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Team:Wellesley Desyne/Notebook/TiffanyNotebook
From 2013.igem.org
Tiffany's Notebook
Contents |
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:
Tuesday: Fixed binding for Name and Direction
Wednesday:
Thursday: Friday:
