Wet Lab: New members began training by learning about sterile technique, bacterial cultures, and DNA purification. Team practiced miniprep protocols.
Product Development: New members conducted survey to find problems to solve in the community. This served as training to improve member engagement within the community.
Wiki: Wiki subteam learned the importance of typography during a one-hour long Wiki/Design Training class. Worked on the webpage replication project to practice Adobe Illustrator (due 3/18).
P & P: On February 27th, P&P worked with YOURS to teach kids about physics and engineering principles by building paper towers to hold up as many books as possible. P&P regrouped to discuss this program and to continue brainstorming for future outreach events. P&P continued brainstorming other outreach events and ideas with the intention of reaching out to the kids at the local Ithaca High school.
Business: Members met to discuss sponsorship options as well as a possible fundraising idea to inform the community about Cornell iGEM. Assigned portions of sponsorship packet that needed updating.
Wet Lab: Members split into training groups and performed PCR on gBlocks from last year’s project. Training involved overviews and run-throughs of cloning, transformation, miniprep, gel extraction, and other protocols.
Product Development: Members familiarize themselves with CADing software autodesk fusion in a workshop. This served as new member training.
Wiki: Wiki subteam learned the basics of HTML and CSS during a one-hour long Wiki/Design Training class. Worked on the HTML/CSS project (due 3/26).
P & P: P&P started planning and finding information for a synthetic biology discussion. Also brainstormed for activities for the annual student outreach event - Splash! at Cornell.
Business: Members met to discuss sponsorship options as well as a possible fundraising idea to inform the community about Cornell iGEM. Assigned portions of sponsorship packet that needed updating.
Product Development: Member familiarized themselves with arduino and LED’s as part of the new member training.
Wiki: Wiki subteam learned the basics of colors, white space, and composition during a one-hour long Wiki/Design Training class. Worked on webpage creation project to practice building information hierarchy (due 4/8).
P & P: P&P brainstormed applications for two possible projects for the team - incorporating synthetic biology with 3D printing or with fourier transforms/band-pass filters.
Business: Members met to finalize specific details about National Garlic Day Fundraiser. Made graphic to spread the word about the event. Continued to reach out to sponsors.
Product Development: Members continue to familiarize themselves with arduino and circuits. Members also learned how to use MOSFETs in a circuit.
Wiki: Wiki subteam learned the basics of JavaScript and jQuery during a one-hour long Wiki/Design Training class. Worked on the JavaScript/jQuery project (due 4/13).
P & P: P&P started finding research contacts to consult for technical advice on creating a band-pass filter in bacteria. P&P compiled a list of questions for the interviews to inform our biological circuit design.
Business: Business continued to organize the fundraiser. Also came up with potential apparel designs for the team.
Product Development: Members familiarize themselves with circuits using circuit lab. Members designed their own circuits and learned how to read circuit part manuels.
Wiki: Wiki subteam evaluated past competition winners’ websites and our past competition websites during a one-hour long Wiki/Design Training class. Worked on designing a webpage for our current project (due 4/23).
P & P: P&P consulted Professor G. Lambert on April 9th regarding our preliminary design of our genetic circuit and any potential issues with the project. On April 10th, P&P interviewed Professor E. Kan about the similar design principles connecting electrical engineering to genetic circuit engineering.
Business: Continued to finalize the fundraising event. Narrowed down apparel options for the team.
Product Development:
Wiki: Wiki subteam learned the basics of Bootstrap and Git/GitHub during a one-hour long Wiki/Design Training class. Worked on the Bootstrap/Github project (due 4/30).
P & P: P&P interviewed Professor J. March on April 20th for assistance in choosing specific protein candidates for our genetic circuit. The discussion also addressed control of circuit kinetics via protein degradation and plasmid copy number and potential applications for our project. P&P also continued planning for Splash! and RawExpo, a creative exposition at the architecture school.
Business: Business held their National Garlic Day fundraiser on 4/19 - earned some money and spread the word about iGEM!
Wet Lab: Wetlab continued training. Members performed a double digestion and practiced using a NanoDrop Spectrophotometer.
Product Development: Members started brainstorming for potential projects and problems to solve for this year’s competition.
Wiki: Wiki subteam met up to discuss iGEM wiki rules and go over the general timeline for the summer and fall.
P & P: The first day of Ithaca High School (IHS) outreach took place on 4/26. P&P introduced Future Problem Solving (FPS) approaches and assigned readings for first topic (spread of infectious diseases).
On April 27th, P&P participated in RawExpo and presented last year’s project, Oxyponics.
P&P hosted an outreach event on April 28th as part of Splash! at Cornell U. We introduced synthetic biology topics including DNA extraction, plasmid transformation, and CRISPR.
Business: Business worked on apparel design for the team and went over fundraising numbers.
