Team:Wellesley HCI/Notebook/SiruiNotebook

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Kathy's Notebook

Week of June 4th

• Monday, 6/4: Jumping right back into research, after so much background readings over the weekend! Today we went to the Microsoft Research Cambridge to get a tutorial of Windows 8. It was particularly interesting because I hadn't had contact with C# nor Visual Basic before, but only got a crash course on it this morning. The new UI was especially interesting, especially the new metro-apps style and the start menu style change. There were also a couple of new gestures that were used with the tablet, such as swiping to corners or gesture-based log-in, that were particularly interesting. It would be great if we could take all these innovations and put them in the ELN design as well.

Metro-styled apps in Windows 8

• Tuesday, 6/5: Today the Wellesley team went to MIT for a basic wet-lab training with Prof. Natalie Kuldell, who used to teach Genetics/BISC 219 labs at Wellesley. Those unfamiliar with synthetic biology received an introduction to the field, and we watched a videotaped presentation from the MIT '06 iGEM team, to gain a better understanding of how the iGEM competition format worked. Also, we were given an extensive introduction to what is expected in the human practices portion of the iGEM competition, and another introduction on doing interdisciplinary research (the different perspectives between engineers and lab scientists).
• Even better, after that we were able to participate in two different basic wet labs, one that is based on the Eau d'Coli lab, and another lab in creating beta-galactosidase assays. My lab partner, Consuelo, and I both realized that the experience was immensely valuable and incredibly eye-opening.
• We both agreed that several factors led to efficient completion of an experiment: labelling, following instructions, and communicating. We ran into problem again and again when we repeatedly mislabeled the tubes and confused our reagents, forcing us to restart repeated. We also found it at times challenging to follow the instructions in the format they were written in, simply because while reactions were happening we didn't have time to both read multiple paragraphs and pipette every 15 seconds. The wet-lab experience was eye-opening, and made us realize if the ELN is to be implemented that several features, such as highlighting, and labeling tools, among many others, needed to be added.

Wendy and Nicole working hard in the wetlab!

Casey and Linda working hard in the lab too!

• Wednesday, 6/6: Today my group- Kara, Nahum, and I- started working on a powerpoint presentation in preparation for the brainstorming meeting with Orit tomorrow. We are working on researching past research in development of ELNs, and dividing up functions based on modality. Casey and I are also looking up research related to microinteractions that can be performed on the beast. We are particularly interested in Sifteo cubes and PaperLens.
• Thursday, 6/7: Today we had a meeting with Orit on things we learned about the ELN, and presented to her in a format of a Powerpoint. Since this is a preview of things we will be presenting about on Monday, the meeting was rather short. Orit suggested that we focus more on things having to do with troubleshooting, and features that can be added to the ELN that deal with visualizing troubleshooting in the lab.
• Friday, 6/8: Casey and I had a meeting with Orit today about microinteractions. Orit suggested that we look more into sifteo cubes as it might be used in the art project for the future, and that we should also focus on interactions that can be done on the bezel. A lot of the research that we thought weren't "feasible" might actually be more realistic than we previously thought- the beauty of HCI!

Week of June 12th

Brainstorming week!! Powerpoints, what we are thinking about....

Nahum and I are brainstorming features for the ELN.

• Monday, 6/12: Visited BU today and finally met the wetlab members, Shawn and Monique. Did a presentation on the basics of HCI, and also did brainstorming for the development of the ELN. Also, we got a crashcourse on topics in biology to be covered this summer in the lab, as well as the MoClo method, which will be the main focus of the wetlab team this summer, as they will be using it to characterize parts.

First meeting of the Wellesley and BU 2012 iGEM teams.

• Tuesday, 6/13: Brainstorming day #1 at Wellesley---> pictures to follow
• Wednesday, 6/14: Brainstorming day #2 at Wellesley---> pictures to follow as well Theme of the summer: create tools that help synthetic biologists troubleshoot in the lab.
• Thursday, 6/15:
• Friday, 6/16: Interview with Professor Chris A. Thoughts to come....

