BAC PACK

NOTEBOOKS

Rachel's Notebook

6/1/2015 : Day 1
Today was the first day in the HCI lab! We had orientation this morning, and I met my teammates Sam and Vivien, today. I also met the other people who will be working in the HCI lab as well this summer. We also had lab orientation and learned more about the HCI lab and all the cool tech in the lab. Before we did anything concerning the multitouch screen, we read up and familiarized ourselves with the iGEM requirements for the community track. We read up on all the qualifications a team needs to get a Bronze, Silver, and Gold medal. We also explored around the iGEM website for a bit. After that, we downloaded Cornerstone SDK, a software development kit that is used to create applications for multitouch screens. One thing we noticed was that C++ was the most common language that is used, and we had decided to use Javascript. So we fiddled around with the few examples in Cornerstone that were in Javascript and used those examples as a baseline for our helloecoli app we were going to start working on this week.

6/2/2015: Day 2
Today we started working on our own application. We initially had randomly colored squares that when tapped on, they duplicated. We changed the squares to circles which also when tapped on, duplicated. At this point, the circles were resizeable with the right hand gesture. The circles also went off the screen. Orit met with us to see what we had so far and gave us the suggestion to make the circles look more like e.coli. We decided to try to change the shape to an ellipse.

6/3/2015: Day 3
Today, we had guests from NYU come in to talk with the other PGHCI team. Sam, Vivien, and I joined them, and they have a very informative talk about genetics. After the talk, we went back to playing around with our app. We changed the circles to ellipses. And when the ellipses consumed/ran into each other, the ellipse being consumed turned into a circle inside the other ellipse. We then brainstormed and decided that we were going to introduce the concept of bacteria and viruses. We decided to make the viruses, circles and the bacteria to be ellipses. And only the virus could be consumed by the bacteria, and the viruses could not consume each other and vice versa for the bacteria. One problem we ran into was the fact that the viruses were still widgets. So when the virus was consumed, it had difficulty staying inside the bacteria. However, after fiddling with Cornerstone, we figured out how to create Children, and the viruses stayed inside the bacteria and did not leave the bacteria.

6/4/2015: Day 4
Thursday was a SUPER productive day. We got a lot done! We FINALLY figured out how to set the boundaries so that the widgets won’t leave the screen. We also got them to bounce of the sides of the screen as well. The viruses and bacteria now randomly move around the screen, independent of touch. We also disabled free rotation and set the scale so that the widgets do not change size when touched. We also introduced marker action and recognition to our app. When you tap a marker on the screen, a new bacterium is created. The bacteria also grew to a certain size and divided into two smaller baby bacteria. This was to mimic (not super accurate) mitosis and the asexual replication of bacteria. It copies the way that bacteria duplicates (increases to double its size and then divides into two at its midline), When a virus is tapped on, more viruses were created. However, we came across an interesting problem. When the widgets ran into each other, sometimes they bounced off of each other. Occasionally, they end up being in a limbo state where they do not bounce off of each other and start to shake.

6/5/2015: Day 5
We have started programming specific actions for specific markers-- now, one marker creates a new Bacteria, one removes that specific Bacteria, and one displays the bacteria’s infection status with a simple attached textbox that states “Infected” or “Not infected”. We explored around with the Image Widget so we can use our own images later for our project. After this week, we really found out how much flexibility we have with this project, and we can do many things with this screen. We decided that we also wanted explore video widgets more in the near future!!!

6/8/15: Day 6
Before natalie came in today, the iGEM team played a bit more around with the cornerstone SDK. Natalie came into today, and she was fabulous. She held a workshop for us, and covered everything from the basics of synthetic biology to summaries of a couple of famous iGEM projects from the past. We also showed her some of our previous projects such as Bac to the Future and Synflo. It was super helpful because she gave us a lot of suggestions about how to make synthetic biology more accessible and more approachable to the general public. We also talked about how to convey that synthetic biology is still very new and it is quite a lengthy process to create new things. We also talked about the ethical concerns that come along with synthetic biology and how to approach in a museum exhibit setting.

6/9/15: Day 7
We also had our potluck today. Johanna brought a beautiful dish and Christina made really yummy gluten free brownies. Around 2:30, we skyped Romie and Anja from the Innovation Museum. They are our collabotors we are working with on this iGEM project this summer! We are super excited to meet them very soon! We presented our brainstorms that we thought of this morning. They provided us with some really great feedback! They told us that they really liked the idea of space exploration for our project, so that can be a project idea possibility!

6/10/15: Day 8
Today, we fiddled around with the multitaction screen a bit more. We introduced the multiple markers to the screen as well as experiment with the marker sizes. We found the smallest optimal size of markers we could use, and we also looked more into the process of marker recognition. For lunch, we went to a program-wide lecture about cyanococchus bacteria. It was really interesting to hear about what other scientists in different fields such as microbiology were doing. We also got free lunch at the lecture today. After lunch, we played around with the multi-taction screen more, and tweaked a couple of things like the background of the screen as well as marker recognition.

6/11/15 Day 9
We got a lot of work done today! We developed prototype for certain designs for our markers today. We also worked on our MarsTest program today. We looked into the hardware of the marker recognition. So we experimented with laser-printed markers vs. inkjet printers to see if the quality of the markers actually influenced the recognition on the multitaction screen. For a lot of the day, we tested out different marker sizes and found the optimal marker size for the screen. We also added functionality that allowed for up to four markers to be recognized by the screen. We also played around with a keyboard widget to add into our program! This was super exciting because in the future, users of our program will be able to add their usernames! We need to play around with this more. Every Thursday we also have a department wide talk during lunch. We had two professors from the CS department talk as well as a physics professor and a math professor talk about their research. I really enjoy going to these talks because it’s really cool to learn about what professors are doing and the fact that even professors still do ongoing research! I really like learning about what other people from various concentrations of science do.

6/12/2015: Day 10
We created a new interface today. We came up with this really cute interface that asked users to pick their favorite flavor. Once they picked their fruit, they can drag it into the flask and the flask is then tipped, another message pops up that says what flavor the user has picked. We also had another google hangout call with Romie and Anja from the Innovation Museum. We are so excited that they are coming into the HCI lab this Monday! We showed them what we have done on the multi-taction screen thus far. We are so excited to brainstorm and collaborate with them next week.

6/15/2015: Day 11
Romie and Anja from from the Tech Museum came to Wellesley today. I was so happy to finally meet them and work with them in person. They talked to us a bit about what the Tech Museum’s philosophy is and what they were looking for in their exhibit. After they told us a little bit about their museum and their work, we proceeded to show them our current prototype programs we created for the past 2 weeks. We also then started phase 1 of brainstorming for what our exhibit will be and also what kind of experience we wanted the visitors of the museum to have. We started brainstorming by using two broad parameters, Big Frame and Places. Then we started to name anything that popped up in our heads. After going back and forth for a bit and discussing what we wanted, we settled with possibly calling the exhibit BacPack and having three extreme environments: Mars, The Deep Ocean Cave, and Antarctica. After that, we came up with some criteria and some goals for this exhibit. We also listed some of the environment details as well as what could possibly be engineered in those different environments. That night, Vivien, Sam, and I were all assigned to research some past iGEM projects

6/17/2015: Day 12
Today was a day full of paper prototyping. I felt like I was in elementary school again from all the paper cutting and coloring. It was honestly a lot of fun and super helpful because I got to really understand every single step of our interaction and our prototype.

6/18/2015: Day 13
Today we did more prototyping, and we actually finished our prototype!!!! Orit’s children also came by to interact with our paper prototype. They were very engaged and interested in the prototype, and we ran through the prototype a few times with both of them. They gave us really interesting and helpful feedback such as adding videos to our project, and challenge states that added more complexity to our prototype. We are going to talk about their feedback in depth tomorrow and next week.

6/19/2015: Day 14
Today we went to the NEGEM meetup at Boston University. A lot of different team from various schools in the New England area came. It was really exciting to see so many people at this meet up. To be honest, I was really nervous to present today because the whole room consisted of people who were very experienced with biology. It was cool to sit through all the presentations about project ideas. NEGEM was really helpful because we got a lot of really helpful feedback from the people participating. It was definitely a great experience.

6/22/2015: Day 15
Today we started creating our first actual prototype for the BacPack iGEM project on the multitaction screen. We started adding some basic widgets such as text widgets and image widgets that we need for our first digital prototype. I am super excited to work more on the multitaction.

6/23/2015: Day 16
We some trouble today with the marker recognition. One cool functionality of the screen is that it can recognize marker codes, and we are planning to use these marker codes for our tangibles. However, there was still some issues with the screen recognizing the markers correctly, so we tried messing around with the settings. However, that didn’t seem to help much. We are hoping that we will figure this out soon. We went out towards the end of work to get some ice cream at JP licks.

6/24/2015: Day 17
Today we worked more on the functionality of the prototype. We also went to the program wide seminar. A Wellesley alum talked about her chemistry career, and it was very inspiring.

