Team:Wellesley HCI/Notebook/SiruiNotebook

• Team
• Project
• Process
  • Methodology
  • Safety
  • Notebook
  • Outreach
• Medal Fulfillment
• Additional Info
  • Acknowledgement
  • Fun

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 Development/Research Center (name?) in cambridge to get a tutorial of Windows 8.
• Tuesday, 6/5: Meeting with Natalie in the lab today!

Wendy and Nicole working hard in the wetlab.

CAPTION HERE.

• INSERT TONS OF PICTURES HERE. What did we learn? Innovations for the ELN....
• Wednesday, 6/6: Meeting with Orit on the ELN--> details to follow
• Thursday, 6/7: Meeting with Orit about microinteractions--> what did you learn? What's interesting? What's not? Sifteo cubes??
• Friday, 6/8:

MIT reflection goes here. Soon.

Week of June 12th

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

caption here

• 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.
• 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: Interview with prof. Sequiera--> thoughts? more to come...

• Tuesday, 6/19:

• Wednesday, 6/20:

• Thursday, 6/21: paper prototyped the MoClo planner, and started to storyboard it. here's what the first panel looks like:

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

• Friday, 6/22: Transcribed the interview with Professor Sequiera. Talk about some trends and interesting things I've noticed in terms of bioethics and human practices.

Week of June 25th

• Monday, 6/25: Continuing interview transcriptions still. These things take an amazing amount of time.

Also started paper prototyping and developing the transitions for the "shutter" design to be made into a 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

MIGHT BE COOL IF I INSERTED A VIDEO HERE.

• 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.

• 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!!

 INSERT A PICTURE OR TWO FROM THE WETLAB VISIT HERE.  Further reflections to follow 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, 7/10: Consuelo, Casey, and I visited the MIT iGEM team and sat in on a morning wet-lab meeting today.
• Initial observations: Right away we noticed that one of the main problems was sharing of visual aid and lack of space, and how that affected the presentation styles of the students.
• Troubleshooting: we also looked at troubleshooting techniques, and noticed several trends.
• Also, started using the product and permute functions on Eugene--> it doesn't seem to work the way we want to??
• Tuesday, 7/11: 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?
• Wednesday, 7/12: Talking with the BU wetlab
• Thursday, 7/13: Interview with Professor Beers
• Friday, 7/14: