Daily Notes
25 May 2015
Arduino Workshop 001(What is Arduino? How to blink a built-in LED and how to use a button to control the LED), Interactive Media Arts Lab Tour, Biology Lab Safety Training, Biology Lab Tour
26 May 2015
Skype meeting with Tristan, who is currently in the States, about our wiki page and final project prototype. Discussions on how to make editing the wiki accessible to everyone, the content of workshops, fundraising, and the coming conference at NCTU. Research on luciferase enzyme, oscillations, and rfc10.
27 May 2015
Bioluminescence presentation given by Ann. Arduino with color sensor+RGB led testing. Research about oscillating systems from previous competitions. Specifics regarding the plasmids we will be implementing. Successfully booked four flights to Taiwan for NCTU Conference in July.
28 May 2015
Skype testing with Tristan for tomorrow’s HTML workshop. Talking with Fudan University about setting up a workshop. Overall unproductive.
29 May 2015
Tristan’s Workshop on HTML via Google Hangout, Reida’s Workshop on plasmids construction, June’s Workshop on penicillin. We also got meal vouchers provided by NYU Shanghai! Hurray!
31 May 2015
We went to EXPLORIUM to hold a workshop with kids and taught them how to visualize their DNA collected from their mouth with detergent, salt, starch, and alcohol.
1 June 2015
Misya’s presentation on E.chromi. IDT representatives visited our lab and showed us how to order DNA on the website. Introduction to transformation lab with arabinose, pGLO, nutrient broth, and ampicillin. Bio majors practiced lab skills and taught Interactive Media Arts majors how to do lab. It was fun! Let’s see if our E.coli can glow tomorrow!.
2 June 2015
Spencer’s presentation on biological oscillators. The results of yesterday’s lab were kind of disappointing. GFP was not expressed and not visible under UV light. Most likely because of old agar plates. Bio majors tested our first transformation using a part from the kit (RFP generator) and made new agar plates. Bruno helped ZZ build our new color-tracking system with a web camera and Processing.
3 June 2015
Bruno, Christian, and Xiaoyue’s workshop on Virtual Reality of the inside of cell with the help of Unity 3D. Got chance to experience the bacteria world with the brand-new and exciting tool. Also, Reida’s RFP plasmid transformation showed a fluorescence in one colony! Prep work for second transformation lab including CFP, RFP, and GFP.
4 June 2015
Xiangxi’s presentation on mathematical modeling. Tristan’s Google Hangout workshop on Java/Animation in HTML. Bio majors made 54 LB agar plates with different concentrations of chloramphenicol resistances (12.5, 25, 34, 50 mg/ml).
5 June 2015
Ann’s presentation on Mini-prep. Everyone did Mini-Prep lab. DAN Quantitation of Mini-Prep we did. Xiangci talked about developing Virtual Reality Project for Human Practice with Christian. Photo shoot for our wiki landing page!
8 June 2015
Research about oscillation sequences. Meet up with Tongji (TJU), Jiaotong (SJTU), IDP students (Indonesia)
9 June 2015
Reida’s presentation on Gel Electrophoresis and Gel Extraction. Lab prep for tomorrow’s Gel Extraction lab. Building up website. Analysis of the medal criteria.
10 June 2015
Human Practice | Bioluminescence + Arduino Workshop in Kongjiang High School
Misya’s presentation on competent cells. Gel Electrophoresis Lab. Workshop about Bioluminescence, Arduino, and the integration of technology and biology in Kongjiang University as one of the series workshops that we are going to have in schools as human practice projects.
11 June 2015
Spencer’s presentation on Art & Design track. Brainstormed more details of our project. pGLO glowed! Bio majors transformed luciferase generator parts from the kit.
12 June 2015
Ann led a recap session before her 2 week leave. Lab team made competent cells. Strikingly page is up for sponsors!
15 June 2015
Started working on Virtual Reality (VR). Made a lot of agar plates and transformed chromoprotein parts.
16 June 2015
RFP glows! Inoculation of chromprotein parts.
17 June 2015
Miniprep of chromoprotein parts. Nanodrop results could have been better...our average was 18.8 ng/uL. We just need a little more practice? Our IMA tech guy introduced some new ideas for our final project, and we discussed with him new ways of integrating the colorful colonies into a step sequencer.
18 June 2015
Spencer's workshop on plasmid construction. Tried to do restriction digest, but no results seen on the gel (ES). We tried following NEB protocol (not iGEM) and it also didn't show on the gel.
19 June 2015
Skype meeting with ZZ to discuss more details of final project. Another round of restriction digest (Xbal and PstI), and it worked!
23 June 2015
More development on the design of the final project. Attempt sequential digest with EcoRI and SpeI. No results.
24 June 2015
Skype meeting with one of our potential sponsors. Developed design of Processing part. Another digest, this time a double digest with EcoRI and SpeI. Digest successful!
25 June 2015
Budget and sponsorship meeting with NYU Shanghai Finance Office and Foundation. Skyped with Vivan Xu to brainstorm our sponsorship/project.
26 June 2015
Getting our member Rachel on board! Development of our interface.
26 June 2015
Coding day for ZZ and Xiangci. Pictures of plates can play notes now. First transformation of ligation products. Sohigh still working on Virtual Reality.
29 June 2015
Coding day for ZZ and Xiangci. Pictures of plates can play notes now. First transformation of ligation products. Sohigh still working on Virtual Reality.
30 June 2015
Lab work presentations with professors. Processing code development. More talks with potential sponsors. Plates photo booth set up.
1 July 2015
Coding coding coding coding. Testing music components. Obtaining linearized backbone through gel electrophoresis and gel extraction.
2 July 2015
Google cardboards arrived! More progress on sponsorship and details of our final interactive genetically inspired music production installation.
3 July 2015
Laser cut a tube rack sample. Lab team did more work on digests and ligations. VR team built a 3D plasmid model. Two official donation agreements sent out. Starting initial wiki design.
6 July 2015
Presentation for the professors on all the stuff besides Biology. Project interface designed in Illustrator. VR team built a skybox in Unity. Made a tube rack prototype.
7 July 2015
Preparation for the iGEM Conference in NCTU. Settled down many cool Arduino stuff that we are going to get from DFRobot. VR tested our Unity project on an Android phone. An academic debate in bio lab over troubleshooting procedures for an unsuccessful ligation. New digestion of promoter and blue chromoprotein with lower reaction volumes.
8 July 2015
Taiwan planning. Tube rack processing code. VR team successfully ran our Unity file on an Android phone! The full construct with Promoter-RBS-Lime green chromoprotein-Terminator grew! But no color seen...
9 July 2015
Planning for Taiwan Conference trip is done! More sponsorship letters sent out.
10 July 2015
No colonies for RFP, YFP, CFP, GFP parts. Why? Luciferase parts successfully transformed into HB101 but still no color seen. Animation work for NCTU Conference begins.
13 July 2015
A lot of transformations. Tested the usb webcame modules. Interviewed bio-artist Vivian Xu, DJ Benjamin Bacon about biology, art, step sequencers, and experimental music. Our Strikingly page made it to the Strikingly discover page! http://igemnyushanghai.strikingly.com
14 July 2015
FUN DAY! Filmed our swag team introduction video for the coming NCTU iGEM conference and took group photos. Got team T-shirts for the NCTU conference! Got a sponsorship package from DFRobot filled with Arduino boards, sliders, buttons, LEDs, and many other cool electronic components for our installation. DFRobot is awesome!
15 July 2015
Miniprep inoculated cultures (promoter + rbs + chromoprotein constructs).Finished editing team video. Poster for NCTU near completion.
16 July 2015
Digest, ligation, and transformation of promoter + rbs + chromprotein + terminator constructs. We should see color tomorrow? Others are animating, coding, making posters, presentations, and updating the budget.
17 July 2015
Getting ready for the Asia conference.
20-24 July 2015
Attended the iGEM Asia Conference hosted by National Chiao Tong University. We learned a lot from other teams and met some really awesome people! We also took a couple days off to explore Taipei area. A good trip.
28 July 2015
Report of our Taiwan trip to our Professors. Potential troubleshooting methods for our lack of color included: adding a RFP reporter gene, sending the parts for seqeuencing, restarting construction from the beginning, and experimenting with arabinose concentrations.
29 July 2015
Our IDT plasmids arrived! Realized only 1000ng of DNA came, thus began designing primers so that we could amplify the sequence (never designed primers before–Snapgene is a great tool!). Sangon agreed to be a donator! Rethinking about our physical installation. Thankful that NEB sent us free Q5 polymerase earlier in the summer.
30 July 2015
Welcoming our new tech helper--Lewei (Richard) Huang! Also interviewed by The Good Life magazine! Figuring out the data transfer of our new installation. Sangon came to pick up our constructed plasmids for sequencing. Realized that iGEM primers are not common primers...we'll see how sequencing goes.
31 July 2015
Went to Fudan University, had lunch with their team members, and learned about the sequencing process, using T-vecors, ordering primers, and general lab procedures. They also gave us their iGEM kits, since we ran out of luciferase generators (our last transformation didn't work). Thank you Fudan iGEM Team!
3 Aug 2015
Consulted Antonius about our coding difficulties and he offered some good suggestions. Two cameras running with one Processing sketch! Yay! Spencer is back from America, back to making chromoprotein constructs.
4 Aug 2015
Virtual Reality project still making progress. Xiangci still coding. Lab meeting held, and new lab policies established to make work more efficient (Friday is inventory check-day, pre-lab requirements, attendance time, etc.)
5 Aug 2015
Getting ready for the 8 iGEM Teams project exhibition at the Shanghai Science and Technology Museum. Gel extraction of digested backbones (PCR is probably a much more efficent way to do this).
6 Aug 2015
Code reconstructed and the we can produce live music now! Hurray! First PCR of the summer–amplified gBlocks recieved from IDT. Found out we needed to add luciferin + ATP to the luciferase generator to generate light.
7 Aug 2015
PCR Purification came out imperfect (a 2.77 260:280 ratio?). Ran another PCR for less non-specific bands. Installation makers and coders hurry to prep for tomorrow.
8 Aug 2015
iGEM Show at Shanghai Science and Technology Museum! Along with Fudan, Shanghai Jiaotong, Tongji Wetware, Tongji Software, Xian-Jiaotong Liverpool, and Zhejiang University. Our bacterial music generator and virtual reality simulations were a success!
10 Aug 2015
Digested and ligated IDT sequences to backbone. If ligation went well, we should see color tomorrow...Sequencing results also back, and all of our previous constructs contained only GFP and CFP, not even a promoter.
11 Aug 2015
No color. Realized that pBAD promoter is inhibited by glucose, and that we've been using SOC media (containing glucose) to do all our transformations. Lesson learned. Talked with Xian-Jiaotong Liverpool University as to how to produce color (they are also working with chromoproteins). Got our LED light strip for our plate stage. Did the test run on the laser cutter for the camera stand.
12 Aug 2015
Ann, Sohigh, and Spencer left for the Beijing University iGEMers Conference! Rachel, ZZ, Xiangci, and June are still working hard in Shanghai.
13-15 Aug 2015
The Beijing Conference was a great experience. We were definitely awe-struck by the level of research and development of the other teams. We also got to try to 'perform' our project--we turned of all the lights on stage before our presentation and it was a wonderfully dramatic experience. Thank you Beijing University! And thank you many other teams (like Shanghai Ocean University and Northeast Forestry University for their advice on working with the pBAD promoter and chromoproteins, respectively.
17 Aug 2015
Last week of iGEM for us (before we all leave to different countries). Everything is a big rush now.
18 Aug 2015
Today Xian-Jiaotong Liverpool University drove all the way from Suzhou (2 hours) to send us plasmids, bacteria containing plasmids, and extra bacteria! THANK YOU XJLTU! They were also working with chromoproteins, and sent us their materials so that we could produce some color in the lab before we left.
19 Aug 2015
Another filming day, this time the final project is completely put together--step sequencer, tube rack, and button control. We planned to start shooting at 10AM, but a lot of difficulties kept coming up, so we ended up starting the shoot around 4pm. It was a really great feeling being able to see everything put together. Today was ZZ and Xiangci's last day.
20 Aug 2015
The last day. We cleaned out the lab fridge. It was very painful throwing away the summer's work of plasmids. We cleaned out the IMA lab and we our classroom 307. We made a round of thank you's to all the administration who helped set up iGEM. The work is still not done... we have the film editing, wiki, VR, T-shirts, presentations, posters, etc. But the next time we meet as a full team will be in Boston. So this is the last daily update of our iGEM journey.