6/25/2015: Day 18
We continued to work on the functionality of the prototype. We had some doubts about the current prototype because it was not taking full advantage of the multitaction screens and the capabilities that come along with the screens. One downside about our current prototype is that it is not collaborative or multi-user and only one user can interact with the screen at a time. This did not make sense to me because one our main goals when we were brainstorming with Romie and Anja was that we needed a collaborative space. We asked Orit about our concerns, and he agreed with us as well. I think we are going to overhaul or initial design and start brainstorming again for a new layout! We also filled out iGEM forms that are due tomorrow. Super excited about iGEM!!!!

6/26/2015: Day 19
The first of our interns came today! Melissa is a sophomore in high school. She is super cool and seemed to be excited to hang out and work with us in the HCI lab. Today, we worked on multiple sketches of our exhibit. One thing that I really emphasized in the layout is having individual workspaces and a shared space that is collaborative. I think Sam and Vivien liked this idea as well, so I think we are going to proceed in this direction. Lauren, one of the Wellesley alums working in the lab, also brought some very cool ideas to the table such as introducing duplication and status bars. In addition, Mike Horn from NorthWestern came to visit us in the lab. He showed us some really cool exhibits and games that he created, and he also gave us a lot of feedback on our current prototypes. He also referred us to a lot of papers for us to read about interactive museum spaces and tabletops.

6/29/2015: Day 20
We started to reiteration process. So THUS BEGAN PAPER PROTOTYPE ROUND 2!!!!! We spent much of the day brainstorming and discussing possible new designs with Orit and the rest of the team. To be honest here, I have a love/hate relationship with paper prototypes. But trust me people, paper prototypes are super important and necessary when designing interfaces. They are so so important, and a lot of thought and detail is put into these prototypes that are valuable when designing the real thing.

6/30/2015: Day 21
A Wellesley alum came to visit us in the lab. She has been in the design industry for a while and gave a lot of great insight and feedback while brainstorming. After having a great discussion with her and reflecting on a lot of her suggestions, the team and I iterated again, the paper prototype. Finally towards the end of the day, we finally came up with the current iteration of our paper prototype.

7/1/2015: Day 22
Today, Natalie came to visit our lab. We gave her a short presentation about our project and then she looked at our paper prototype. She gave us a lot of suggestions and feedback for us, and it was super helpful to have someone who is a synthetic biologist to come in and look over our project. The other interns came today as well. We spent most of the day filming our paper prototype. We also sent a video of our new paper prototype in action to The Tech today as well. Casey, who has worked in the lab previously and has participated in previous iGEMS also came into as they are helping us with a lot of the graphics for our project.

7/2/2015: Day 23
Today we worked on finishing up our paper prototype as well as editing our word choice and phrasing of words. We also went to the CS/Math/Physics lecture today during lunch time. The editing and word choice was pretty in depth and very detail oriented so it took us a while to determine all the phrasings in the project that are going to be used.

7/7/2015: Day 24
Casey came and visited us. We talked about design and we also discussed the challenges with our design. They had some really good sketches planned out already which is super exciting. I always wished I was super good a drawing and designing, and I was super amazed by how awesome Casey is! ! ! !

7/8/2015: Day 25
We have a presentation at the department presentations tomorrow. I’m pretty nervous because this is our first presentation at Wellesley as a team. While we had some practice talking at NEGEM, I was nervous because in the audience will be friends and professors that I know well. We revamped our entire presentation layout and aesthetic, and we even included some videos of our multitaction prototype.

7/9/2015: Day 26
Presentation at department talks: We had our presentation today! Sam, Vivien, and I were pretty nervous, but we finished successfully. Our fellow classmates gave us some good feedback, and we are happy that it got positive responses at this talk.

7/10/2015: Day 27
We went to the Museum of Science! I became an emotional mess at the Pixar Exhibit. Orit recommended that we take a lab outing to the newly opened Pixar exhibit for some inspiration. The exhibit itself was phenomenal. I did not realize how much work and iterations that went into creating these films.

7/13/2015: Day 28
Casey sent us some really cool artwork. We started adding and using their artwork into our prototype. It was really cool seeing our project looking more space-y.

7/15/2015: Day 30
Today we did a lot of math. We had a difficult time with figuring out the math for the flasks tilting towards the Mars environment. After a few hours and a lot of tinkering with equations, we finally got our flasks to empty towards the center! Hallelujah! Later in the afternoon, the MIT app inventor team came by and looked at what was going on in the lab.

7/16/2015: Day 31
Today, I got to listen to a lot of my friends’ presentations from the other departments. My roommate actually presented today on her physics research. It was super cool to see what others have done. We also went to Larry’s machine shop today. It was really cool to get laser cutting trained. We learned how to laser cut, and it was a lot of fun!

7/17/2015: Day 32
We did a lot of work before the iGEM meet-up tomorrow. We added more functionality to our project such as adding message bubbles that instructed people on how to proceed.

7/18/2015: Day 33
MIT and the BU iGEM team came over to Wellesley today. We had a lot of fun testing our prototype with students that came today. Also we got to hear their feedback on our project and they gave us some wonderful suggestions. Also, we got to hear what the other teams have been working on since we last met. It was super cool for them to come over and play with all the gadgets in the lab!

7/20/2015: Day 34
We spend a lot of time on functionality today as well.

21/7/2015: Day 35
We got the status bars to work today! They were easier to make than we expected them to be. The status bars decrease automatically as time passes! We also talked to Anja and Romie briefly. They gave us feedback on our current prototype and also gave us updates on the wetlab portion that they are working on.

22/7/2015: Day 36
Today, Casey sent us more images. They sent us message bubbles for us to insert into our prototype. So we incorporated the new message bubbles that guide users during the experience. In addition, we also tested the prototype with 3 high school interns. We looked to see how they interacted with our current prototype. We also asked them for feedback.

23/7/2015: Day 37
This morning, WE FIXED ONE OF THE MAJOR BUGS THAT WE HAVE BEEN STRUGGLING WITH FOR THE PAST WEEK. Wohoo, we realized that there was something wrong with how we constructed the marker recognition. We fixed by simply creating a new array when the plasmid is cleared. It was such a simple fix. We also realized that Johanna is a wonderful human and gave us a lot of suggestions. If Johanna is around, everything ends up working out. Also, around 50 kids from Upward Bound came in today to test our prototype and provided us with a lot of wonderful feedback.

24/7/2015: Day 38
We worked on various things. We wrote and submitted our two abstracts that are due for the Wellesley Summer Science Research. We also looked at the various bugs that we found yesterday, and we fixed a couple. We also changed some formatting and switched from buttons to tabs for some of the information that will accompany the exhibit.

27/7/2015: Day 39
WOW can’t believe it is the final stretch! We got a lot done today!!!!!!!! Casey sent us more art so we updated all the animations. We also made the status bars glow when they are updated. We also programmed the bacteria to go to a certain part of Mars based on their “haves” when deployed. I fixed all the tabs and made them look more integrated with the environment, and we also fixed the never-ending duplicating in flask bug that we have been fiddling around with for the last couple of days. Here are some of the things that we checked off our to-do list!!! Update art from Casey Make decreasing status bars more visible Program bacteria to go to a certain part of Mars make tabs larger fix neverending duplication

28/7/2015: Day 40
It’s really crunch time. We spent a lot of time coding and adding final touches to BacPack.

30/7/2015: Day 41
Wow today was the poster session! I can’t believe that this experience at Wellesley summer research has come to an end. I am not too sad still, because I will still be in the lab this fall. It was interesting and really fun to present BacPack to the Wellesley students, professors, and community. We got a lot of interesting feedback from them, and they helped us out by playing around with the prototype.

31/7/2015: Day 42
We started planning out what our wiki would look like, and what the content inside of it would be. We had a skype call with Romie and Anja today. They gave us feedback on what to modify before we went over to the Tech next week. We also decided that we wanted to introduce error states to our prototype. Monday, August 1st: Vivien and I tweaked BacPack a little bit. We introduced general error states that popped up when the wrong resource was used.

8/6/2015: Day 43
Almost everyone in the lab left! Lauren, Jasmine, and I are the only people here now. It was pretty sad and lonely today, not seeing all our other lab buddies come to work today. I made the error states more customized. The error message printed out what resource was not available.

8/7/2015: Day 44
Today I flew to California!! It’s still surreal that I am in San Jose to test our prototype! I am still in shock. We landed at the airport and went straight to the Tech Museum. Romie and Anja were there to greet us!!! There we set up the multitaction and went over how we are going to do user studies Saturday and Sunday. RIght after, Lauren and I went back to the hotel and passed out.

8/8/2015: Day 45
First day of testing!!!!! I was exhausted after a full day of testing. It was really cool to see how people interacted with the prototype. I found that most people were very interested and excited to play with our exhibit. It was also cool to see Romie and Anja set up a mobile wetlab, and to also see how kids interacted with the wet lab component as well.

8/9/2015: Day 46
Final day of testing. We decided to move our user study location to a more central part of the museum. This was a good idea because we got a lot more people that fit the age demographic we were concentrating our learning goals on. We also asked post-interaction questions to see how much the kids learned from briefly interacting with the prototype. Later, Romie and Anja let us explore the Tech Museum. It was so much fun wandering around and playing with some of the coolest exhibits! I’m sad that this is my last day in San Jose, but I really enjoyed doing these user studies!!!