Wet Lab: Members practiced double digest and ligation of digested inserts into pSB1C3 vector.
Product Development: Members continued the brainstorming process and presented our ideas to other members for feedback.
P & P: P&P continued IHS outreach on 5/3 by going over a practice FPS future scenario about the spread of infectious diseases and introducing the problem-solving process.
Product Development: Members continued learning about Pmos and Nmos along with other circuitry components.
P & P: P&P continued reaching out to faculty and experts for consultation on our band-pass filter biological circuit and mapped out the schedule for summer work.
Product Development: MMembers started CADing components of a model car separately.
Wiki: Started discussing possible concepts to consider for the 2018 wiki design, such as going with a dark color scheme (not necessarily black, something more along the lines of a dark color like navy blue) and incorporating geometric aspects. Also went over some brainstorming already done in April.
Wiki: Discussed idea of using templates to make implementation of the wiki easier. Assignment to look up templates that could work for possible wiki designs for 2018 project.
Wet Lab: We had our first team meeting on Thursday the 21st where we outlined goals for the summer. We also had a group training session on Sunday the 23rd to complete training for new members. In the lab, we attempted to transform stock PSB1C3 into NEB 5-alpha Competent E. coli, however the transformation was not successful.
Product Development: PD met with wet lab members to discuss the project while also exploring possible modeling methods.
Wiki: Discussed themes we found that represented elements we would like to see in a potential wiki design. Reached out to team lead for more information and clarification on the project and Product Development’s role.
P & P: P&P outlined the events and goals for the summer while planning for 4-H. One major goal was to finish creating a customizable plasmid kit and to use it for collaboration.
Wet Lab: Wet Lab ran PCR reactions for PhrpL and sigmaF and Confirmed the lengths of each construct by running through a gel. The PCR was cleaned up and nanodropped resulting in high DNA concentration. Wet Lab began a wet culture from NEB 5-alpha E. coli transformed with PSB1c3. The wet culture was miniprepped and then ran through a gel. However, no bands were visible for PSB1C3 indicating an unsuccessful miniprep.
Product Development: PD had a modeling meeting to look into simbiology and other ways to model online. We also began translating the wet lab work into a math model.
P & P: P&P taught a class on synthetic biology during 4-H career explorations on June 27th. Various topics were introduced, including CRISPR, DNA extraction, and phage transduction/plasmid transformation. The first iteration of the plasmid kit was laser cut and used at 4-H. We asked the students about their opinions on its use in pedagogy for feedback to improve our design. P&P began pursuing an educational collaboration with the Greater Ithaca Activities Center nearby.
P&P also began reaching out to professors at Washington University in St. Louis for consultation on our band-pass filter biological circuit.
Business: Members began reaching out to potential sponsors.
Wet Lab: We ran PCR on our DNA constructs PhrpL, Sigmaf, and PF2. After several failed attempts, the lengths of each construct was confirmed by running a gel and nanodropping to determine the respective concentrations of each construct.
Product Development: PD brainstormed ideas for a hardware application, worked on and finished a basic model for simbiology and began developing a system of ODEs as a math model.
Wiki: Called together three of our Wiki subteam members to help design the wiki this summer. Went over the project description to catch up other members of the design team. Assigned each design member to make mock-up(s) of a home page (due 7/12).
P & P: P&P reflected on 4-H and the feedback about the plasmid kit. Issues included its transparent color, lack of visibility, and difficulty in assembly. A new plasmid kit was designed for laser cutting. P&P also worked on consolidating materials for IHS outreach in the fall and reached out to the NY Affiliate Director.
Business: Members are still reaching out to potential sponsors.
Wet Lab: We ran PCR on our DNA constructs PhrpL, Sigmaf, PF2, High pass 1b, Low pass 1b. Confirmed the lengths of each construct by running through a gel. Miniprepped PSB1C3 bacteria with low yields.
Product Development: PD started a literature review and began searching for parameter values to fit the mathematical models.
Wiki: Design team went over each member’s home page design. Discussed what we liked/disliked for each person’s design. Picked best design out of the three. Assigned each design member to edit the chosen home page design (due 7/17).
P & P: On July 9th, P&P interviewed Professor M. DeLisa, who interrogated the circuit design, provided suggestions on the placement different protein degradation tags on different components of the system. P&P also consulted him on the emerging technology and public opinion side of synthetic biology.
On July 10th, P&P interviewed Professor G. Lambert about modelling and testing the biological circuit.
P&P continued brainstorming potential outreach events, including a hackathon and activities for Ithaca High School in the Fall.
Business: Members are still reaching out to potential sponsors.
Wet Lab: Team ligated Phrpl, mf-lon, High Pass 1b and Low Pass 1b into pSB1C3 vectors. Team unsuccessfully attempted to transform plasmids into competent cells on chloramphenicol plates.
Product Development: PD began working on CAD (computer aided design), continued to identify parameter values for the model, and started working on the graphs for the wiki.
Wiki: Design team went over each team member’s revised home page design and listed out what features/components to include for the final home page design. Reached out to leads and former members who contributed to design for feedback. Assigned each design member to make mock-up(s) of sub-page (due 7/21).
Design team went over sub-page designs and listed out what features/components to include for final sub-page design. Designated assignments for making team page design, notebook/attributes page design, and looking into incorporating animation into the wiki (due).
P & P: On July 17th, P&P hosted a workshop at GIAC about synthetic biology teaching 1st graders about parts of a cell by representing different parts with different candies. Additionally, the plasmid kit was painted with methods that did not give a good final aesthetic. P&P contacted NY 4H for outreach opportunities at the upcoming NY State fair.
Business: Members are still reaching out to potential sponsors.
Wet Lab: Wet Lab PCRed High Pass 1a, High Pass 1b and Low Pass 1c. We ran the PCR product on a gel, which confirmed a successful PCR. We then cleaned up the PCR product and nanodropped the cleanups. The PCR cleanup was cleaned up, while PSB1c3 was linearized and digested. The digestion were cleaned up and nanodropped. Wet Lab also miniprepped a wet culture that had been started earlier in the week of PSB1C3 transformed bacteria and nanodropped the results.
Product Development: PD completed data parsing and created basic graphs. We also worked on updating parts of the model that required adjusting.
P & P: On July 24th, P&P returned to GIAC and made aluminum boats with the kids to learn about engineering principles, buoyancy, and physics. Plasmid kits were designed, cut, and painted for testing for UT-Austin
Business: Members are still reaching out to potential sponsors.
Wet Lab: We ligated previously digested High Pass 1a and High Pass 1b into pSB1C3 (to create High Pass 2a) as well as High Pass 1a and High Pass 1c into pSB1C3 (to create high Pass 2b). We performed PCR reactions for some parts we were running low on and then digested and ligated mf-Lon, sigmaF, and PhrpL, High Pass 1a, High Pass 1b, High Pass 1c, Low Pass 1b, and Low Pass 1c individually into pSB1C3 vectors. We heat inactivated and transformed our ligations into NEB 5-alpha Competent E. coli. Since we had been having trouble with transformations, we used SOC instead of LB for our outgrowth steps, with a positive outcome - colonies grew on all plates. We used isolated colonies to inoculate 5 mL liquid cultures which we miniprepped after overnight incubations. We also performed colony PCR reactions on assembled pSB1C3 vectors with High Pass 2a and and mf-lon inserts. We will continue with colony PCRs and run gels for them next week.
Product Development: PD began developing proofs and identifying characters of model via direct analysis and also worked on updating the graphics of the graphical model.
Wiki: Design team discussed and made final decisions for sub-page and team page designs. Went over and made final decisions for animation. Assigned design team members to make these finalized designs.
P & P: On July 31st, P&P played polymerase tag and made oobleck with the kids at GIAC. P&P interviewed Dr. L. Pierce and Dr. N. Argyres of Washington University in St. Louis in two separate interviews on 8/1 about the potential risks and regulations relevant to our project (see interview notes for specific interview contents).
Business: Members are still reaching out to potential sponsors.
Wet Lab: We performed colony PCR reactions on assembled pSB1C3 vectors with inserts. We ran the colony PCR products on agarose gels but got only bands of about 300 base pairs, which indicated that our biobricks had not been successfully inserted into our vectros. After some troubleshooting, we realized that the antarctic phosphatase we had been using to dephosphorylate the pSB1C3 to prevent re-ligation was expired and likely inactive. We ordered new quick CIP.
Product Development: PD identified algorithms for stochastic simulation model, found more parameter values, and updated graphics.
Wiki: Wiki started setting up the internal structure of the wiki. Wiki set up the wiki repository.
P & P: P&P interviewed Professor Swingle on August 6th, focusing on understanding methods to test and gather characterization data for modeling of the proteins HrpR and HrpS, which are integral to the biological circuit. New plasmid kits were ready for laser cutting, but the laser cutter was down.
Business: Members finalized sponsor list.
Wet Lab: [HIATUS]
Product Development: PD continued to work on the math model.
Wiki: Wiki started setting up the layout of the home page and considering what kind of framework to use to set up the layout.
Wet Lab: Break continued for wet lab members. At the end of the week, members returned to campus.
Product Development: PD continued to work on the math model.
Wiki: Wiki decided to use CSS grid to implement the layout of the wiki. Wiki did more setup of the wiki.
P & P: P&P had a Skype call interview on 8/22 with Professor M. Baccara from Washington University in St. Louis about the process and ethics of moving a product from science to business.
P&P resumed work on the project, outlining the fall semester outreach events and synthesizing information from various human practices and policies readings and interviews with experts.
P&P met with the IHS teacher on 8/24 to go over lesson plans and how FPS might fit in with the BioBuilder Club activities for the fall semester.
Wet Lab: Members took inventory and made a plan to finish cloning quickly with the new CIP.
Product Development: PD continued to work on the math model and completed the graph-model animation.
Wiki: Wiki had its first weekly subteam meeting. Wiki started implementing the nav bar, footer, home page, and standard page template.
P & P: P&P worked on state fair materials, including a trifold and portable plasmid kits for our outreach efforts on 9/3.
Wet Lab: Members continued ligating and transforming components into pSB1C3, and began both colony PCRs and test digestions to confirm the success of transformed parts.
Product Development: Members came back and learned about the modeling which began this summer.
Wiki: Wiki implemented the home page banner, footer, and description. Wiki implemented the side bar for the standard page template.
P & P: On September 3rd, P&P traveled to Syracuse, New York, to share our project with the local community. We promoted discussions with the fairgoers about what synthetic biology means to them and engaged younger children with our smaller plasmid kits.
Wet Lab: Began ligation of multiple Biobrick inserts to create high and low pass filters and reporters. Tried a variety of techniques, including both Standard and 3A assembly. Successfully transformed LP1ac and HP1ac using Standard assembly.
Product Development: Member helped with WIKI to develop interactive web pages. Members also continued to work on the models.
Wiki: Wiki implemented the nav bar, standard page text section, and notebook page. Wiki started implementing the team page and the sub-descriptions area of the home page.
P & P: P&P received a response from the NY Affiliate Director with more information on the timeline and registration process for Future Problem Solving, which was then forwarded to Ms. Arti Jewett at Ithaca High School.
P&P led the general body meeting on September 15th to conduct Application Day as a team exercise to brainstorm possible applications of our project in various industries. We compiled all of the responses and narrowed the scope to five main areas: co-culturing, process control, biological clocks, medical devices, and cell therapy. We had two additional ideas that we thought were interesting but had a bit of difficulty conceptualizing: biological data storage and microfluidics.
Business: Business began compiling a project overview for the potential business model.
Wet Lab: Successfully transformed multiple part constructs LP1ab and Hp1ab into pSB1C3 with Standard assembly. Transformed mf-lon into pSB1C3 and continued verification of single part constructs.
Product Development: Members continued helping wiki create interactive web pages and continued to work on the stochastic and deterministic models.
Wiki: Wiki implemented the safety page and the standard page banner. Wiki continued implementing the team page and sub-descriptions area of the home page. Wiki started implementing the sponsors page and the no-picture banner.
P & P: P&P brainstormed designs for the Human-Centered Design and Outreach wiki pages at Wiki Workday.
Business: Business established that the foundational nature of the project would lead to gaps in the business model and consequently switched focus to looking at alternative business applications.
Wet Lab: Began preparing completed constructs for testing. Transformed PF2 into pSB1C3 and began verification of transformants by sequencing.
Product Development: Members ordered parts for the hardware application of the project. Members continued helping wiki create interactive web pages and continued to work on the stochastic and deterministic models.
Wiki: Wiki implemented the Attributions page. Wiki finalized and uploaded the Home, Sponsors, Safety, and Notebook pages.
P & P: P&P continued to write and modify the designs for wiki content to be added to the wiki pages.
Business: Business decided to schedule a meeting with Launchpad, a Cornell Entrepreneurship Program in order to pitch the prior year’s project for potential sponsorship.
Wet Lab: Wet Lab began testing low pass and high pass filters independently. PD’s model predicted a period of 2 hours for the temperature signal would fall within the band, and wet lab tested at this frequency, as well as at a 1 hour period.
Product Development: Members started working on the stochastic model simulation along with the deterministic model simulation. Members continue working on the interactive webpage.
Wiki: Wiki started implementing the Wet Lab and P&P pages. Wiki started working on creating a plasmid and DNA helix for the Public Engagement and Practices pages respectively.
P & P: P&P emailed information about Future Problem Solving to Ms. Arti Jewett at Ithaca High School to distribute to students. P&P also sent a link to a survey to gauge the students’ interest in participating in Global Issues Problem Solving.
Wet Lab: Continued testing to find the cutoff frequencies.
Product Development: Finished up Wiki content.
Wiki: Wiki started implementing the Wet Lab and P&P pages. Wiki started working on creating a plasmid and buttons for the Public Engagement and Practices pages respectively.
P & P: P&P finished up wiki content and finalized designs for the wiki pages.
Business: Business worked on the Wiki page content.
Wiki: Wiki finished uploading the wiki to the iGEM server. Wiki did final checks to make sure everything was OK.
P & P: P&P finished up wiki content.
Business: Business finalized Wiki pages.