Team:Wellesley HCI/Notebook/NahumNotebook


Wellesley HCI iGEM Team: Nahum's Notebook

Nahum's Notebook


Jun 4: My first day in lab

Today was my first day in the lab. I was warmly welcomed by a group of girls who had an ungodly amount of energy at 9 am in the morning. After all of the introductions to my lab mates, I started work by going through a tutorial on some surface applications using Visual Basic and the surface software development kit. I made my first mistake in lab today by wearing my headphones while working. I learned that headphones impeded my ability to communicate with my fellow lab mates. After working on the touch surfaces, I was allowed some time to meet with my “mini-team” to discuss the topic we would be working on for the brainstorming phase of the competition. I will be focusing on the electronic lab notebook for the next two weeks! A little later, I enjoyed my first lab Starbucks run of the summer. Around 3pm , we all head over to Microsoft to get a tutorial with some of the new tablet and Windows 8 technology. The trip was great. I had the opportunity to get a peep into the operations of a huge corporation while also learning a lot of new things about different software technologies. I will admit though, at points I felt very confused with some of the topics that the software developers were talking about. Being a biologist and a computer science lab wil be very interesting this summer…

Jun 5: A day in the wet lab

In an MIT Wet Lab

Today I did not have to make the commute to Wellesley because we had our workshop on MIT’s campus with one of my previous professors. The purpose of the workshop was to give the computer scientists a taste of what synthetic biology is all about. We reviewed some basic biological concepts, looked at previous iGEM projects, and did some wet lab work. I was much more knowledgeable on the material we studied today and found myself being a source of help for a lot of my labmates. This team is interesting because we are all very intelligent but hold very different academic strengths. It’s a very useful and humbling experience to be dependent on your teammates for certain topics while being depended on for others. It makes for a very collaborative environment.

June 6: The Research Begins

This morning and afternoon was dedicated to doing research on the electronic notebook. It was nice to have so many other people in the lab during the hours of research because researching for hours can get monotonous and tiring. Whenever I needed a break from the work, I could just close my laptop for a few minutes and talk to one of my fellow labmates. At 3pm, I had my first meeting with Orit Shaer, the PI for our lab, to discuss some of my thoughts on the electronic notebook. She was very helpful in making me see the bigger picture of the project rather than getting bogged down in the specifics of one technical aspect of the notebook or another. I left the meeting with a more refined direction for my research.

Jun 7: Research and birthday cake

After our meeting with Orit yesterday, all of today was dedicated to additional research and brainstorming on the electronic notebook. Luckily there was some additional excitement in the lab because it was Veronica’s birthday. We kind of ruined the surprise by accidentally ruined the surprise we were planning for here by including her in the email thread where we actually planned what we were going to do. Regardless, the celebration was fun. We had cake and cookies! Besides the birthday, I had periodic meetings with my electronic lab notebook “mini-team” to organize the topics we researched and discuss how to most efficiently represent the information we were researching for the rest of our labmates. We used Google documents and Dropbox to organize ourselves.

Jun 8: Work, Work, Work, and Chipotle!

Friday brought a much more relaxed attitude to the lab. Everyone was energetic and excited about the weekend. We all continued working on our specific projects but off-topic chatter was much higher today. At 12:30 pm, we all attended a group of talks by different computer science professors at Wellesley. We got to learn about a lot of cool projects that were going on in the computer science department this summer. After the talks, we all went to Chipotle Mexican Grill as a lab for lunch. It is tradition that every Friday, the lab goes out to lunch together which is nice. After lunch, my mini-team and I did additional research on the electronic notebook. We will be presenting our project to the rest of the lab next week so it was important that we be on top of our work. This is my first time participating in iGEM and have been having a little bit of trouble determining how extravagant I should be with my ideas. My labmates who have done iGEM before have helped me a bit with this problem by telling me that I should not limit any of my ideas (at least for the brainstorming phase…).

Jun 11: Project updates and my birthday!

Brainstorming for the ELN.

Today was a bit stressful. It was finally our time to present everything we had learned about the electronic lab notebook to the rest of the lab. My team spent the entire morning working to perfect our powerpoint presentation. We were the first to present today. It ended up being a lot less scary than I thought it would be. Everyone was very attentive during our presentation and provided a lot of useful commentary that made me think in ways I had not before. The new perspectives were extremely useful. Afterwards, I listened to the presentations from the other “mini-teams” and was amazed at just how refined the presentations were for just one week of work. Today is also my birthday (seems like we have one everyday…). My labmates bought me cake and cookies and we feasted before heading home. It was great!