Sam's Notebook

6/1/2015: Day 1
Today was the official start of summer research and work in the HCI Lab. We spent the first half of the day in general orientation, then started work in our teams. Rachel, Vivien, and I are the three Wellesley members of the Wellesley - The Tech Museum of Innovation team for iGEM 2015. Our afternoon was split between getting acquainted with the technical environment and getting acquainted with the iGEM contest and synthetic biology. We got the Cornerstone SDK software, and looked at examples of code and documentation to become familiar with its capabilities. We also looked at previous years’ iGEM teams, specifically the Wellesley ones. This years project is a continuation of sort of the 2012 Wellesley iGEM project SynFlo, so we paid particular attention to that. We’re just starting off, but it seems like a good start!

6/2/2015: Day 2
Second day at the lab! Today was dedicated to exploring the functionality of the cornerstone software. We made our first HelloWorld app in Javascript. Cornerstone also offers functionality using C++, but we decided on Javascript as a more malleable and accessible language to use. Our first app consisted of a few rectangles on the screen, which can be moved around by the users and duplicate when tapped on. Our long-term goal is to develop customized Widgets that would simulate bacteria and viruses, so later in the day we began exploring drawing customized shaped. By the end of the day, we had circles! Tomorrow we’ll explore more of the shape and customization possibilities.

6/3/2015: Day 3
Similar to yesterday (and likely the rest of this week), today was spent playing around with the available Widget features. We changed the shape of the Widgets to ellipses, hopefully moving towards a more E.coli-like shape in the future. We also defined some interaction between the widgets. We started off with bacteria being able to “eat” other bacteria: when two bacteria were close enough, the bigger one would consume the smaller one, with the latter then becoming a circle in the bigger one’s surface area. We then later differentiated between bacteria and viruses, another step towards a more accurate (though obviously still simplified) simulation. Bacteria are now bigger and elliptical, while viruses are smaller circles. Viruses can be replicated by tapping on them, and we currently have not define a mechanism for creating new bacteria. Bacteria can become “infected” by a virus through interacting with it. The issue we ran into was the fact that viruses were still individual widgets even when within bacteria, which meant that tapping on a virus inside a bacterium would still create new viruses, and it was possible to move a virus outside a bacterium’s body. At the very end of the day, we decided to use the addChild() function in widgets, which successfully restricted the virus’s movement within the bacterium. Ideally, tomorrow we’ll work on disabling any interaction with the virus once it is within a bacterium.

6/4/2015: Day 4
Today was a big day with a lot of progress! First, we explored changing the rendering function of bacteria, so now when a bacterium becomes infected, rather than containing the virus widget itself, a little circle is drawn within its body (and the virus widget is removed from the screen). Adding instance variables to the widgets really extended the possibilities for interaction, so we decided that if an infected bacterium encounters a non-infected bacterium, the latter one would also become infected with the same colored virus (we currently have three different viruses: red, blue, and purple). We then restricted the widget’s movement so that neither bacteria nor viruses can be dragged off screen, something we’ve been trying to accomplish since yesterday. Once that was working, we expanded the app so that viruses and bacteria would now float freely within the “tank”, even when not being dragged by users. In the afternoon, we explored marker functionality, and defined any marker interaction with the screen to produce a new bacterium at that spot. The last successful change we made today was to make bacteria be able to reproduce: a bacterium now starts out small and grows continuously, until it reaches a size after which it divides and makes two new bacteria! At the very end of the day we started looking into having different bacteria and viruses bounce off of each other when they collide, but we ran into some issues, which would occasionally prevent them from moving at all and get interlocked. We’ll continue to look into that tomorrow.

6/5/2015: Day 5
Today we continued working on animating the widgets, but ran into the same issues when two widgets collide. We tried several different approaches and equations, but all of them seemed to have some borderline cases that would not display properly On a more successful note, we managed to get marker recognition working: we assigned different markers different roles. Tapping one kind of marker on the screen creates a new bacterium; tapping a bacterium with a specific marker display information about it, and tapping it with a different marker removes it from the tank. We also explored future customization, in terms of using custom images as the bacteria (instead of drawn shapes), but only tested it with a sample image. More works needs to be done in creating a customized bacteria image for the actual project. We will probably spent most of next week focusing on that, and on exploring more accurate SynBio concepts. Overall, it was a good first week!

6/8/2015: Day 6
Today was dedicated to learning Biology. Natalie Kulldel came to visit and gave us a basic Synbio 101, since most of the people in the lab (myself included) have a limited Bio background. Then we talked about some of the science behind previous iGEM projects, including Bacterial Photography, e-Chromi, and making bacteria smell like bananas! It was really fascinating to see just how much synthetic biology is like computer science, which also opens up a lot of possibilities for the direction in which to take our project. We also had a brainstorming session, talked about bacterial superpowers, and applications of Synbio research. At the end, we discussed the ethical implications and overcoming the distrust people might have regarding “engineered” organisms, in the context of the museum exhibit. Tomorrow we’re having a call with Anja and Romie from the Tech, so we are starting to develop concepts and preliminary designs for the actual project. One week in, we’re getting down to business!

6/9/2015: Day 7
We spent the better part of the day brainstorming ideas for the project. We started out with more general brainstorming, but by the early afternoon narrowed it down to three specific exhibit designs (Bac to Mars, BacFarm, and BacMan). They were all conceptually centered around letting users engineer bacteria to perform a particular task, given a list of tasks, but they had different “storylines” and engagement techniques. This is the very early stages of development, so we do expect all of these to change drastically, and possibly not even make an appearance in the final project we settle on. In the afternoon, we talked to Anja and Romie from the Tech, who gave us feedback on our ideas and designs, as well as provided us with more concrete information on what they expect out of the exhibit. As expected, our preliminary designs did not necessarily align with their thoughts, but we all shared the common theme of emphasising engineering and creative spirit in the exhibits. We will continue working on fine-tuning the ideas, and the rest of the week will probably be dedicated to exploring technical possibilities for getting the exhibit to work.

6/10/2015: Day 8
We are back to tinkering with Cornerstone. Since yesterday all of us agreed that it would be good if users had a tangible token they can carry around and put together while exploring the exhibit, we got started with looking into recognizing multiple markers activity on the MultiTaction screen. We also looked into optimizing the size of the markers, and trying to get them as small as possible (to minimize the size of the possible future token). We discovered that the smallest size the MultiTaction can reliably recognize for our purposes is 4x4cm, which should be small enough. In the afternoon, we started working on a new app (expanding on the one we made last week), to introduce a more varied range of interaction with the widgets, for example clicking on a widget to expand and display information about it. We also got some basic functionality in terms of widgets recognizing when they’re tapped on with three markers and changing their state appropriately. Overall, despite the slight frustration (and a lot of cutting out paper squares) of the morning, today was a successful day in terms of functionality and design. We’re really moving forward with your prototype!

6/11/2015: Day 9
Today was a productive day. We worked on different marker functionality, so that each combination of four markers tapped on a bacteria creates a distinct plasmid combination for that bacteria. We also made infoboxes, both on top of the screen (visible at all times), and next to the bacteria (when it’s pulled up close). We also spent some time talking about the physical token that could be part of the exhibit, thinking about how to make markers fit nicely with each other in a single device.

6/12/2015: Day 10
We spent the morning developing another application to explore simulating wetlab actions, such as dragging things into flasks and petri dishes. We decided to just stick with a basic “pick a fruit flavor and ‘extract’ that gene” metaphor that lets users choose one of four fruits into a flask, then drag the flask to a petri dish, which would display an overlay letting the user know what DNA piece they need to insert into the physical plasmid token to get that gene. Of course, this is still very abstract high-level functionality that is just with testing purposes, but it was also nice to see how much quicker we’re getting in using the surface and the Cornerstone API after a couple of weeks. In the afternoon, we had another call with Anja and Romie (before they come visit on Monday!), just to show them the couple of prototypes we’ve developed since Tuesday. Since we decided we’re in a good place in terms of working with the MultiTaction, we spent the rest of the day brainstorming more concrete ideas about the exhibit and getting a more realistic and fleshed-out prototype.

6/15/2015: Day 11
Today was a busy day! Anja and Romie from the Tech Museum are visiting us for two days, and we’re spending most of those two days brainstorming ideas for the project. We had a Scientific Ethics training in the morning as part of the Summer Research program, but after that we got to work. Romie and Anja gave a brief overview of the other museum exhibits and what they would expect of the exhibit we develop. In the afternoon, we spent a lot of time brainstorming ideas for the project. We focused on the “storylines” and the “environment” part. The name BacPack was born, and we decided that the general story behind the exhibit would be that the visitors are scientists engineering bacteria to help explorers on different missions. We decided on three extreme environments/new frontiers: Mars (everyone’s favorite), the Deep Sea, and the Antarctic. We also started looking into BioBricks we could use for the digital exhibit; we each picked a topic to research for homework tonight.