Week of June 18th

• Monday, 6/18: Today Kara and I interviewed Professor Sequeira. It was a very informative interview. Professor Sequeira gave us a lot of tips on how to visualize a troubleshooting tree, and how her team graphs progress when they are doing a long-term research project. Also, she gave us a lot of suggestions on features to add for the ELN. The next thing we need to do is transcribe the interview, and focus on designing the MoClo planner.
• Tuesday, 6/19- Wednesday, 6/20: I spend almost all day reading the MoClo paper and trying to understand how to visualize fusion sites and restriction sites for the MoClo planner- this thing is much more complicated than I thought... Orit also asked us to look up additional information, such as related research, to design the MoClo planner.
• Thursday, 6/21: The team paper-prototyped the MoClo planner using Balsamiq, and we started to storyboard it. There will be a primer designer incorporated into the design, as well as access to fact sheets and related research. It'll be similar to gnome surfer, but instead of extended desktops, the levels are vertical "shutters". Here's what the first panel looks like:

Here's a panel from the MoClo planner designer that we storyboarded.

• Friday, 6/22: I transcribed the interview with Professor Sequiera, which took a very long time, with annotations. Next week, the goal is to make a video for the MoClo planner after we've refined the details, and then send the video to Traci for evaluation before we dive in and start implementing our design.

Week of June 25th

• Monday, 6/25: Continuing interview transcriptions; between the two interviews so far, there are a lot of material covered. Nahum, Kara, and I started making a refined version of the MoClo planner for the video, and talked more in details about the transitions. There is a huge difference between what we designed for the Balsamiq prototype, and what is designed as the paper prototype for the video. I think it might be a good idea for me to go back and document everything, for later.
• The idea of "shutters" that we've used is finally clarified. Ready for the video tomorrow!
• Tuesday, 6/26: Created a paper prototype video for the MoClo planner. The youtube link is: http://www.youtube.com/watch?v=IPr-D4vAGAM

We sent this video to Traci, and got the response that overall the design was good, but that it might also be important to insert the destination vectors as well.

• Wednesday, 6/27: We got some feedback from Traci today on the design for the MoClo planner. She would also like us to include in the primer designer component the reverse complement sequence created for the reverse primer. Also, I guess we also forgot some really important information for primer designer that we included in the Optimus Primer design last year- stuff like checking for different kinds of dimers, secondary structures, melting temperatures, etc. We will have to add that for later.

Also, I started looking more into Eugene today.

• Thursday, 6/28: Continued looking more into Eugene and getting familiarized with the terminology. It seems that there is great flexibility in the language when it comes to syntax and definition.

We took down observations in different wet labs.

• Friday, 6/29: We met the MIT 2012 iGEM team today, and had social hour with the BU team as well. We went to an interesting physics lecture talk by Professor Walter Lewin, which was taped by NHK, the Japanese national broadcasting station. Members of the team visited the MIT iGEM wet-lab. We'll be back to visit team meetings in the future as well!!

Week of July 2nd

• Monday, 7/2: Continued looking into Eugene, and reviewing the Optimus Primer code from last year. I'm anticipating getting into the nitty-gritty details of the coding soon!
• Tuesday, 7/3: Started working today on the rules and definitions needed to create a Level 1 module. This should be really interesting since I'm not familiar with C# nor Java nor Eugene yet. But I'm learning!
• Wednesday, 7/4: Happy 4th of July! Kim, Kara, and I saw "The Amazing Spider-Man". There was a very cool tree visualization in one of the scenes that could totally be applied to our troubleshooting tree. It's interested how a lot of the things mentioned are already feasible in the field of HCI. Even better? "Cross-species genetics"... synthetic biology?
• Thursday, 7/5: Finished the Level1 module rules for Eugene. Fiddling around with the C# code for displaying the permutations by referencing the primer designer code we were working with last year, but having some difficulties.
• Friday, 7/6: Sat down with Casey and slowly got introduced to the C# code for the Eugene module. Ran simulated data through Eugene and were able to make to print the codes in the command window. Next step: work on figuring out how product/permute works in the eugene code. Talked to Ernst; Eugene code will be updated soon, and we can view the sample code later.

