worked on editing the protocol. It's starting to look pretty good! Orit took a look at it for us and made some really helpful comments, and now we will take into account her changes for testing our lab mates tomorrow. Evan is helping us style the presentation to the lab colors of orange and blue. We are going to practice today and be ready for the presentation tomorrow afternoon.

Friday: Today, we finished up our presentation, and practiced a few times for our friends in the lab. Then we gave our presentations in front of our fellow students in the math and computer science departments. I believe our project was pretty well received and that people found it interesting, despite the fact that our work is very far away from the direction of focus of the projects of people in the audience.

Week 9: July 29 - August 2

Monday: Eugenie pilot studies day 1! Catherine and I had been working on the user study protocol last week and over the weekend. The both of us had already worked on the Tabula user studies so we know that sometimes protocols need to be edited because they are not working as smoothly as the study runner would like for various reasons (the instructions for the task are not clear or concise enough, there is not enough instruction). Also, sometimes it takes running the study a few times before it runs smoothly. The Eugenie team was really looking forward to getting some feedback for our project!

I heavily recruited from the lab I previously worked in at Wellesley, headed by my major advisor, Yui Suzuki, http://www.wellesley.edu/biology/faculty/suzukiy. My former lab mates were happy to oblige me in my request for guinea pig test users in exchange for some cupcakes and other snack foods. Only one person from that group had had experience in or knowledge of synthetic biology. Overall, the response was extremely positive, and using the system was very easy to pick up for all of our test users.

Orit requested that we also conduct pair user-studies the next day to take a look at the collaborative nature of the project in strangers.

Tuesday: Poster printing day! I spent the morning putting the finishing touches on the poster. As a team, we decided what the font should be because our original choice of Helvetica Neue was not quite up to par. As a somewhat last minute decision, I asked Evan to help me write a blurb about the visual language that we had devised. They wrote up a really awesome description which fit perfectly into the poster, and then we were off to the presses for our 12:30 poster printing slot. Thankfully, it was a beautiful day, so we didn't have to worry about our poster getting rained on in transport. I'm really proud of how the poster turned out!

Wednesday: More user-testing! Catherine and I gathered up video cameras, a tripod, two iPads, one tablet, and a huge bundle of chargers and headed off to Boston University to do user-testing for our current iteration for Eugenie from the BU iGem team! We had some issues finding the building, resulting in getting there a bit late, but it turned out fine. The BU students who were there liked the program and gave us some great feedback. There are two members of the team that weren't there, but I will schedule some other user studies with them when it is convenient for all parties involved.

Thursday: Presentation day! The Eugenie, zMol/zTree, and Bac to the Future teams finally had the opportunity to show off their projects to the rest of the Wellesley Summer Research Program. It was a great day and people were really interested in the work that we were doing.

It was the official end to the Wellesley Summer Science Research Program, but there is still much to do before iGem competition! I'm looking forward to the rest of the summer.