6/16/2015: Day 12
In the morning we presented the results of the research we did last night, and made a list of all the BioBricks that could be helpful. We then spent time researching and talking about the conditions and resources available in each environment, and made a list of their “haves” and “needs”. In the afternoon, we created a simplified paper prototype of what we envisioned the exhibit to look like. We went through several iterations of brainstorming and changing the design, until we settle on a design that would split a single MultiTaction screen into two parts, and would allow each user to have their personal “workbench” space as well as a testing environment. Tomorrow, we are going to develop a more detailed prototype and test it with children on Thursday.

6/17/2015: Day 13
Most, if not all, of today was spent making a paper prototype and refining our design from yesterday. We spent some time deciding on the layout of the workspace, as well as the representation of the bacteria, and after that it was pretty much just cutting things out and gluing them together. I look forward to testing it tomorrow!

6/18/2015: Day 14
We finished our paper prototype in the morning, and Orit’s children came to visit us in the afternoon. They’re aged 6 and 9, so they’re the exact age of our target audience. They seemed to enjoy playing around with the prototype and understood the concept behind the project. We asked them to assess the difficulty level, and they said that it’s not “too easy or too difficult”.

6/19/2015: Day 15
The NEGEM Meetup was today! We took the train to Boston bright and early, and got there with a bit of time to spare so we met some of the other teams. The presentations were very interesting, and it was great to hear what the other teams are doing. I didn’t really understand all of the science, since all the other teams are working with actual BioBricks, but it was still nice to see the more technical details and the foundation of what we’re building. The time we spent on socializing and talking about collaboration with the other teams was also very helpful, as were the feedback forms they gave us. A lot of the teams suggested we make the protocol and procedures used in a wet lab a more prominent part of the software, which is an important aspect to consider.

6/22/2015: Day 16
We started work on the computer prototype today! We did the basic layout of the program, using sample images. We based everything on the paper prototype from last week, so the workflow was easy. So far, it’s going easier than expected; we haven’t run into any significant coding challenges, but we also haven’t started work on any of the functionality, so we’ll see how tomorrow goes.

6/23/2015: Day 17
Today was another day dedicated to programming. We started adding functionality and worked on marker recognition.

6/24/2015: Day 18
We spent the morning adding more functionality to the prototype. In the afternoon, we introduced a major change to the layout: now the entire screen is dedicated to only one user, with the workbench and the environment each taking up half of the screen respectively.

6/25/2015: Day 19
We continued working on the functionality. We have been feeling a bit uncertain with the current layout of the design, so in the afternoon we talked to Johanna and Orit, and discussed possible changes to the layout. We spent some time brainstorming alternative versions, to emphasize collaboration and to allow multiple users to share the screen. This was to be expected; and iterative design process inherently has the potential for minor or major changes as we go along. We will start exploring new layouts, and we will also start talking to graphic designers about the images we would like to include as part of the design.

6/26/2015: Day 20
Today was another day of brainstorming. Mike Horn came to the lab, and we discussed museum exhibits and children’s interaction. We also looked at some of the project that he has been working on, in order to discuss more design ideas and get inspiration. In the afternoon, we “tested’ the prototype of a game he is working on, which was a lot of fun (we did get quite competitive). We spent more time finalizing layouts and talking about possible designs. It all seems kind of uncertain right now, but I’m sure we’ll be able to come up with a solid new design in no time--we just have to narrow our ideas a bit further.

6/29/2015: Day 21
We spent time talking about the ideas we’d developed last week and discussing how each one promotes collaboration and learning. We have a pretty solid agreement on the general layout of the screen, but we are still undecided on how to incorporate the Environment or Collaboration areas. We have discussed the values of having each space on the screen, and the likelihood that users will use it. We started on a simple paper prototype, which helped narrow down our ideas a bit.

6/30/2015: Day 22
We finished the paper prototype and then Stephanie Houde came to the lab to talk to us about our design. She is an interaction designer and a Wellesley alumna, so it was very nice talking to her. She gave us some very useful and concrete feedback on our prototype, so we are narrowing down our ideas even further. By the end of the day, we actually had a very solid and finalized version of it.

7/1/2015: Day 23
Today was another busy day. Natalie came to give us feedback on our latest iteration. We also had a conversation about aspects of the scientific process that we would like to include in the digital component without making the interaction too overwhelming, and how the wet lab component can complement that experience. We also met with Casey to talk about potential art and design for BacPack, including backgrounds, overall theme, and color choices. At the end of the day, we had a redesigned version of our paper prototype.

7/2/2015: Day 24
We did some more work with the paper prototype today. We tested it with several users from the research program who had never seen it before, and incorporated their feedback into the design. We also went through a set of design cards with requirements for interactive exhibits by age group, and we wrote up how our exhibit design satisfies each of the requirements.

7/3/2015: Day 25
We had the day off today because of the holiday tomorrow!

7/6/2015: Day 26
We started working on the computer prototype. We now have a very solid idea of what the software will look like, so it is much easier to program to that end. A lot of the programming also depends on the visuals and animations, so we only have the basic motions and functionality so far.

7/7/2015: Day 27
Today we continued working on the prototype and the phrasing write-up of all the prompts and information in the application. In the afternoon, Casey visited the lab again and brought some of the sketches and mock-ups of their initial design ideas. We discussed the artwork we’ll need, and agreed that some of the animation will be crucial for getting the functionality down, so Casey will begin working on that in the next few days.

7/8/2015: Day 28
As part of the Summer Research program at Wellesley, we have to give a presentation on the research we are doing. Our presentation is scheduled for tomorrow, so we spent most of today working on that. We started building off of the NEGEM presentation we gave, but changed it accordingly so that we spent more time explaining the basic science behind our project, since oru disciplinary group is the Computer Science, Math, Astronomy, and Physics, and no one has much biology in their background. It was good practice to make sure that we can convey the basic concepts, and it was a lot of fun making our presentation more engaging and animated (literally, we added a whole bunch of nice transitions and animations on the slides).

7/9/2015: Day 29
Our presentation was at lunch today, so we spent most of the morning finishing it up. The presentation went fine; people asked a few questions afterwards. In the afternoon, Casey sent us some more of the design work they’ve done, so we incorporated the flask animation and the new background into our design. It is starting to actually look good now. I’m excited to continue working on it next week, since tomorrow we are going to the Science Museum!

7/10/2015: Day 30
Today was so much fun! We went to the Science Museum early in the morning, and got tickets to the “Science behind Pixar” exhibit as well as the Ice Age 4D screening. The Pixar exhibit was so, so inspiring and entertaining; we all pretty much left determined to work at Pixar one day. We also looked at the fish exhibit, which was a partial inspiration in the early stages of our work, and which we’d read several papers about, but it was so much better to see it in person. There were many exhibits that had components similar to ours, so it was helpful to see how they are integrated with the rest of the design. Overall, it was a very fun and educational visit!

7/13/2015: Day 31
We spent most of the day working on the prototype. We added the new animations that Casey sent in, and most of the functionality has been laid down with the most recent changes.

7/14/2015: Day 32
We spent a large part of today figuring out the math for the animation and widget response. Since the entire background is one widget (both the workbench and the environment area), we needed to define when a flask is dragged into Mars (and at what point it happens). We used the distance from the center of the Environment semicircle, which was simple enough for the two horizontal widgets. However, the two widgets on the side are rotated, so it took a while to figure out how the coordinate system work and how to get a flask’s absolute coordinates on the screen (as opposed to its coordinates in relation to its parent widget). We did figure it out eventually though, so that felt satisfying!

7/15/2015: Day 33
Today was another Math day! We spent most of the morning fixing the rotation of the flasks so that when they enter Mars, they’d turn to point towards its center (so that the bacteria exists towards it and not in some random direction). In the afternoon, the MIT App Inventor team came to visit us, and we had some time for demos and a presentation. We spent the rest of the time we had after that talking about the art we’ll need, and finalizing some of the designs we’ve been working on.

7/16/2015: Day 34
We got laser cutter training this morning! It was so much fun. We are probably going to be cutting out our tangibles next week (Casey’s been working on designing them), so it really feels like the project is coming together. Casey also sent us a lot of new animations and art, so we worked on incorporating those into our design.

7/17/2015: Day 35
Today was dedicated to getting ready for tomorrow’s collaboration meeting. The BU and MIT iGEM teams are coming to the lab on Saturday so that we can demo our prototype to them and run some user studies, and we are giving them feedback on their presentation and methods. We incorporated the image of a static status bar in the design, and added functionality that lets a group of bacteria appear on Mars when the flask empties. I hope tomorrow goes well!

7/20/2015: Day 36
Saturday was so much fun! We spent the morning testing our prototype and demoing other technology we have in the lab, and the BU and MIT teams gave us so much useful feedback. Hearing their presentations in the afternoon was also very interesting. Today, we are continuing working on the animation and the feel of the interface. We will be doing more user tests this week, so the prototype is really starting to come together.

7/21/2015: Day 37
We finished the functionality of the status bar today! It now updates dynamically so that resource level decrease at random intervals, and when users send bacteria to Mars, the appropriate resource level increases. At this point, we have practically all of the functionality, but we need to continue working on the design for testing it tomorrow.

7/22/2015: Day 38
We tested the prototype with three of the Outreach program interns who are at the science center this summer. We had the opportunity to change some things before we test it with the students from Upward Bound tomorrow. We added more informational messages on the side, which will hopefully make the interaction easier.