To do for next week: Start parsing real data for feeding into the C# code, get Eugene to work, contact more PIs/post-grads/grads/profs for interviews on troubleshooting, start working on things for L2 module and primer designer with the background info Traci gave us, and contact other iGEM teams for observations/participation.

Week of July 9th

• Monday, 7/9: Consuelo, Casey, and I visited the MIT iGEM team and sat in on a morning wet-lab meeting today.
• Initial observations: We made observations on how the space restricted/augmented conversation and group interactions. Also, we looked at the variety of visual aids that were used by the PIs and students in the presentations. We also paid careful attention to conversations on troubleshooting techniques, and noticed several trends. It would really great once we're done with the MoClo planner that the MIT team come and test it out at Wellesley.

Eugene

• Also, we started using the product and permute functions on Eugene. It seems that product and permute do not actually work the way we want them to for Level 1 modules. We want variations of concrete parts in the same order, replacing the absDevice(prom, RBS, CDS, term) pattern with real biobrick parts. However, permute changes the order of the parts so that the absDevice would have variations of (RBS, prom, term, CDS) or (term, RBS, CDS, prom), etc on the inside. This function will be extremely useful once we get to creation of Level 2 modules, but it is not pertinent to creating Level 1 modules.
• Tuesday, 7/10: Started fiddling with parsing real data. Somehow it's really difficult retrieving RBS data from the Registry! Do you search "RBS", their family names, or something else all together? What if the RBS doesn't have a family it belongs in? Nicole and Veronica have been working on semantic search for a while, and used their skills to also mine the Registry for pertinent information for the MoClo planner. However, as a result of using different parameters to classify different backbone parts, the rules that I wrote earlier for Eugene must now all be redefined. For example, I realized today that instead of creating 4 separate categories of promoters (constitutive, hybrid, repressible, inducible) that the promoter type can just be defined as a property" of promoters inside of a promoter type. The same pattern can also be followed for RBS, CDS, and terminators.
• Wednesday, 7/11: Consuelo, Wendy, and I sat in on a wet-lab meeting at BU. This week BU is focusing on creating their level1 modules, and Traci ordered a record-breaking 128 primers!! Back in the comp lab, we are working with Eugene still; with a lot of help from Casey I finally was able to parse some fake data, and get that to print out. The next step would of course be to use real data. But as a result of the parsing, I realized that a lot of the Eugene rules I had written had to be reworded.
• Thursday, 7/12: We worked on integrating my code with the front end done by Kara and Nahum. We decided that since permute nor product does what we thought they did, we should only use "permute" in Eugene for Level2 modules, and that for Level1 modules we create only a nested for-loop. Today I worked on integrating that into the MoClo Planner design, but as usual, ran into a lot of problems with syntax. We wanted to interview Professor Beers today, but there was a conflict and the interview is delayed to another time.
• Friday, 7/13: Starting to work on the backend behind Level 2, especially on Eugene. Things are especially interesting because creating a hybrid device might not work the way we thought in Eugene. So far, to test hybrid device functionality, we are creating four abstract devices with the same non-specific backbone parts, and then permuting them once they are all defined to be a single hybrid device. The problem is, will the permutations show the differences between the pieces of the hybrid device?
• So far, permutations are working- we can create 720 permutations of a level2 device from 6 abstract level 1 devices; this can be done by defining the abstract devices with the same parts inside (prom, RBS, CDS, term) while they are all abstract, and create a hybrid device composed of all 6 abstract devices. Then, the permutation is of the abstract devices inside the hybridDevice, which come out at 6!, or 720 permutations.