Jun 12: BU

Today we were at BU working with their iGEM wetlab team. They gave us short explanations of things they were working on and we game them short explanations of what we are working on. Discussions with the BU team was extremely useful because it gave us our first opportunity to bounce some of our software ideas off of people actually working in the lab. Plus, we got free pizza for lunch! We also spent some time organizing a few social events for our teams and possibly more of the Massachusetts teams including laser tag and ultimate frisbee!

Jun 13: Brainstorming

Brainstorming at Wellesley

We were back at Wellesley today with the BU iGEM team and a representative from Agilent Technology. We had our first of two days of brainstorming today. Each one of the Wellesley “mini-teams” set up a station in one of the larger rooms at Wellesley and had everyone rotate around these stations. At each station, individuals had the opportunity to ask each “mini-team” questions about their project and propose some new ideas. The BU wet lab team helped us ground some of our ideas and realize what was actually useful and what was superfluous. The representative from Agilent Technology was able to provide us with a lot of input on the technical feasibility of a lot of the things we were working on. The brainstorming session answered a lot of questions but created even more. We have our work cut out for us!

Jun 14: Brainstorming: Part II

Today was day 2 of brainstorming. We had Natalie Kuldull, a biological engineering lab professor at MIT, come in this morning to help us out with the electronic lab notebook. She provided a unique perspective on the electronic lab notebook as a professor. She introduced ideas of administrative controls versus student controls as well as mechanisms to provide oversight over the work that students may do in the lab. After our brainstorming session, the entire team met to isolate specific topics that we need to do additional research on. I will be doing some additional research on digital pens and styluses as well as doing some research on some of the work that the BU iGEM team will be working on.

June 15: Our first interview

This morning, we had an interview with a professor about the electronic lab notebook. We interviewed Christopher Arumainayagam, the head of the Wellesley chemistry department. He held a lot of the same perspectives as many of the professors quoted in the literature. He was generally hesitant to move away from paper and go digital but he was will to consider the possibilities. One of my favorite features that he suggested was a troubleshooting tree that would allow a researcher to input a problem that he ran into during an experiment and the solution he used to get around this problem. This tree would be able to be referenced anytime in the future so that if the problem occurs again, the solution will be well documented. After the interview, the lab went on our weekly food run to Chipotle again which was great. The remainder of the day was spent doing research on digital pens.

Jun 18: First glance at MoClo

Today we began to do extensive research on the MoClo technique. MoClo seems to be a revolutionary biological technique for designing multigene networks. I read the paper today and it was extremely dense but this seems to be a consistent them amongst biological papers. Beyond this initial research, we are also continuing to do research on unique modalities for an electronic notebook. We are focusing our research on modalities to headcams, digitial pens and stylus. At the end of today, we had to present all of our findings on the electronic notebook and explain why we thought that this was a project that we should pursue for the rest of the summer. Personally, I think that the electronic notebook is a rather vague project with a lot of modalities being beyond our technological reach. I felt like most of the lab felt the same way by the end of the day.

Jun 20: MoClo Continued

Brainstorming at BU

Research on the electronic notebook has essentially been terminated for the summer. I am now working on creating a MoClo Planner. This planner will be used to make the design of multi-gene networks using this technique simpler and more intuitive. One big emphasis in our lab this semester has been using standard tools and languages that have been established by the synthetic biology community. Therefore, Kara, Kathy, and I have begun to research the Eugene coding language while developing our MoClo planner. Our hope is that we will be able to incorporate Eugene into the development of our application. All this coding language research is difficult…

Jun 21: Eugene

I spent the majority of today trying to make sense of Eugene. I finally began to understand some of the basic structure of the language and Kara and I even started to create parts and write properties for these parts. Alongside the Eugene work, Kara, Kathy, and I began to create paper prototypes of the MoClo planner in order to get the ball rolling on the design of the MoClo planner.

Jun 22: Let the coding begin...

We began coding today in Visual Studio. The electronic notebook is all but dead at this point and Kara and my focus has been directed to the MoClo planner. Thank god Kara has some familiarity with coding because I was entirely lost. I really look forward to trying to tackle a new skill but having no idea what I was doing today was quite the humbling experience. Kara was great though in teaching me what she knows and not making me feel to bad every time (and there were a lot of times) I made a mistake.

Jun 26: Paper prototypes, video demos, and more

FOOD! And discussions of progress...

Today was a very busy day. Kara, Kathy, and I spent the majority of the day setting up a more meticulous paper prototype of the MoClo planner in order to create a video demo for the iGem and synthetic biology community. For the later portion of the day, Kara and I went back to work on the user interface of the MoClo planner. I’m starting to get a hang of the XAML language but the C# back code is still beyond my grasp of understanding. Everyone keeps telling me that it will make more sense with time. I sure hope so…

Jun 27 & 28: Coding, coding, and more coding

The past two days have been spent in front of the computer coding for hours. When things are going well and the code does what you want it to, coding can actually be quite a bit of fun. When the code continuously breaks, however, coding can be one of the most mentally exhausting exercises the mind can take on. We now have all of the “layers” of our MoClo planner up and running and they are moving correctly relative to each other. We have even started coding for some of the behavioral aspects of the program by giving functionality to certain navigation buttons. We have also added context menus. A lot can happen in two days…

Jun 29: A day at MIT

Today, we got a break from all the coding and spent the day at MIT. We watched a physics lecture by professor Walter Lewin and then met up with the MIT iGem team for lunch. I had to leave after lunch, but the rest of the team spent the day checking out the MIT iGEM team’s lab and hearing about their project.

Jul 2 & 3: Back to MoClo

Me and Kara have continued our work on the MoClo designer. Much of the structure and layout of the user interface is falling into place and we have begun to focus on the behavioral aspects of the planner. The big feature we need to tackle is getting drag and drop properties to work on all parts of the planner. Seems a little complex to me but Kara and I have already hurdled over some speed bumps so hopefully this shouldn’t be a huge problem.

Jul 5 & 6: Drag and Drop

Still working on the UI. We have gotten a lot of smaller functions such as a search box, mock parts adders, and other things working but drag and drop is giving us a lot more trouble than we had hoped for. Even when we get drag and drop to work in one area of the program, the type of drag and drop need in another part of the program is different and requires a new set of methods.

July 10: Progress

We've been struggling with drag and drop for a couple of days but we are finally getting it to work consistently. We were having the most trouble transferring data between different workspaces. We have consistently taken the approach of creating a duplicate of an object on a touch down event, having the duplicate take the place of the original object, and dragging the original object between workspaces.

July 11: Lonely at the Lab

I spent much of today touching up the UI of the MoClo planner so that I can begin more work on the backend of the planner. Consuelo, Wendy, and Kathy were gone to BU today so the lab was a bit quiet today. It was eerie...

July 16: Backend

I spent today working on the backend of the MoClo planner. I was working on making sure that the data sheet populated with the correct data from the registry of standard biological parts and I began a bit of work on making the publications page populate with the correct information.

July 18: Beach Day

It was a nice break from work!

July 19: Upward Bound

Kim presenting SynFlo to Upward Bound Students

Upward Bound kids joined the lab today. I believe they were getting a demo on SynFlo and the beast. I was not involved in the demo. I just had my headphones on and continued working on the backend of the MoClo planner.

July 24: User studies

Today we had a round of user studies for the MoClo planner. I satin on 2 of the studies and it was one of the most difficult experiences I have had this summer. It is difficult to watch watch people use your work in fear of it breaking. In fact, the program crashed once and we had to restart the study. Although difficult, the study was very informative.

July 25: Debugging

Kara and I spent the majority of the day debugging a lot of the problems that we ran into during the user study. The filters, in particular, take a very long time to load all the parts so we worked on optimizing that function of the program. We also modified some of the swipe and trash functionality so that it was more consistent along all workspaces.

Friday 27: MIT User Studies

Today, Consuelo, Kathy, and I headed out to MIT. These user studies were even more difficult that the Wellesley user studies. For some reason, MIT students love trying to break programs. They would often get distracted from the task at hand and look for flaws in planner. It was difficult to watch (but also helpful). At least we got some delicious pad thai for lunch. Transferring Uppi (our large table top surface) to MIT and back was pretty difficult.

August 1: Poster Session Prep

Preparing for the Science Center Poster Presentation.

We have spent the past 3 days balancing work on the MoClo planner and on our poster. The poster session is tomorrow so we have spent much of the past few days working on abstracts for all the different projects in the lab as well as working as our "elevator speil" for our particular projects. We have also have been working on a giant task list of problems with the MoClo planner that we created after the user studies.

August 2: Poster Session

I can't believe today is the last day of the summer! We spent the morning working with Orit on our presentations as well as how to answer different types of questions. The poster session went great although I felt that the science center was a little overcrowded with all the summer projects. Afterwards, we ended the summer with a lab dinner. We went out for Cuban food and relied on Consuelo's expertise for choosing our dishes. It was a really great way to end the summer.