7/23/2015: Day 39
Today we tested with the students from Upward Bound. There was a total of almost 50 students, so we got to test with 10 groups of 3-5 students each. It was very informative to observe such large groups interact with the surface. Overall, we found that we need more informational messages, and many people liked the idea of having instructional videos to incorporate into the design.

7/24/2015: Day 40
We’re almost there! We continued working on the functionality and incorporating features the test users suggested. We decided to make the information on the side a tabbed panel split into several categories so we can display more information.

7/27/2015: Day 41
We got a lot done today. Casey sent us a lot of new art over the weekend, so we incorporated that into our design. Now the plasmids are color-coded based on their outputs. We also made the bacteria on Mars cluster around the resources they are using. We fixed the duplication bug we were having, and added a glowing outline to the changing status bars.

Vivien's Notebook

6/1/2015: Day 1
Today was the first day and I feel so overwhelmed (in the best way) and excited to be introduced to all of these new CS softwares and applications of CS in education. We began with a lab orientation, and then split off into our teams to begin brainstorming and training.
The iGEM team (Rachel, Sam, and I) started by researching iGEM medal requirements and gaining a deeper understanding of the iGEM competition. We had already done some prior research about the iGEM competition and previous Wellesley iGEM teams’ projects, but getting familiar with iGEM requirements made me begin to more fully grasp the great effort and time that would be put into these projects- but also made me all the more excited to be pursuing them.
We downloaded the software that we would be using (Cornerstone SDK) and spent the rest of the day exploring the provided examples and examining the different ways we could interact with the Widgets. I feel very excited and optimistic about the upcoming work.

6/2/2015: Day 2
Today we began work on our own example application! We created our own basic “Hello World”-level app that featured rectangles, which upon tapping specific ones, would duplicate below where your finger touched the screen. We started playing around with the shapes, and changed the rectangles to circles. The signature for creating circles seemed to be very simple and similar to drawing rectangles, but by examining the different parameters that each method took in, we became introduced to new concepts such as Nimble Vector2fs. As of now, we are trying to restrict the Widgets to the screen and prevent them from accidentally being pushed offscreen and becoming inaccessible.

6/3/2015: Day 3
After changing the Widget shapes to circles, we ultimately changed our main Widget shape to be an ellipse. This choice made us start to consider other ways that we can apply basic concepts of synthetic biology to our project, so we decided to have two forms of Widgets-- large white “E. Coli” and smaller, more colorful widgets that represent viruses. We hoped to display and share the concept of bacteria absorbing or “eating” a virus. Currently in our app, if a E.Coli and virus intersect, the E. Coli “eats” the virus and the virus appears within the E.Coli to represent its infection. When an infected E.Coli collides with a non-infected E.Coli, the second E.Coli displays the same virus to represent contamination. When you tap a virus, three new viruses are created to simulate the virus growing on its own. We are struggling with keeping the virus within the boundaries of the E.Coli parent widget, and working on inspecting the Widgets’ locations and reference points so that we can better understand how to work with them.

6/4/2015: Day 4
Today was a very successful day! We added movement to the Widgets so that when left unattended, the E.Coli and viruses float about on their own. The use of markers has also been incorporated, so that tapping a marker to the screen creates a new Bacteria. In addition, we managed to set boundaries around the screen to prevent the Widgets from going out of frame. Another exciting new addition is that the E.Coli now individually grow in size and once they reach a certain size, divide into two separate E.Coli. If the original E.Coli was infected with a virus, the new E.Coli will also display its infection. This process is accurate and true to the natural E.Coli growth and division process. Our next step is hopefully to keep the Widgets from overlapping and to eventually make them bounce off of one another upon intersection.

6/5/2015: Day 5
We have started programming specific actions for specific markers-- now, one marker creates a new Bacteria, one removes that specific Bacteria, and one displays the bacteria’s infection status with a simple attached textbox that states “Infected” or “Not infected”. We have also introduced ImageWidgets into our app so that we can have custom images deployed onto our app. We have only just started to realize the vast number of directions that this app/exhibit can go in and the many different concepts it can teach, and this textbox that will share the bacteria’s status is a great example of the different possibilities we can teach and display. For our next steps, we want to program the widgets to bounce off of another, and eventually try introducing video and text to the screen that can play and display independently.

6/8/2015: Day 6
Today Natalie Kuldell stopped by the lab and led a few discussions about presenting and teaching synthetic biology as well as the complexities and controversies surrounding the topic. It was quite a wonderful experience-- I definitely admire a lot of the work Natalie has done- teaching and developing curriculum at multiple undergraduate institutes, founding BioBuilder Educational Foundation (a non-profit that teaches biology/synthetic biology topics online, making this knowledge widely available and accessible), working as a visiting scientist in labs… she clearly communicated her deep understanding of teaching and interacting with others and the greater implications and questions of synthetic biology.
We began our day with a short presentation by Natalie where she defined the study of synthetic biology and, upon learning that most of the team-members had more of a computer science background than biology background, began introducing these biological concepts as forms of coding. She also explained the link between biology and engineering by passing out small educational kits comprised of mini-breadboards, wires, batteries, LED lights, and more where we could explore how biology functions to create its own “hardware”. She then gave us a brief but very interesting lecture on the actual science behind how genes are expressed. I understand that our exhibit will probably focus on the user being able to “make and tinker” than on the actual science, but it is still helpful for us to better understand what we may eventually represent and display. I loved hearing Natalie teach-- she is very present and energetic.
We then went on to discuss some of the most famous synthetic biology experiments and previous iGEM submissions such as bacterial photography, E. chromi, Eau that Smell, Colorful World, etc.
Throughout the day, Natalie kept giving tips of what to keep in mind when designing a museum exhibit- such as taking into account the convenience of recovering/restoring materials (both accessibility and in monetary value), considering the attention span of the museum-goers, understandability (e.g. would a facilitator or written instructions be needed?), and how concrete or abstract the concepts that we would eventually teach would be. Each point was definitely helpful, and something that I had not fully considered at that time. This has been true during this summer research program thus far, as well as through previous years of experience-- but the more that I learn, the more I realize how little I actually understand in the world. However, I only feel that much more energized and excited to fill in the gaps and pursue what I don’t know. Today was a very full day-- we learned a lot of hard biology, we chatted about how museum-goers would experience our product, we discussed how to bring up this sensitive topic… I feel optimistic and ready to move forward tomorrow and the rest of the summer!

6/9/2015: Day 7
Today was an intense session of brainstorming. We spent the morning coming up with three separate, very different possible museum exhibit ideas and designs to show Romie and Anja during our Skype call at 2:30. Our current ideas are affectionately titled “BacMan”, “BacFarm”, and “Bac to Mars”, and I’m excited to pursue work on any of them!
During the call, they were both very pleasant and seem very committed to cultivating a creative space where museum-goers can learn in novel ways, and I’m definitely excited to work closer with them over the next few months. We left the Skype call with the intention of beginning to pursue one of the ideas (probably the Mars exhibition, affectionately titled Bac to Mars) with the more specific technical goal of furthering our understanding of Cornerstone markers-- figuring out how to get the screen to recognize multiple and respond differently to a set. By then, we were pretty worn out from a day of such brainstorming and creative thinking, so we spent the last hour helping transcribe interviews gathering information for another project happening in the HCI lab. I’m looking forward to coming in tomorrow and tackling markers.

6/10/2015: Day 8
We began the day with the goal of further exploring and understanding the Cornerstone Marker documentation. We were able to program our app to detect and act if two markers touched the screen at the same time, but discovered that the app was inconsistent when identifying individual marker codes. As the markers that the lab already had were a little worn out and folded on the corners, we decided to try printing out new markers and fiddle around to see the smallest marker that the app could still accurately detect. Using the MarkerFactory application, we created, saved, and printed new markers of varying sizes to test against the app.
We created the smallest markers that could still be detected on the screen, and then began incorporating them into the app.

6/11/2015: Day 9
Today we simplified our code to match the “Bac to Mars” idea that we had shared with Romie and Anja. Now, the starting screen appears with five bacteria with “empty” plasmids. When you click on the bacteria, it increases in size and a text box appears with information about the bacteria. Once you tap on the bacteria with four different markers, a new plasmid pops up of four different colors based on what markers you used to tap. The text-box then pops up, listing the markers’ codes of the colors within the plasmid.
We also brainstormed possible plasmid token/physical representation ideas-- as of now, we are thinking of some large, donut-shaped object with spots for physical representations of different genes to fit in, like a puzzle.
We then hit a few dead ends in terms of technical stuff-- the screen sometimes has trouble recognizing the markers correctly/at all, which can be problematic in the future when the users are creating their customized plasmids. In addition, we wanted to incorporate a TextEditWidget where a keyboard appears on screen and users are able to name their own bacteria, but for some reason the interface crashes upon inspection. We sent a few questions to one of the Cornerstone engineers and are eagerly awaiting his response so we can proceed!

6/12/2015: Day 10
We had a very productive morning creating another possible interface, that allows users to choose the gene that they want to insert into their plasmid-- we began with a fun “flavor” example. Users can drag a fruit representing their favorite flavor into a flask, which represents extracting a flavor-gene from the fruit and eventually showing it as a physical object that the user can place into their plasmid.
We then had a quick Google Hangout check-in with Romie and Anja to show them the two applications. They seemed pleased, and I’m definitely excited to meet with them in person on Monday!

6/15/2015: Day 11
We began today with an ethics workshop where we discussed the fundamental guidelines and foundations of ethics in scientific experiments. The lecture was mainly focused on plagiarism- its definition, its use with or without the intent to deceive, the amount of previous knowledge that people enter college/grad school with, and its consequences. We also had a conversation about ownership, and it was just a very odd concept to me that upon submitting an article to a journal, the journal now owns those words and you cannot re-use your own words without asking for permission. Overall, this was quite an interesting workshop-- all throughout elementary school and middle school I’ve heard “Don’t plagiarize! Or else…” but I’ve never had a very full understanding of what fits into that definition and the possible repercussions. It was definitely a useful time.
We then had a large, collaborative brainstorming and sharing session with Romie and Anja. Both the Wellesley-side and The Tech-side shared our available resources-- we introduced them to the educational tools and technology we have in the HCI lab, and they shared the current and future exhibits that they are working on as well as the technology that are available alongside those exhibits. It was very exciting to see what The Tech is working on and the educational concepts that they want to teach, and there were definitely moments where they shared hopeful ideas (such as representing bacterial growth and development) and I thought, “We can definitely program that!” I’m glad that we had the first two weeks to tinker around and further understand Cornerstone.
Tonight, we’ve all been assigned to find possible biobricks that can be applied in our project from the Registry of Standard Biological Parts. Finding these biobricks requires going through previous iGEM projects which is absolutely fascinating-- I’m so amazed at the incredible creativity and scientific ability of some of the teams! Looking forward to returning to the lab tomorrow to share my findings and hear about what others discovered.

6/16/2015: Day 12
This morning we all shared the individual research we had done last evening and took inventory of all of the biobricks we had discovered. Afterwards, we continued to brainstorm and flesh out possible ideas. We finalized Mars, Deep Sea (Cave), and Antarctica as locations for our users to explore, and then moved on to brainstorm possible storylines and discuss what expectations the users approach the exhibit with. I am learning that there are so many other things to consider and discuss outside of just the software/back-end-- we’re doing so much more than just coding, which I’m glad about- I love this design and brainstorming bit and I want to learn more about what has to go about for an entire exhibit to come together.
Now set in the storyline of creating bacteria that can help the user survive Mars, the deep sea, and Antarctica, we began furthering our ideas of the actual interface on a MultiTaction. Romie and Anja presented us with a paper prototype they had used for a separate museum exhibit to give us an idea of the look and function of a paper prototype. We then started created our own paper prototypes-- we sat on the ground, crowded around a single piece of paper, discussing and sketching, and the entire time I just felt my heart was rising up in excitement. I’m very interested in education and teaching STEM subjects from a young age, and creating an interface introducing synthetic biology that is tailored to be accessible and understandable for young children merges all of these dreams. The experience was even better because I was around really passionate, intelligent, down-to-earth people all just as committed to making this project the best it could be.
From now until Friday, our team has to actually create a paper prototype, test it on some young children (probably Orit’s kids!), start actually programming the back-end, and come up with a presentation to share our project at the iGEM meetup this Friday. Wow. This all sounds like a lot, but I am also thinking of previous times/projects where it seemed like I could not possibly get everything done and it all worked out-- and now, I am working with a very dedicated and lovely team, so I know we will work it out. I plan on going to bed early tonight and coming in fresh and rejuvenated tomorrow morning!

6/17/2015: Day 13
Today we focused on creating our paper prototyping. Even though right now, it doesn’t look like much, actually creating the prototype initiated a lot of conversations and discussions. We had to chat about many aspects of how our application would run that we hadn’t considered before. It was my first experience creating a paper prototype, and I really enjoyed it! Looking forward to introducing it to Orit’s kids tomorrow.

6/18/2015: Day 14
Today was a busy day! We worked all morning on finishing up our prototype to show Orit’s kids Ben and Daniel. Once they came in, we ran through a couple of test scenarios on paper.
They were both very engaged and interested in the prototype, and also had some great feedback and ideas, including incorporating videoclips onto the screen and making the “Challenges” more difficult. We will definitely incorporate some of these into our project! It was very exciting to see people actually interact with what we had made so far-- I couldn’t wait to hear their feedback and see how they responded.

6/19/2015: Day 15
Today's NEGEM meet up went (surprisingly) well! Our presentations were very well received by the other iGEM teams-- we definitely stood out as a team competing on the community lab track and thus focusing on making synthetic biology more accessible and educating others about general synbio concepts rather than actually doing the science. A majority of the other undergrads participating in iGEM are studying a form of biology-- synthetic biology, computational biology, biochemistry-- which made me a little nervous about presenting our project, but people were actually very interested and curious about our software and the technology we were using.
Later in the day there was an hour allotted for all attendees to discuss their current progress, next steps, and possible collaborations in a smaller group. There (and in our evaluation forms!) we got some excellent feedback for making the science more accurate. I especially enjoyed chatting with some members from the MIT and BU iGEM teams who made suggestions on certain key aspects of the scientific process to include in our program. I have so much respect for these students who are so learned in synthetic biology and spoke to us with so much patience and willingness to help.
Traci Haddock brought up a very good point that we are in Boston, the hub of synthetic biology-- besides just doing our user testings on young kids to see how they respond, we should also reach out to some experts in the field to gauge how accurate the science is, how well they think that process is portrayed, etc. I think that the HCI lab has many possible contacts who would be happy to help out, from trained professionals to members of other iGEM teams!
Overall, today was really wonderful! Looking forward to incorporating some of these ideas on Monday!

6/22/2015: Day 16
Today we began programming the basic layout of the widgets and planning everything out in the most effective way. As we begin today, I understand the true importance of making a paper prototype before actually programming so we can all be on the same page of how features will work and the software’s layout.

6/23/2015: Day 17
Today we finalized the basic layout and made certain features (such as the scanner) functional, but the software is still having trouble with marker recognition. We reprinted out markers and attached them to new vessels with which to use them, but it’s still a bit funky. We’ll come back and try again tomorrow!

6/24/2015: Day 18
We finished most of the basic functionality today. In the afternoon, we were informed that due to the way that the MultiTaction screens are set up at The Tech, we cannot use the set up that we had had of two “scenes” on one screen. We began re-designing, and continued on functionality.

6/25/2015: Day 19
Today, we checked in with Orit and discussed our next few steps- we’ve been working on functionality, but now we are beginning to see more of a need for an alternative design that is more collaboration-focused. We continued to brainstorm possible designs.

6/26/2015: Day 20
We spent the morning going over our designs and listening pros and cons of each, and then after lunch we met Mike Horn, an assistant professor at Northwestern and the director of Northwestern’s TIDAL (Tangible Interaction Design and Learning) lab. He showed us some of the projects that TIDAL is working on and it was so incredibly exciting to see the ways his lab applies computational thinking and computer science to education. He also shared some helpful literature with us, including Thomas Humphrey’s Fostering Active Prolonged Engagement, which was very interesting to read and very applicable to what we’re working on. Today was such an exciting day.

6/29/2015: Day 21
We devoted all of today to brainstorming and creating a new paper prototype! A busy day.

6/30/2015: Day 22
Today we finished the paper prototype and chatted with Stephanie Houde, a Wellesley grad with a lot of graphic design experience. She shared a lot of tips, including taking photos of each step and how to consider animations that inform the user how to proceed, including exaggeration and “amping up” to introduce movement/animation about to occur.

7/1/2015: Day 23
What a big day! Natalie stopped by to see how we were doing. It had been a month since we’d seen her, so obviously things had progressed quite a bit- since then, we had (for the most part) finalized our concept, goals to teach, design layout, and paper prototype. She gave a lot of helpful feedback, especially on the actual scientific accuracy. We had an interesting conversation about what aspects of the scientific process we would have in the software side (without being too complex and confusing for users!) and what we would have in the actual wetlab component.
We also looked at possible artistic designs with Casey. It was great to walk through the paper prototype with them since they have had so much experience with iGEM. It’s exciting to know that actual designs are on their way!
Finally after Natalie and Casey’s feedback, we had a new version of our paper prototype! We created a video for Romie and Anja to keep us updated.
The lab had a few other new people today as well-- two high school interns arrived today! Since both have had some C++ experience, over the next few weeks they’ll be playing around with Cornerstone as well and creating their own apps.

7/2/2015: Day 24
Today we examined the suggestions given by the lab’s design cards and jotted down how our project fulfills each requirement. We also created a document to note our official phrasing and write-ups for the prototype/project. Finally, we conducted a few user studies with some other Wellesley students who had little background knowledge of how we’d prepared the
Tomorrow we’ll work on: finalize among us phrasing and consider design possibilities

7/6/2015: Day 25
We’re continuing to work towards fulfilling basic functionality of our software, and planning a meetup with the BU and MIT iGEM teams! I’m so excited for the chance to meet with two other teams and to share ideas and feedback. Tomorrow we’ll be meeting with Casey, a recent Wellesley grad who has participated in many previous iGEM competitions, to discuss artwork and designs for the final project!

7/7/2015: Day 26
Today, Casey came in and showed us their notebook and concept art thus far-- everything looks so incredible, and having a lot of potential! It’s very helpful that they’re familiar with iGEM and designing for clients, but they also have a great designer’s eye and are so artistic.

7/8/2015: Day 27
Today we continued to work on our presentation, and work on adding functionality & incorporating.

7/9/2015: Day 28
Today we gave our presentation at the student talks-- it overall went very well! People were definitely very interested in actually getting to know what projects we are working on in the lab and it was exciting on our end to be able to share how the project has changed over various iterations of brainstorming, designing, and redesigning. Preparing for this presentation has also been a great opportunity to put into words the process and ideas and concepts that we’ve been using this summer, which will come in handy for our actual iGEM presentation and for writing future articles and such.

7/10/2015: Day 29
Our lab took the day off to visit the Museum of Science’s special exhibit on Pixar! It was an incredible experience and an opportunity to see the incredible amount of math and physics that goes on behind the scenes to add lights, flesh out characters, design a set, and create the world in a Pixar film.

7/13/2015: Day 30
Today we continued to incorporate Casey’s artwork into our project-- the beautifully designed pieces add so much to our program experience! We also worked on our project description, looked into more iGEM requirements, and discussed possibly meeting with Wellesley’s science center machinist, Larry, to work with the laser cutter to create our tangibles!

7/14/2015: Day 31
We’re still working on the functionality -- today we specifically looked at the tracking of coordinates and math to tell the flasks when they’re “on Mars”. We determined the background image’s points, at what coordinates Mars began, ended, and the length of its radius. We then checked the points of the flasks, and calculated the distance of the flask from Mars’ “midpoint”-- if its distance was less than the length of Mars’ radius, we programmed the animation to display deploying the bacteria to Mars. This ended up being trickier than expected because the Widgets displaying the petri dishes on the two sides are rotated, and thus their X and Y values are flipped. Furthermore, each Widget is a child Widget of a larger Widget, and their coordinates are relative to their Parent Widget. Figuring out the absolute locations of the Widgets and thus calculating their distances took some time, but we finally got it!

7/15/2015: Day 32
Today we built off of the victory of yesterday and programmed the flasks to rotate in the direction of Mars’ center to create the illusion that the flasks deploy the bacteria onto Mars. We checked in with our PI, sent out an updated list of designs and artistic things needed to Casey, and scheduled a meeting with Larry to receive laser cutter training. Then, the HCI lab met with the MIT App Inventor team and showed them some demos of the research we were working on. It was very exciting to meet everyone on the team and learn about their very cool work (and some of their ties with iGEM!)

7/16/2015: Day 33
This morning we had our training with Larry on laser cutting basics-- it was so exciting to be in the machine shop and see all of the machinery at work. We made a simple “Hello World”-esque plaque for Johanna, and explored the other things and opportunities in the shop! Casey also sent us a lot of beautiful artwork and designs that we incorporated-- very exciting :)

7/17/2015: Day 34
Today we’ve been doing our best to pull everything together and have the best possible prototype for when the BU and MIT iGEM teams come visit us tomorrow! We’re also discussing next steps to take!

7/20/2015: Day 35
Today we reflected on how the BU/MIT iGEM teams’ comments and made some adjustments to our project accordingly. In particular, people wanted specific instructions at every step of the process, so we created “bubble instructions” and contact Casey to ask for a template of message images and icons. We also continued to look into creating the tangibles, including contacting Larry about materials and googling pros and cons of different materials and where to order them from.

7/21/2015: Day 36
Today we continued discussing how to obtain different materials with Larry, added status bar functionality, and generally prepped for prototyping-- tomorrow, three high school interns will be coming to our lab to try out the project. I am very excited to see how people interact with it and how they feel, especially since I couldn’t attend the BU/MIT meet up!
In the afternoon, Lauren, Lily and I headed over to the Museum of Science for their Building with Biology Event training. Building with Biology is an event for scientists and the public to have open conversations about the synthetic biology field and its applications, and clear up public misconceptions. It’s exciting to be helping out at this event and continue working on public perceptions of synthetic biology. There are a lot of prominent synthetic biologists presenting at the event, including Natalie Kuldell!

7/22/2015: Day 37
Casey sent us the art for message templates-- a way for us to communicate with the user what their next step is! We created the bubble-like messages and added them to the screen, we feel excited and ready to be testing with some high school interns at noon!
When the interns came in to play around with our exhibit, they were definitely excited by the premise and platform of the project-- they liked making different combinations of genes, but without the animation of the plasmid entering the bacteria they found it difficult to understand the actual scientific process that the tangibles represented. Will be making changes to make this process more transparent.

7/23/2015: Day 38
We spent this morning focused on debugging, and figured out how to make the marker recognition more consistent and reliable.
Today was a big day in terms of user testing-- the MIT/Wellesley Upward Bound program of fifty high school students visited our lab and interacted with our prototype in groups of four or five. It was a wonderful experience-- it was very helpful to see how people first approached the exhibit and what questions they had along the way. We learned that we definitely need more explicit instructions and labeling of items on the screen, and also discovered a bunch of new bugs that had never showed up before!
With learning all of this new information and finishing the last week before the poster session and when we leave, we are realizing how much work there still is! It’s really crunch time: we listed everything left to do and divided it over the last days of work. We’re ready to come in tomorrow fresh and ready to redesign.

7/24/2015: Day 39
Hello! This is crunch week, and we’re ready to go. Today we finished our research abstracts- a general one, and one targeted for a more scientific audience-- both of which are required as part of our summer spent doing research at Wellesley. We also have decided to incorporate videos into our exhibit, and so we’ve asked the interns to find some informational and educational videos about synthetic biology and the cell duplication process.
We also confirmed an appointment with Larry to go down to the machinery and cut the tangibles out. Our materials arrived, and we’re looking forward to meeting with Larry to cut next Wednesday!
In the afternoon, we updated the “reset” functionality so that the petri dishes fully reset when the user clicks the “Reset” button-- previous there were some bugs that included the bacteria and other buttons still appearing when they should have been removed from the screen.

7/27/2015: Day 40
Over the weekend, Casey sent us some beautiful art files. When we came in today, we immediately updated everything that they had sent us-- their art makes our work look so much better and makes the exhibit so much easier to understand! For example, they’ve sent us a glowing flask and animations of a plasmid entering a bacteria, which greatly help users understand how to proceed and what their actions are representing. Other art changes include a glowing animation around status bars which draws attention to the change due to the user’s work. We also finished the logic for programming the bacteria to go to a certain part of Mars depending on their “Have” or “If”, and fixed a bug that was displaying the wrong animation at certain points. Looking forward to continuing to work tomorrow!

7/28/2015: Day 41
We stayed late today to finish our exhibit!!! Yay!!! This included creating and adding information messages, sending Larry our tangible files to prepare for laser cutting tomorrow (!), researching and adding additional scientific background for each gene, incorporating the rest of Casey’s animations, making editing when the status bars flicker, and adding videos to the project. I love how it looks, and I’m so proud of how far this exhibit has come.

7/29/2015: Day 42
This morning we met with Larry to laser cut our tangibles! It was such an exciting process to see them being made and have the physical parts present. We created a video of the current prototype for Romie and Anja, and then focused most of our day on building our poster. It is very visual and colorful, and I love it!

7/30/2015: Day 43
Today was poster session day!! We started the day off by printing our beautiful poster and finishing up details with the tangibles, practiced our presentations, and went down to the science library to present!
I felt very excited and proud to show what we had worked so hard on to create. The Multitaction itself drew many interested attendees, and we were swamped with people asking questions and asking to test it out. The best part was having some younger attendees (probably age 7 - 9) playing with it-- they were enthralled! They kept making different combinations of genes and trying to provide resources to Mars to fill the resource status bars. Most of our prototype testing had been with an older audience, so it was very relieving and exciting to see how captivated the younger audience was.

Christina's Notebook

Brainstorming with Romie and Anja
Today Romie and Anja came to help us brainstorm ideas for our iGEM project. All of us worked together to come up with ideas that would be able to be converted into a museum exhibit. The energy in the lab was truly amazing and we all really gave all that we had. It was one of the precious times in the lab where everyone was working together on the exact same thing and was 100% focused. We also turned all the lab walls into brainstorming space, sticking post-its with ideas on the walls and writing around them to group them together. It was also very interesting to see what other people were coming up with. It also felt like coming up with science fiction ideas that could be made into reality. My favorite things being mentioned involved changing elements in food to make them better and easier for consumption.

NEGEM
Today was the New England GEM meeting (NEGEM). All teams from the New England area came together at Boston University, where we all presented our ideas for what our iGEM project would be. The atmosphere in the room was amazing and it was really interesting to see what other teams were working on. It was also very informative since I was coming from a computer science perspective when everyone else was on syn-bio track. It was also a very good way to get feedback from other teams on our ideas and our progress. We also were able to find teams to collaborate with, which will be very useful for our progress. In general, it was a great experience and very educational one. I am looking forward to more meetings until the competition and our collaboration with the BU and MIT teams.

BU/MIT Meetup
Today we came into the lab on a Saturday to meet up with the BU and MIT teams to show them our work and to view theirs. It all had a really good time and it was very useful to receive feedback for our project. Both of the other teams are on the syn-bio track so they had very different projects than the one we are working on. In addition, the feedback that we got was unique since it was coming from a completely different perspective. I also really appreciated the atmosphere in the lab where people from different backgrounds got to play around with all the different gadgets that we have. In general, I think that it was a great experience for all parties involved and that we all got very informative feedback that we integrated into our projects.

Jasmine's Notebook

Brainstorming with Romie and Anja
Prior to today the lab had tossed around some general ideas as to what our iGem project was going to be, but Romi and Anja's visit marks our first real brainstorming session. Since we're creating an interactive exhibit for The Tech Museum of Innovation in California, it's important that we got a chance to speak to both of them since they will be the exhibit's curators. This brainstorming session was one of the few times everyone in the lab was together working on the same project. As a group we managed to come up with and finalize a direction to take our project in. I'm really looking forward to our final project and think museum visitors will be enticed to give it a go!

NEGEM
I was able to attend NEGEM, a meetup of all the iGem teams in the New England area, last year and was looking forward to going again this year. It was fun seeing the new faces and hearing about the projects local teams have decided to tackle. NEGEM is held at Boston University. In addition to having lunch together, all the teams in attendance are given 20 minutes to present and receive feedback on their projects. Wellesley brought in the only team that didn't have any biology or chemistry major members, but despite that we were able to give some solid feedback on the other presentations. In addition to getting good feedback on our own iGem project, we were also able to find collaborators (Boston University and MIT). Once everyone has had a time to come back together and reflect on what was said during NEGEM, we'll start setting up a day to meet with BU and MIT later in the summer.

BU/MIT Team Meet Up at Wellesley
We don't normally have to come into the lab on Saturdays, but today it was necessary so we could meet up with BU and MIT. We started the day with tours of the HCI Lab and Wellesley's Science Center and then got to business listening to short presentations everyone had prepared. Since there are no biologists in the HCI lab, presenting to us was a good opportunity for the BU and MIT teams to check if their presentations and projects were understandable to a less knowledgeable audience. Similarly, the Wellesley team got a chance to see if our interactive exhibit and digital interpretation of synthetic biology stayed true to its roots. I think everyone came away from this meetup with some important things to think about (one of the things we have to look at is making interactions more intuitive) and look forward to seeing what comes of it.

Lily's Notebook

NEGEM
We headed to Boston University today for our first official NEGEM meeting. I will admit it was a little nerve racking to be in a room full of biology-focused science students, after all that is what the iGEM competition is about. It was a bit intimidating hearing a lot of the presentations before us because of our lab’s computer science background and limited exposure to biology prior to this summer. However the twenty minute Q&A helped with understand much more than I want to admit.I thought that because we were doing the “community track” we wouldn’t have anything to contribute to these other students. After we presented our project I felt so much more at ease. People came up to us and asked questions and seemed to be genuinely interested in what we were doing. A lot of people commended us on doing something different and thought it was really cool. After all the presentations and question periods, we broke into groups to discuss these worksheets to help us engage each other about our opinions and research and it was really nice hearing from so many different people and their different lab experiences across universities.

BU/MIT meetup
Today we had the Boston University and MIT’s iGEM teams come to our lab today to collaborate and share our iGEM presentations and work. I had a lot of fun getting to know the students from other schools. We got to use them as test subjects or rather perform user studies on them as they tried our our iGEM multi-touch program and also helped test other projects going on in the lab. This meetup was our lab’s first time showing it and having our project tested so it was a little bit like a milestones in our progress. We got some great feedback on ways to improve, likes and dislikes of the projects. It was great to get insight on different types It was extremely valuable to have the time to get to know our peers in this competition as competitors and on a personal level. We got down to business the first half of the day, full of presenting our respective power points and brainstorming ways for each other’s team to enhance their research and asking questions. Our lunch break was my favorite part of the day because we played Catch-a-phrase, and I guess when you have a bunch of driven college students in one room it can get a little crazy. It was competitive and fun and really helped us get to know the other teams.

Upward Bound Testing
Today was a hectic day in the lab. We had the pleasure of hosting the Upward bound group to at the lab for a few hours. Getting to show people all the awesome things in the lab is always fun so it was especially great to be able to share that experience with high school students who were excited to learn more about our lab. Everyone in the lab was in charge of a different “station”, and I got to work with the Leap Motion. In addition to technology like the Leap Motion and Oculus, it was great for these students to see the Multi-touch device and fiddle around with our iGEM prototype which was very helpful to see how a removed party interacted with it. The lab was buzzing with questions and my fellow co-workers explaining their various technology they were stationed at. Even though we all were pretty winded after standing up for a few hours straight opposed to working around the multi-touch and noses buried in computers, it was a blast and a great change of pace.

Melissa's Notebook

Today was my first day working in the Wellesley HCI lab. This summer I am working with the iGEM team on their competition project. From what I can understand they are working on creating a program that will teach synthetic biology concepts to children through a multitaction cell. As of today, the design is in its planning stages. However, we are getting close to what will be the final design, which is very exciting! I am looking forward to spending the summer working with Sam, Vivien, and Rachel. I hope to learn as much as I can from them. Hopefully they can help me with learning some coding skills over the course of my time here at Wellesley. I can already tell this will be a great summer with the enthusiasm and positive energy that I felt in the lab today.

Today the upward bound kids came to help us test run our prototype. Upward Bound is a summer program that 9-12 grade students take part in on Wellesley's campus. It was interesting to see how they interacted with our prototype. I saw the full range of what someone felt coming up to the multitaction. Some were hesitant to touch it at first while others were excited to run up and start playing. This also helped is with the design process of our prototype. Without this user test, we would not have found some flaws that occurred within our program. For example, a few of the users suggested after interacting with the program that it might be more helpful if there were some more written instructions for them to read as they went along creating their bacteria. Another huge part that they helped us with was allowing us to see how different users worked with the tangibles that we provided them with. Some were not sure what at all to do with them, while others got it right away and were able to get the relation that we tried to convey through the common images on the screen. From that observation, it allowed us to know to add a statement in the instructions for the user on the screen about the tangible element. Currently, our tangibles are still cardboard cutouts. However, shortly we will be laser cutting acrylic to make new tangibles for the final product which is very exciting. But, that also means that things are starting to wrap up for the summer which means that we are so close to what will be the final version of our program.

Today was my last day here in the HCI lab for the summer. Looking back, I realize just how much I learned. Besides gaining some coding languages and skills, I learned a lot about the human component of programming. I learned that you need to think about how someone would try to interact with your program with no knowledge of what to do. As I finish this summer my main goal is to keep learning more coding languages. Also, I am looking forward to rejoining the team in September for the competition. I am excited and thankful to be able to experience this unique opportunity. This summer, the HCI lab and the iGEM team helped to give me a look into what is possible in the computer sciences and what I could do going into the future. I now have a slightly more concentrated view of what I want to do in college and possibly as a profession. Overall, this summer was one never to forget.

Nicole's Notebook

Tuesday, 6/30 -
Today was my first day at Wellesley College. The other interns and I first went to the large open area in the science building to talk about our internship requirements and other housekeeping information. Soon after we arrived our mentors joined us and took us back to the labs for a brief tour. My mentors Sam and Christina showed me the HCI lab and gave me an introduction to the projects the lab was working on. I learned about the PGHCI project and the iGEM project.

Tuesday, 7/7 -
I started working on learning Javascript and html using Codecademy. Also, I helped the PGHCI team by giving them input on how I would organize certain health conditions into categories. This helped the team decide how to sort the diseases and conditions to make it easier for users to understand their genomic information.

Tuesday, 7/21-
I continued to work on learning Javascript on Codecademy. I later helped the iGEM team research biobricks to use in their project, which was creating an interactive museum exhibit to help non-expert museum patrons understand synthetic biology concepts. The biobricks we researched were ones which could be used in bacteria on mars to create a more hospitable environment for human explorers.

Priyanka's Notebook

Throughout the month of July, I worked with the iGEM team and the other two interns, Nicole and Melissa, on the BacPack for New Frontiers project, an interactive display in which bacteria use available resources in extreme environments to make products important for human survival in those areas. For example, on Mars, resources include carbon dioxide, solar energy, soil, ice, and waste, which can be used to make oxygen, water, food, heat, and fuel. One of the tasks that we completed make the project easier to understand for younger students, we came up with simplified definitions for each resource and its use. In addition, we researched basic concepts related to the project such as the definitions of genes, bacterial reproduction, and bacterial colonies.

The third week, some interns from other labs came and tried the interactive display, and we observed them. Their feedback was useful in figuring out which aspects of the project can be improved upon, so that the display is more user-friendly. In addition, in order to explain synthetic biology, we helped add a video with subtitles to the display.

Throughout our time at the HCI lab, we learned JavaScript so that we could understand the code behind the project better. We also experimented with various virtual reality tools, so that we could learn about the kinds of feats that the HCI field can accomplish.

Team:Wellesley TheTech/Team/Notebooks